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11 pages, 4550 KiB

Open AccessArticle

Unveiling Lathyrus aphaca L. as a Newly Identified Host for Begomovirus Infection: A Comprehensive Study

by Tehmina Bahar, Fasiha Qurashi, Muhammad Saleem Haider, Murad Ali Rahat, Fazal Akbar, Muhammad Israr, Ahmad Ali, Zahid Ullah, Fazal Ullah, Mohamed A. El-Sheikh, Ryan Casini and Hosam O. Elansary

Genes 2023, 14(6), 1221; https://doi.org/10.3390/genes14061221 - 03 Jun 2023

Cited by 1 | Viewed by 1497

Abstract

The Begomovirus genus of the family Geminiviridae comprises the largest group of geminiviruses. Begomoviruses are transmitted by the whitefly complex (Bemisia tabaci) and infect dicotyledonous plants in tropical and subtropical regions. The list of begomoviruses is continuously increasing as a result [...] Read more.

The Begomovirus genus of the family Geminiviridae comprises the largest group of geminiviruses. Begomoviruses are transmitted by the whitefly complex (Bemisia tabaci) and infect dicotyledonous plants in tropical and subtropical regions. The list of begomoviruses is continuously increasing as a result of improvements in the methods for identification, especially from weed plants, which are considered a source of new viruses and reservoirs of economically important viruses but are often neglected during diversity studies. Lathyrus aphaca L. weed plants (yellow-flowered pea) with varicose veins and discoloration of the leaves were found. Amplified genomic DNA through rolling circular amplification was subjected to PCR analysis for the detection of the viral genome and associated DNA-satellites (alphasatellites and betasatellites). A full-length sequence (2.8 kb) of a monopartite begomovirus clone was determined; however, we could not find any associated DNA satellites. The amplified full-length clone of Rose leaf curl virus (RoLCuV) reserved all the characteristics and features of an Old World (OW) monopartite begomovirus. Furthermore, it is the first time it has been reported from a new weed host, yellow-flowered pea. Rolling circle amplification and polymerase chain reaction analysis of associated DNA satellites, alphasatellite, and betasatellite, were frequently accomplished but unable to amplify from the begomovirus-infected samples, indicating the presence of only monopartite Old World begomovirus. It is observed that RoLCuV has the capability to infect different hosts individually without the assistance of any DNA satellite component. Recombination in viruses is also a source of begomovirus infection in different hosts. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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17 pages, 5311 KiB

Open AccessArticle

Genome-Wide Characterization and Sequence Polymorphism Analyses of Glycine max Fibrillin (FBN) Revealed Its Role in Response to Drought Condition

by Muhammad Zeshan Zafer, Muhammad Hammad Nadeem Tahir, Zulqurnain Khan, Muhammad Sajjad, Xiangkuo Gao, Muhammad Amir Bakhtavar, Ummara Waheed, Maria Siddique, Zhide Geng and Shoaib Ur Rehman

Genes 2023, 14(6), 1188; https://doi.org/10.3390/genes14061188 - 29 May 2023

Viewed by 1102

Abstract

The fibrillin (FBN) gene family is widely distributed in all photosynthetic organisms. Members of this gene family are involved in plant growth and development and their response to various biotic and abiotic stress factors. In this study, 16 members of FBN [...] Read more.

The fibrillin (FBN) gene family is widely distributed in all photosynthetic organisms. Members of this gene family are involved in plant growth and development and their response to various biotic and abiotic stress factors. In this study, 16 members of FBN were identified in Glycine max and characterized by using different bioinformatics tools. Phylogenetic analysis classified FBN genes into seven groups. The presence of stress-related cis-elements in the upstream region of GmFBN highlighted their role in tolerance against abiotic stresses. To further decipher the function, physiochemical properties, conserved motifs, chromosomal localization, subcellular localization, and cis-acting regulatory elements were also analyzed. Gene expression analysis based on FPKM values revealed that GmFBNs greatly enhanced soybean drought tolerance and controlled the expression of several genes involved in drought response, except for GmFBN-4, GmFBN-5, GmFBN-6, GmFBN-7 and GmFBN-9. For high throughput genotyping, an SNP-based CAPS marker was also developed for the GmFBN-15 gene. The CAPS marker differentiated soybean genotypes based on the presence of either the GmFBN-15-G or GmFBN-15-A alleles in the CDS region. Association analysis showed that G. max accessions containing the GmFBN-15-A allele at the respective locus showed higher thousand seed weight compared to accessions containing the GmFBN-15-G allele. This research has provided the basic information to further decipher the function of FBN in soybean. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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15 pages, 2210 KiB

Open AccessArticle

First Description of the Nuclear and Mitochondrial Genomes and Associated Host Preference of Trichopoda pennipes, a Parasitoid of Nezara viridula

by Mesfin Bogale, Shova Mishra, Kendall Stacey, Lillie Rooney, Paula Barreto, Gina Bishop, Katherine Bossert, Kalista Bremer, Daniel Bustamante, Lila Chan, Quan Chau, Julian Cordo, Alyssa Diaz, Jordan Hacker, Lily Hadaegh, Taryn Hibshman, Kimberly Lastra, Fion Lee, Alexandra Mattia, Bao Nguyen, Gretchen Overton, Victoria Reis, Daniel Rhodes, Emily Roeder, Muhamed Rush, Oscar Salichs, Mateo Seslija, Nicholas Stylianou, Vivek Vemugunta, Min Yun, Anthony Auletta, Norman Leppla and Peter DiGennaro Show full author list Hide full author list

Genes 2023, 14(6), 1172; https://doi.org/10.3390/genes14061172 - 27 May 2023

Viewed by 1873

Abstract

Trichopoda pennipes is a tachinid parasitoid of several significant heteropteran agricultural pests, including the southern green stink bug, Nezara viridula, and leaf-footed bug, Leptoglossus phyllopus. To be used successfully as a biological control agent, the fly must selectively parasitize the target [...] Read more.

Trichopoda pennipes is a tachinid parasitoid of several significant heteropteran agricultural pests, including the southern green stink bug, Nezara viridula, and leaf-footed bug, Leptoglossus phyllopus. To be used successfully as a biological control agent, the fly must selectively parasitize the target host species. Differences in the host preference of T. pennipes were assessed by assembling the nuclear and mitochondrial genomes of 38 flies reared from field-collected N. viridula and L. phyllopus. High-quality de novo draft genomes of T. pennipes were assembled using long-read sequencing. The assembly totaled 672 MB distributed among 561 contigs, having an N50 of 11.9 MB and a GC of 31.7%, with the longest contig at 28 MB. The genome was assessed for completeness using BUSCO in the Insecta dataset, resulting in a score of 99.4%, and 97.4% of the genes were single copy-loci. The mitochondrial genomes of the 38 T. pennipes flies were sequenced and compared to identify possible host-determined sibling species. The assembled circular genomes ranged from 15,345 bp to 16,390 bp and encode 22 tRNAs, two rRNAs, and 13 protein-coding genes (PCGs). There were no differences in the architecture of these genomes. Phylogenetic analyses using sequence information from 13 PCGs and the two rRNAs individually or as a combined dataset resolved the parasitoids into two distinct lineages: T. pennipes that parasitized both N. viridula and L. phyllopus, and others that parasitized only L. phyllopus. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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23 pages, 6891 KiB

Open AccessArticle

Genome-Wide Identification, Characterization and Expression Analysis of Plant Nuclear Factor (NF-Y) Gene Family Transcription Factors in Saccharum spp.

by Peter Swathik Clarancia, Murugan Naveenarani, Jayanarayanan Ashwin Narayan, Sakthivel Surya Krishna, Prathima Perumal Thirugnanasambandam, Ramanathan Valarmathi, Giriyapur Shivalingamurthy Suresha, Raju Gomathi, Raja Arun Kumar, Markandan Manickavasagam, Ramalingam Jegadeesan, Muthukrishnan Arun, Govindakurup Hemaprabha and Chinnaswamy Appunu

Genes 2023, 14(6), 1147; https://doi.org/10.3390/genes14061147 - 25 May 2023

Cited by 5 | Viewed by 1759

Abstract

Plant nuclear factor (NF-Y) is a transcriptional activating factor composed of three subfamilies: NF-YA, NF-YB, and NF-YC. These transcriptional factors are reported to function as activators, suppressors, and regulators under different developmental and stress conditions in plants. However, there is a lack of [...] Read more.

Plant nuclear factor (NF-Y) is a transcriptional activating factor composed of three subfamilies: NF-YA, NF-YB, and NF-YC. These transcriptional factors are reported to function as activators, suppressors, and regulators under different developmental and stress conditions in plants. However, there is a lack of systematic research on the NF-Y gene subfamily in sugarcane. In this study, 51 NF-Y genes (ShNF-Y), composed of 9 NF-YA, 18 NF-YB, and 24 NF-YC genes, were identified in sugarcane (Saccharum spp.). Chromosomal distribution analysis of ShNF-Ys in a Saccharum hybrid located the NF-Y genes on all 10 chromosomes. Multiple sequence alignment (MSA) of ShNF-Y proteins revealed conservation of core functional domains. Sixteen orthologous gene pairs were identified between sugarcane and sorghum. Phylogenetic analysis of NF-Y subunits of sugarcane, sorghum, and Arabidopsis showed that ShNF-YA subunits were equidistant while ShNF-YB and ShNF-YC subunits clustered distinctly, forming closely related and divergent groups. Expression profiling under drought treatment showed that NF-Y gene members were involved in drought tolerance in a Saccharum hybrid and its drought-tolerant wild relative, Erianthus arundinaceus. ShNF-YA5 and ShNF-YB2 genes had significantly higher expression in the root and leaf tissues of both plant species. Similarly, ShNF-YC9 had elevated expression in the leaf and root of E. arundinaceus and in the leaf of a Saccharum hybrid. These results provide valuable genetic resources for further sugarcane crop improvement programs. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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13 pages, 1447 KiB

Open AccessArticle

Genome-Wide Integrative Transcriptional Profiling Identifies Age-Associated Signatures in Dogs

by Hyun Seung Kim, Subin Jang and Jaemin Kim

Genes 2023, 14(6), 1131; https://doi.org/10.3390/genes14061131 - 23 May 2023

Viewed by 1723

Abstract

Mammals experience similar stages of embryonic development, birth, infancy, youth, adolescence, maturity, and senescence. While embryonic developmental processes have been extensively researched, many molecular mechanisms regulating the different life stages after birth, such as aging, remain unresolved. We investigated the conserved and global [...] Read more.

Mammals experience similar stages of embryonic development, birth, infancy, youth, adolescence, maturity, and senescence. While embryonic developmental processes have been extensively researched, many molecular mechanisms regulating the different life stages after birth, such as aging, remain unresolved. We investigated the conserved and global molecular transitions in transcriptional remodeling with age in dogs of 15 breeds, which revealed that genes underlying hormone level regulation and developmental programs were differentially regulated during aging. Subsequently, we show that the candidate genes associated with tumorigenesis also exhibit age-dependent DNA methylation patterns, which might have contributed to the tumor state through inhibiting the plasticity of cell differentiation processes during aging, and ultimately suggesting the molecular events that link the processes of aging and cancer. These results highlight that the rate of age-related transcriptional remodeling is influenced not only by the lifespan, but also by the timing of critical physiological milestones. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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11 pages, 2644 KiB

Open AccessArticle

Investigation of Resistance Genes in Genus Vigna Reveals Highly Variable NLRome in Parallel Domesticated Member Species

by Jehanzaib Asif, Fatima Qureshi, Muhammad Zain, Hamza Nawaz, Effat Naz, Shahid Fareed, Aqsa Bibi, Sehar Nawaz, Fozia Saleem, Muhammad Shafique, Saba Tabasum, Umer Maqsood, Saad Serfraz and Saad Alkahtani

Genes 2023, 14(6), 1129; https://doi.org/10.3390/genes14061129 - 23 May 2023

Cited by 1 | Viewed by 1722

Abstract

Vigna is a unique genus that consist of multiple crop species that are domesticated in parallel fashion between 7–10 thousand years ago. Here we studied the evolution of nucleotide-binding site leucine-rich repeat receptor (NLR) genes across five crop species of genus Vigna. [...] Read more.

Vigna is a unique genus that consist of multiple crop species that are domesticated in parallel fashion between 7–10 thousand years ago. Here we studied the evolution of nucleotide-binding site leucine-rich repeat receptor (NLR) genes across five crop species of genus Vigna. In total identified 286, 350, 234, 250, 108 and 161 NLR genes were from Phaseolous vulgaris, Vigna. unguiculata, Vigna mungo, Vigna radiata, Vigna angularis and Vigna umbellata respectively. Comprehensive phylogenetic and clusterization analysis reveals the presence of seven subgroups of Coiled coil like NLRs (CC-NLR) genes and four distinct lineages of Toll interleukin receptor like NLRs (TIR-NLR). Subgroup CC_G10-NLR shows large scale diversification among Vigna species suggesting genus specific distinct duplication pattern in Vigna species. Mainly birth of new NLR gene families and higher rate of terminal duplication is the major determinants for expansion of NLRome in genus Vigna. Recent expansion of NLRome in V. anguiculata and V. radiata was also observed which might suggest that domestication have supported their duplication of lineage specific NLR genes. In short, large scale difference in the architecture of NLRome were observed in diploid plant species. Our findings allowed us to hypothesized that independent parallel domestication is the major drivers of highly divergent evolution of NLRome in genus Vigna. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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27 pages, 3925 KiB

Open AccessArticle

Genome-Wide Identification and Gene Expression Analysis of Sweet Cherry Aquaporins (Prunus avium L.) under Abiotic Stresses

by Ariel Salvatierra, Patricio Mateluna, Guillermo Toro, Simón Solís and Paula Pimentel

Genes 2023, 14(4), 940; https://doi.org/10.3390/genes14040940 - 19 Apr 2023

Cited by 1 | Viewed by 1719

Abstract

Aquaporins (AQPs) are integral transmembrane proteins well known as channels involved in the mobilization of water, small uncharged molecules and gases. In this work, the main objective was to carry out a comprehensive study of AQP encoding genes in Prunus avium (cv. Mazzard [...] Read more.

Aquaporins (AQPs) are integral transmembrane proteins well known as channels involved in the mobilization of water, small uncharged molecules and gases. In this work, the main objective was to carry out a comprehensive study of AQP encoding genes in Prunus avium (cv. Mazzard F12/1) on a genome-wide scale and describe their transcriptional behaviors in organs and in response to different abiotic stresses. A total of 28 non-redundant AQP genes were identified in Prunus spp. Genomes, which were phylogenetically grouped into five subfamilies (seven PIPs, eight NIPs, eight TIPs, three SIPs and two XIPs). Bioinformatic analyses revealed a high synteny and remarkable conservation of structural features among orthologs of different Prunus genomes. Several cis-acting regulatory elements (CREs) related to stress regulation were detected (ARE, WRE3, WUN, STRE, LTR, MBS, DRE, AT-rich and TC-rich). The above could be accounting for the expression variations associated with plant organs and, especially, each abiotic stress analyzed. Gene expressions of different PruavAQPs were shown to be preferentially associated with different stresses. PruavXIP2;1 and PruavXIP1;1 were up-regulated in roots at 6 h and 72 h of hypoxia, and in PruavXIP2;1 a slight induction of expression was also detected in leaves. Drought treatment strongly down-regulated PruavTIP4;1 but only in roots. Salt stress exhibited little or no variation in roots, except for PruavNIP4;1 and PruavNIP7;1, which showed remarkable gene repression and induction, respectively. Interestingly, PruavNIP4;1, the AQP most expressed in cherry roots subjected to cold temperatures, also showed this pattern in roots under high salinity. Similarly, PruavNIP4;2 consistently was up-regulated at 72 h of heat and drought treatments. From our evidence is possible to propose candidate genes for the development of molecular markers for selection processes in breeding programs for rootstocks and/or varieties of cherry. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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15 pages, 3359 KiB

Open AccessArticle

Identification of the Function of the Pathogenesis-Related Protein GmPR1L in the Resistance of Soybean to Cercospora sojina Hara

by Yeyao Du, Nooral Amin, Naveed Ahmad, Hanzhu Zhang, Ye Zhang, Yang Song, Sujie Fan and Piwu Wang

Genes 2023, 14(4), 920; https://doi.org/10.3390/genes14040920 - 15 Apr 2023

Cited by 4 | Viewed by 1109

Abstract

Pathogenesis-related proteins, often used as molecular markers of disease resistance in plants, can enable plants to obtain systemic resistance. In this study, a gene encoding a pathogenesis-related protein was identified via RNA-seq sequencing analysis performed at different stages of soybean seedling development. Because [...] Read more.

Pathogenesis-related proteins, often used as molecular markers of disease resistance in plants, can enable plants to obtain systemic resistance. In this study, a gene encoding a pathogenesis-related protein was identified via RNA-seq sequencing analysis performed at different stages of soybean seedling development. Because the gene sequence showed the highest similarity with PR1L sequence in soybean, the gene was named GmPR1-9-like (GmPR1L). GmPR1L was either overexpressed or silenced in soybean seedlings through Agrobacterium-mediated transformation to examine the resistance of soybean to infection caused by Cercospora sojina Hara. The results revealed that GmPR1L-overexpressing soybean plants had a smaller lesion area and improved resistance to C. sojina infection, whereas GmPR1L-silenced plants had low resistance to C. sojina infection. Fluorescent real-time PCR indicated that overexpression of GmPR1L induced the expression of genes such as WRKY, PR9, and PR14, which are more likely to be co-expressed during C. sojina infection. Furthermore, the activities of SOD, POD, CAT, and PAL were significantly increased in GmPR1L-overexpressing soybean plants after seven days of infection. The resistance of the GmPR1L-overexpressing lines OEA1 and OEA2 to C. sojina infection was significantly increased from a neutral level in wild-type plants to a moderate level. These findings predominantly reveal the positive role of GmPR1L in inducing resistance to C. sojina infection in soybean, which may facilitate the production of improved disease-resistant soybean cultivars in the future. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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11 pages, 2966 KiB

Open AccessArticle

Investigation of NLR Genes Reveals Divergent Evolution on NLRome in Diploid and Polyploid Species in Genus Trifolium

by Amna Areej, Hummera Nawaz, Iqra Aslam, Muhammad Danial, Zohaib Qayyum, Usama Akhtar Rasool, Jehanzaib Asif, Afia Khalid, Saad Serfraz, Fozia Saleem, Muhammad Mubin, Muhammad Shoaib, Muhammad Shahnawaz-ul-Rehman, Nazia Nahid and Saad Alkahtani

Genes 2023, 14(4), 867; https://doi.org/10.3390/genes14040867 - 04 Apr 2023

Cited by 4 | Viewed by 1955

Abstract

Crop wild relatives contain a greater variety of phenotypic and genotypic diversity compared to their domesticated counterparts. Trifolium crop species have limited genetic diversity to cope with biotic and abiotic stresses due to artificial selection for consumer preferences. Here, we investigated the distribution [...] Read more.

Crop wild relatives contain a greater variety of phenotypic and genotypic diversity compared to their domesticated counterparts. Trifolium crop species have limited genetic diversity to cope with biotic and abiotic stresses due to artificial selection for consumer preferences. Here, we investigated the distribution and evolution of nucleotide-binding site leucine-rich repeat receptor (NLR) genes in the genus of Trifolium with the objective to identify reference NLR genes. We identified 412, 350, 306, 389 and 241 NLR genes were identified from Trifolium. subterraneum, T. pratense, T. occidentale, subgenome-A of T. repens and subgenome-B of T. repens, respectively. Phylogenetic and clustering analysis reveals seven sub-groups in genus Trifolium. Specific subgroups such as G4-CNL, CCG10-CNL and TIR-CNL show distinct duplication patterns in specific species, which suggests subgroup duplications that are the hallmarks of their divergent evolution. Furthermore, our results strongly suggest the overall expansion of NLR repertoire in T. subterraneum is due to gene duplication events and birth of gene families after speciation. Moreover, the NLRome of the allopolyploid species T. repens has evolved asymmetrically, with the subgenome -A showing expansion, while the subgenome-B underwent contraction. These findings provide crucial background data for comprehending NLR evolution in the Fabaceae family and offer a more comprehensive analysis of NLR genes as disease resistance genes. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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22 pages, 2001 KiB

Open AccessArticle

Genomic Regions Associated with Milk Composition and Fertility Traits in Spring-Calved Dairy Cows in New Zealand

by J. M. D. R. Jayawardana, Nicolas Lopez-Villalobos, Lorna R. McNaughton and Rebecca E. Hickson

Genes 2023, 14(4), 860; https://doi.org/10.3390/genes14040860 - 01 Apr 2023

Cited by 2 | Viewed by 1958

Abstract

The objective of this study was to identify genomic regions and genes that are associated with the milk composition and fertility traits of spring-calved dairy cows in New Zealand. Phenotypic data from the 2014–2015 and 2021–2022 calving seasons in two Massey University dairy [...] Read more.

The objective of this study was to identify genomic regions and genes that are associated with the milk composition and fertility traits of spring-calved dairy cows in New Zealand. Phenotypic data from the 2014–2015 and 2021–2022 calving seasons in two Massey University dairy herds were used. We identified 73 SNPs that were significantly associated with 58 potential candidate genes for milk composition and fertility traits. Four SNPs on chromosome 14 were highly significant for both fat and protein percentages, and the associated genes were DGAT1, SLC52A2, CPSF1, and MROH1. For fertility traits, significant associations were detected for intervals from the start of mating to first service, the start of mating to conception, first service to conception, calving to first service, and 6-wk submission, 6-wk in-calf, conception to first service in the first 3 weeks of the breeding season, and not in calf and 6-wk calving rates. Gene Ontology revealed 10 candidate genes (KCNH5, HS6ST3, GLS, ENSBTAG00000051479, STAT1, STAT4, GPD2, SH3PXD2A, EVA1C, and ARMH3) that were significantly associated with fertility traits. The biological functions of these genes are related to reducing the metabolic stress of cows and increasing insulin secretion during the mating period, early embryonic development, foetal growth, and maternal lipid metabolism during the pregnancy period. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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14 pages, 7200 KiB

Open AccessArticle

Identification and Characterization of Phytocyanin Family Genes in Cotton Genomes

by Muhammad Bilal Tufail, Muhammad Yasir, Dongyun Zuo, Hailiang Cheng, Mushtaque Ali, Abdul Hafeez, Mahtab Soomro and Guoli Song

Genes 2023, 14(3), 611; https://doi.org/10.3390/genes14030611 - 28 Feb 2023

Cited by 3 | Viewed by 1414

Abstract

Phytocyanins (PCs) are a class of plant-specific blue copper proteins that have been demonstrated to play a role in electron transport and plant development. Through analysis of the copper ligand residues, spectroscopic properties, and domain architecture of the protein, PCs have been grouped [...] Read more.

Phytocyanins (PCs) are a class of plant-specific blue copper proteins that have been demonstrated to play a role in electron transport and plant development. Through analysis of the copper ligand residues, spectroscopic properties, and domain architecture of the protein, PCs have been grouped into four subfamilies: uclacyanins (UCs), stellacyanins (SCs), plantacyanins (PLCs), and early nodulin-like proteins (ENODLs). The present study aimed to identify and characterise the PCs present in three distinct cotton species (Gossypium hirsutum, Gossyium arboreum, and Gossypium raimondii) through the identification of 98, 63, and 69 genes respectively. We grouped PCs into four clades by using bioinformatics analysis and sequence alignment, which exhibit variations in gene structure and motif distribution. PCs are distributed across all chromosomes in each of the three species, with varying numbers of exons per gene and multiple conserved motifs, and with a minimum of 1 and maximum of 11 exons found on one gene. Transcriptomic data and qRT-PCR analysis revealed that two highly differentiated PC genes were expressed at the fibre initiation stage, while three highly differentiated PCs were expressed at the fibre elongation stage. These findings serve as a foundation for further investigations aimed at understanding the contribution of this gene family in cotton fibre production. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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12 pages, 2976 KiB

Open AccessArticle

Dynamic Evolution of NLR Genes in Dalbergioids

by Shamiza Rani, Ramlah Zahra, Abu Bakar, Muhammad Rizwan, Abu-Bakar Sultan, Muhammad Zain, Amna Mehmood, Muhammad Danial, Sidra Shakoor, Fozia Saleem, Ali Serfraz, Hafiz Mamoon Rehman, Rao Sohail Ahmad Khan, Saad Serfraz and Saad AlKahtani

Genes 2023, 14(2), 377; https://doi.org/10.3390/genes14020377 - 31 Jan 2023

Cited by 3 | Viewed by 2271

Abstract

Dalbergioid is a large group within the family Fabaceae that consists of diverse plant species distributed in distinct biogeographic realms. Here, we have performed a comprehensive study to understand the evolution of the nucleotide-binding leucine-rich repeats (NLRs) gene family in Dalbergioids. The [...] Read more.

Dalbergioid is a large group within the family Fabaceae that consists of diverse plant species distributed in distinct biogeographic realms. Here, we have performed a comprehensive study to understand the evolution of the nucleotide-binding leucine-rich repeats (NLRs) gene family in Dalbergioids. The evolution of gene families in this group is affected by a common whole genome duplication that occurred approximately 58 million years ago, followed by diploidization that often leads to contraction. Our study suggests that since diploidization, the NLRome of all groups of Dalbergioids is expanding in a clade-specific manner with fewer exceptions. Phylogenetic analysis and classification of NLRs revealed that they belong to seven subgroups. Specific subgroups have expanded in a species-specific manner, leading to divergent evolution. Among the Dalbergia clade, the expansion of NLRome in six species of the genus Dalbergia was observed, with the exception of Dalbergia odorifera, where a recent contraction of NLRome occurred. Similarly, members of the Pterocarpus clade genus Arachis revealed a large-scale expansion in the diploid species. In addition, the asymmetric expansion of NLRome was observed in wild and domesticated tetraploids after recent duplications in the genus Arachis. Our analysis strongly suggests that whole genome duplication followed by tandem duplication after divergence from a common ancestor of Dalbergioids is the major cause of NLRome expansion. To the best of our knowledge, this is the first ever study to provide insight toward the evolution of NLR genes in this important tribe. In addition, accurate identification and characterization of NLR genes is a substantial contribution to the repertoire of resistances among members of the Dalbergioids species. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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19 pages, 7146 KiB

Open AccessArticle

Identification and Molecular Characterization of RWP-RK Transcription Factors in Soybean

by Nooral Amin, Naveed Ahmad, Mohamed A. S. Khalifa, Yeyao Du, Ajmal Mandozai, Aimal Nawaz Khattak and Wang Piwu

Genes 2023, 14(2), 369; https://doi.org/10.3390/genes14020369 - 31 Jan 2023

Cited by 4 | Viewed by 1764

Abstract

The RWP-RK is a small family of plant-specific transcription factors that are mainly involved in nitrate starvation responses, gametogenesis, and root nodulation. To date, the molecular mechanisms underpinning nitrate-regulated gene expression in many plant species have been extensively studied. However, the regulation of [...] Read more.

The RWP-RK is a small family of plant-specific transcription factors that are mainly involved in nitrate starvation responses, gametogenesis, and root nodulation. To date, the molecular mechanisms underpinning nitrate-regulated gene expression in many plant species have been extensively studied. However, the regulation of nodulation-specific NIN proteins during nodulation and rhizobial infection under nitrogen starvation in soybean still remain unclear. Here, we investigated the genome-wide identification of RWP-RK transcription factors and their essential role in nitrate-inducible and stress-responsive gene expression in soybean. In total, 28 RWP-RK genes were identified from the soybean genome, which were unevenly distributed on 20 chromosomes from 5 distinct groups during phylogeny classification. The conserved topology of RWP-RK protein motifs, cis-acting elements, and functional annotation has led to their potential as key regulators during plant growth, development, and diverse stress responses. The RNA-seq data revealed that the up-regulation of GmRWP-RK genes in the nodules indicated that these genes might play crucial roles during root nodulation in soybean. Furthermore, qRT-PCR analysis revealed that most GmRWP-RK genes under Phytophthora sojae infection and diverse environmental conditions (such as heat, nitrogen, and salt) were significantly induced, thus opening a new window of possibilities into their regulatory roles in adaptation mechanisms that allow soybean to tolerate biotic and abiotic stress. In addition, the dual luciferase assay indicated that GmRWP-RK1 and GmRWP-RK2 efficiently bind to the promoters of GmYUC2, GmSPL9, and GmNIN, highlighting their possible involvement in nodule formation. Together, our findings provide novel insights into the functional role of the RWP-RK family during defense responses and root nodulation in soybean. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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18 pages, 5344 KiB

Open AccessArticle

Wide-Range Portrayal of AP2/ERF Transcription Factor Family in Maize (Zea mays L.) Development and Stress Responses

by Cheng Cheng, Likun An, Fangzhe Li, Wahaj Ahmad, Muhammad Aslam, Muhammad Zia Ul Haq, Yuanxin Yan and Ramala Masood Ahmad

Genes 2023, 14(1), 194; https://doi.org/10.3390/genes14010194 - 11 Jan 2023

Cited by 12 | Viewed by 2275

Abstract

The APETALA2/Ethylene-Responsive Transcriptional Factors containing conservative AP2/ERF domains constituted a plant-specific transcription factor (TF) superfamily, called AP2/ERF. The configuration of the AP2/ERF superfamily in maize has remained unresolved. In this study, we identified the 229 AP2/ERF genes in the [...] Read more.

The APETALA2/Ethylene-Responsive Transcriptional Factors containing conservative AP2/ERF domains constituted a plant-specific transcription factor (TF) superfamily, called AP2/ERF. The configuration of the AP2/ERF superfamily in maize has remained unresolved. In this study, we identified the 229 AP2/ERF genes in the latest (B73 RefGen_v5) maize reference genome. Phylogenetic classification of the ZmAP2/ERF family members categorized it into five clades, including 27 AP2 (APETALA2), 5 RAV (Related to ABI3/VP), 89 DREB (dehydration responsive element binding), 105 ERF (ethylene responsive factors), and a soloist. The duplication events of the paralogous genes occurred from 1.724–25.855 MYA, a key route to maize evolution. Structural analysis reveals that they have more introns and few exons. The results showed that 32 ZmAP2/ERFs regulate biotic stresses, and 24 ZmAP2/ERFs are involved in responses towards abiotic stresses. Additionally, the expression analysis showed that DREB family members are involved in plant sex determination. The real-time quantitative expression profiling of ZmAP2/ERFs in the leaves of the maize inbred line B73 under ABA, JA, salt, drought, heat, and wounding stress revealed their specific expression patterns. Conclusively, this study unveiled the evolutionary pathway of ZmAP2/ERFs and its essential role in stress and developmental processes. The generated information will be useful for stress resilience maize breeding programs. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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15 pages, 8293 KiB

Open AccessArticle

Volatile Profiling and Transcriptome Sequencing Provide Insights into the Biosynthesis of α-Pinene and β-Pinene in Liquidambar formosana Hance Leaves

by Yongquan Li, Yanfang Gao, Lin Deng, Huiming Lian, Wei Guo, Wei Wu, Bine Xue, Baobin Li, Yuzhen Su and Hui Zhang

Genes 2023, 14(1), 163; https://doi.org/10.3390/genes14010163 - 06 Jan 2023

Cited by 2 | Viewed by 1341

Abstract

Liquidambar formosana Hance is a pinene-rich deciduous plant species in the Altingiaceae family that is used as a medicinal plant in China. However, the regulatory mechanisms underlying α-pinene and β-pinene biosynthesis in L. formosana leaves remain unknown. Here, a joint analysis of the [...] Read more.

Liquidambar formosana Hance is a pinene-rich deciduous plant species in the Altingiaceae family that is used as a medicinal plant in China. However, the regulatory mechanisms underlying α-pinene and β-pinene biosynthesis in L. formosana leaves remain unknown. Here, a joint analysis of the volatile compounds and transcriptomes of L. formosana leaves was performed to comprehensively explore the terpene synthase (TPS) that may participate in α-pinene and β-pinene biosynthesis. Headspace solid-phase microextraction (HS-SPME) and gas chromatography–mass spectrometry (GC–MS) jointly detected volatile L. formosana leaves. Trees with high and low levels of both α-pinene and β-pinene were defined as the H group and L group, respectively. RNA sequencing data revealed that DXR (1-deoxy-D-xylulose-5-phosphate reductoisomerase), HDS [(E)-4-hydroxy-3-methylbut-2-eny-l-diphosphate synthase], and TPS may be the major regulators of monoterpenoid biosynthesis. We identified three TPSs (LfTPS1, LfTPS2, and LfTPS3), which are highly homologous to α-pinene and β-pinene synthases of other species in phylogenetic analysis. Four TPS genes (LfTPS1, LfTPS2, LfTPS4, LfTPS5) may be critically involved in the biosynthesis and regulation of α-pinene and β-pinene in L. formosana. Bioinformatic and transcriptomic results were verified using quantitative real-time PCR. We identified LfTPS1, LfTPS2 as candidate genes for α-pinene and β-pinene biosynthesis that significantly improve the yield of beneficial terpenoids. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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17 pages, 3076 KiB

Open AccessArticle

The Evolution of tRNA Copy Number and Repertoire in Cellular Life

by Fenícia Brito Santos and Luiz-Eduardo Del-Bem

Genes 2023, 14(1), 27; https://doi.org/10.3390/genes14010027 - 22 Dec 2022

Cited by 4 | Viewed by 3242

Abstract

tRNAs are universal decoders that bridge the gap between transcriptome and proteome. They can also be processed into small RNA fragments with regulatory functions. In this work, we show that tRNA copy number is largely controlled by genome size in all cellular organisms, [...] Read more.

tRNAs are universal decoders that bridge the gap between transcriptome and proteome. They can also be processed into small RNA fragments with regulatory functions. In this work, we show that tRNA copy number is largely controlled by genome size in all cellular organisms, in contrast to what is observed for protein-coding genes that stop expanding between ~20,000 and ~35,000 loci per haploid genome in eukaryotes, regardless of genome size. Our analyses indicate that after the bacteria/archaea split, the tRNA gene pool experienced the evolution of increased anticodon diversity in the archaeal lineage, along with a tRNA gene size increase and mature tRNA size decrease. The evolution and diversification of eukaryotes from archaeal ancestors involved further expansion of the tRNA anticodon repertoire, additional increase in tRNA gene size and decrease in mature tRNA length, along with an explosion of the tRNA gene copy number that emerged coupled with accelerated genome size expansion. Our findings support the notion that macroscopic eukaryotes with a high diversity of cell types, such as land plants and vertebrates, independently evolved a high diversity of tRNA anticodons along with high gene redundancy caused by the expansion of the tRNA copy number. The results presented here suggest that the evolution of tRNA genes played important roles in the early split between bacteria and archaea, and in eukaryogenesis and the later emergence of complex eukaryotes, with potential implications in protein translation and gene regulation through tRNA-derived RNA fragments. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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21 pages, 4303 KiB

Open AccessArticle

Harnessing on Genetic Variability and Diversity of Rice (Oryza sativa L.) Genotypes Based on Quantitative and Qualitative Traits for Desirable Crossing Materials

by Sanjoy K. Debsharma, Md. Abu Syed, Md. Hannan Ali, Sheikh Maniruzzaman, Popy R. Roy, Marian Brestic, Ahmed Gaber and Akbar Hossain

Genes 2023, 14(1), 10; https://doi.org/10.3390/genes14010010 - 21 Dec 2022

Cited by 10 | Viewed by 2292

Abstract

Yield is a complex parameter of rice due to its polygonal nature, sometimes making it difficult to coat the selection process in the breeding program. In the current study, 34 elite rice genotypes were assessed to evaluate 3 locations for the selection of [...] Read more.

Yield is a complex parameter of rice due to its polygonal nature, sometimes making it difficult to coat the selection process in the breeding program. In the current study, 34 elite rice genotypes were assessed to evaluate 3 locations for the selection of desirable rice cultivars suitable for multiple environments based on genetic diversity. In variance analysis, all genotypes have revealed significant variations (p ≤ 0.001) for all studied characters, signifying a broader sense of genetic variability for selection purposes. The higher phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) were found for yield-associated characteristics such as the number of grains panicle⁻¹ (GP), panicles hill⁻¹ (PPH), and tillers hill⁻¹ (TILL). All of the characters had higher heritability (greater than 60%) and higher genetic advance (greater than 20%), which pointed out non-additive gene action and suggested that selection would be effective. The most significant traits causing the genotype variants were identified via principal component analysis. In the findings of the cluster analysis, 34 elite lines were separated into 3 categories of clusters, with cluster II being chosen as the best one. The relationship matrix between each elite cultivar and traits was also determined utilizing a heatmap. Based on multi-trait genotype-ideotype distance index (MGIDI), genotypes Gen2, Gen4, Gen14, Gen22, and Gen30 in Satkhira; Gen2, Gen6, Gen7, Gen15, and Gen30 in Kushtia; and Gen10, Gen12, Gen26, Gen30, and Gen34 in Barishal were found to be the most promising genotypes. Upon validation, these genotypes can be suggested for commercial release or used as potential breeding material in crossing programs for the development of cultivars suitable for multiple environments under the future changing climate. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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19 pages, 13414 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of Kinesin Family in Barley (Hordeum vulgare)

by Zhaoshun Ye, Zhen Yuan, Huan Xu, Leiwen Pan, Jingsi Chen, Anicet Gatera, Muhammad Uzair and Dawei Xu

Genes 2022, 13(12), 2376; https://doi.org/10.3390/genes13122376 - 16 Dec 2022

Cited by 2 | Viewed by 1614

Abstract

Kinesin, as a member of the molecular motor protein superfamily, plays an essential function in various plants’ developmental processes. Especially at the early stages of plant growth, including influences on plants’ growth rate, yield, and quality. In this study, we did a genome-wide [...] Read more.

Kinesin, as a member of the molecular motor protein superfamily, plays an essential function in various plants’ developmental processes. Especially at the early stages of plant growth, including influences on plants’ growth rate, yield, and quality. In this study, we did a genome-wide identification and expression profile analysis of the kinesin family in barley. Forty-two HvKINs were identified and screened from the barley genome, and a generated phylogenetic tree was used to compare the evolutionary relationships between Rice and Arabidopsis. The protein structure prediction, physicochemical properties, and bioinformatics of the HvKINs were also dissected. Our results reveal the important regulatory roles of HvKIN genes in barley growth. We found many cis- elements related to GA3 and ABA in homeopathic elements of the HvKIN gene and verified them by QRT-PCR, indicating their potential role in the barley kinesin family. The current study revealed the biological functions of barley kinesin genes in barley and will aid in further investigating the kinesin in other plant species. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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18 pages, 5119 KiB

Open AccessArticle

Ploidy Status, Nuclear DNA Content and Start Codon Targeted (SCoT) Genetic Homogeneity Assessment in Digitalis purpurea L., Regenerated In Vitro

by Yashika Bansal, A. Mujib, Zahid H. Siddiqui, Jyoti Mamgain, Rukaya Syeed and Bushra Ejaz

Genes 2022, 13(12), 2335; https://doi.org/10.3390/genes13122335 - 11 Dec 2022

Cited by 4 | Viewed by 1883

Abstract

Digitalis purpurea L. is a therapeutically important plant that synthesizes important cardiotonics such as digitoxin and digoxin. The present work reports a detailed and efficient propagation protocol for D. purpurea by optimizing various PGR concentrations in Murashige and Skoog (MS) medium. The genetic [...] Read more.

Digitalis purpurea L. is a therapeutically important plant that synthesizes important cardiotonics such as digitoxin and digoxin. The present work reports a detailed and efficient propagation protocol for D. purpurea by optimizing various PGR concentrations in Murashige and Skoog (MS) medium. The genetic homogeneity of in vitro regenerants was assessed by the flow cytometric method (FCM) and Start Codon Targeted (SCoT) marker technique. Firstly, the seeds inoculated in full MS medium added with 0.5 mg/L GA₃ produced seedlings. Different parts such as hypocotyl, nodes, leaves and apical shoots were used as explants. The compact calli were obtained on BAP alone or in combinations with 2, 4-D/NAA. The hypocotyl-derived callus induced somatic embryos which proliferated and germinated best in 0.75 mg/L BAP-fortified MS medium. Scanning electron microscopic (SEM) images confirmed the presence of various developmental stages of somatic embryos. Shoot regeneration was obtained in which BAP at 1.0 mg/L and 2.0 mg/L BAP + 0.5 mg/L 2,4-D proved to be the best treatments of PGRs in inducing direct and indirect shoot buds. The regenerated shoots showed the highest rooting percentage (87.5%) with 24.7 ± 1.9 numbers of roots/shoot in 1.0 mg/L IBA augmented medium. The rooted plantlets were acclimatized in a greenhouse at a survival rate of 85–90%. The genome size and the 2C nuclear DNA content of field-grown, somatic embryo-regenerated and organogenic-derived plants were estimated and noted to be 3.1, 3.2 and 3.0 picogram (pg), respectively; there is no alteration in ploidy status and the DNA content, validating genetic uniformity. Six SCoT primers unveiled 94.3%–95.13% monomorphic bands across all the plant samples analyzed, further indicating genetic stability among in vitro clones and mother plants. This study describes for the first time successful induction of somatic embryos from hypocotyl callus; and flow cytometry and SCoT marker confirmed the genetic homogeneity of regenerated plants. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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19 pages, 3065 KiB

Open AccessArticle

Genomic Analysis of Pseudomonas asiatica JP233: An Efficient Phosphate-Solubilizing Bacterium

by Linlin Wang, Fangyuan Zhou, Jianbo Zhou, Paul R. Harvey, Haiyang Yu, Guangzhi Zhang and Xinjian Zhang

Genes 2022, 13(12), 2290; https://doi.org/10.3390/genes13122290 - 05 Dec 2022

Cited by 3 | Viewed by 1756

Abstract

The bacterium Pseudomonas sp. strain JP233 has been reported to efficiently solubilize sparingly soluble inorganic phosphate, promote plant growth and significantly reduce phosphorus (P) leaching loss from soil. The production of 2-keto gluconic acid (2KGA) by strain JP233 was identified as the main [...] Read more.

The bacterium Pseudomonas sp. strain JP233 has been reported to efficiently solubilize sparingly soluble inorganic phosphate, promote plant growth and significantly reduce phosphorus (P) leaching loss from soil. The production of 2-keto gluconic acid (2KGA) by strain JP233 was identified as the main active metabolite responsible for phosphate solubilization. However, the genetic basis of phosphate solubilization and plant-growth promotion remained unclear. As a result, the genome of JP233 was sequenced and analyzed in this study. The JP233 genome consists of a circular chromosome with a size of 5,617,746 bp and a GC content of 62.86%. No plasmids were detected in the genome. There were 5097 protein-coding sequences (CDSs) predicted in the genome. Phylogenetic analyses based on genomes of related Pseudomonas spp. identified strain JP233 as Pseudomonas asiatica. Comparative pangenomic analysis among 9 P. asiatica strains identified 4080 core gene clusters and 111 singleton genes present only in JP233. Genes associated with 2KGA production detected in strain JP233, included those encoding glucose dehydrogenase, pyrroloquinoline quinone and gluoconate dehydrogenase. Genes associated with mechanisms of plant-growth promotion and nutrient acquisition detected in JP233 included those involved in IAA biosynthesis, ethylene catabolism and siderophore production. Numerous genes associated with other properties beneficial to plant growth were also detected in JP233, included those involved in production of acetoin, 2,3-butanediol, trehalose, and resistance to heavy metals. This study provides the genetic basis to elucidate the plant-growth promoting and bio-remediation properties of strain JP233 and its potential applications in agriculture and industry. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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21 pages, 6383 KiB

Open AccessArticle

Genome-Wide Identification and Expression Profiling of Heat Shock Protein 20 Gene Family in Sorbus pohuashanensis (Hance) Hedl under Abiotic Stress

by Xiangyu Qi, Zexin Di, Yuyan Li, Zeren Zhang, Miaomiao Guo, Boqiang Tong, Yizeng Lu, Yan Zhang and Jian Zheng

Genes 2022, 13(12), 2241; https://doi.org/10.3390/genes13122241 - 29 Nov 2022

Cited by 3 | Viewed by 1559

Abstract

Small heat shock proteins (HSP20s) are a significant factor in plant growth and development in response to abiotic stress. In this study, we investigated the role of HSP20s’ response to the heat stress of Sorbus pohuashanensis introduced into low-altitude areas. The HSP20 gene [...] Read more.

Small heat shock proteins (HSP20s) are a significant factor in plant growth and development in response to abiotic stress. In this study, we investigated the role of HSP20s’ response to the heat stress of Sorbus pohuashanensis introduced into low-altitude areas. The HSP20 gene family was identified based on the genome-wide data of S. pohuashanensis, and the expression patterns of tissue specificity and the response to abiotic stresses were evaluated. Finally, we identified 38 HSP20 genes that were distributed on 16 chromosomes. Phylogenetic analysis of HSP20s showed that the closest genetic relationship to S. pohuashanensis (SpHSP20s) is Malus domestica, followed by Populus trichocarpa and Arabidopsis thaliana. According to phylogenetic analysis and subcellular localization prediction, the 38 SpHSP20s belonged to 10 subfamilies. Analysis of the gene structure and conserved motifs indicated that HSP20 gene family members are relatively conserved. Synteny analysis showed that the expansion of the SpHSP20 gene family was mainly caused by segmental duplication. In addition, many cis-acting elements connected with growth and development, hormones, and stress responsiveness were found in the SpHSP20 promoter region. Analysis of expression patterns showed that these genes were closely related to high temperature, drought, salt, growth, and developmental processes. These results provide information and a theoretical basis for the exploration of HSP20 gene family resources, as well as the domestication and genetic improvement of S. pohuashanensis. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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20 pages, 4641 KiB

Open AccessArticle

Genome-Wide Identification and In Silico Analysis of ZF-HD Transcription Factor Genes in Zea mays L.

by Md. Abir Ul Islam, Juthy Abedin Nupur, Muhammad Hayder Bin Khalid, Atta Mohi Ud Din, Muhammad Shafiq, Rana M. Alshegaihi, Qurban Ali, Qurban Ali, Zuha Kamran, Mujahid Manzoor, Muhammad Saleem Haider, Muhammad Adnan Shahid and Hakim Manghwar

Genes 2022, 13(11), 2112; https://doi.org/10.3390/genes13112112 - 14 Nov 2022

Cited by 6 | Viewed by 2034

Abstract

Zinc finger-homeodomain proteins are amongst the most prominent transcription factors (TFs) involved in biological processes, such as growth, development, and morphogenesis, and assist plants in alleviating the adverse effects of abiotic and biotic stresses. In the present study, genome-wide identification and expression analyses [...] Read more.

Zinc finger-homeodomain proteins are amongst the most prominent transcription factors (TFs) involved in biological processes, such as growth, development, and morphogenesis, and assist plants in alleviating the adverse effects of abiotic and biotic stresses. In the present study, genome-wide identification and expression analyses of the maize ZHD gene family were conducted. A total of 21 ZHD genes with different physicochemical properties were found distributed on nine chromosomes in maize. Through sequence alignment and phylogenetic analysis, we divided ZHD proteins into eight groups that have variations in gene structure, motif distribution, and a conserved ZF domain. Synteny analysis indicated duplication in four pairs of genes and the presence of orthologues of maize in monocots. Ka/Ks ratios suggested that strong pure selection occurred during evolution. Expression profiling revealed that the genes are evenly expressed in different tissues. Most of the genes were found to make a contribution to abiotic stress response, plant growth, and development. Overall, the evolutionary research on exons and introns, motif distributions, and cis-acting regions suggests that these genes play distinct roles in biological processes which may provide a basis for further study of these genes’ functions in other crops. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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10 pages, 2127 KiB

Open AccessArticle

Analysis of Heat Shock Proteins Based on Amino Acids for the Tomato Genome

by Meshal M. Almutairi and Hany M. Almotairy

Genes 2022, 13(11), 2014; https://doi.org/10.3390/genes13112014 - 02 Nov 2022

Cited by 1 | Viewed by 1363

Abstract

This research aimed to investigate heat shock proteins in the tomato genome through the analysis of amino acids. The highest length among sequences was found in seq19 with 3534 base pairs. This seq19 was reported and contained a family of proteins known as [...] Read more.

This research aimed to investigate heat shock proteins in the tomato genome through the analysis of amino acids. The highest length among sequences was found in seq19 with 3534 base pairs. This seq19 was reported and contained a family of proteins known as HsfA that have a domain of transcriptional activation for tolerance to heat and other abiotic stresses. The values of the codon adaptation index (CAI) ranged from 0.80 in Seq19 to 0.65 in Seq10, based on the mRNA of heat shock proteins for tomatoes. Asparagine (AAT, AAC), aspartic acid (GAT, GAC), phenylalanine (TTT, TTC), and tyrosine (TAT, TAC) have relative synonymous codon usage (RSCU) values bigger than 0.5. In modified relative codon bias (MRCBS), the high gene expressions of the amino acids under heat stress were histidine, tryptophan, asparagine, aspartic acid, lysine, phenylalanine, isoleucine, cysteine, and threonine. RSCU values that were less than 0.5 were considered rare codons that affected the rate of translation, and thus selection could be effective by reducing the frequency of expressed genes under heat stress. The normal distribution of RSCU shows about 68% of the values drawn from the standard normal distribution were within 0.22 and −0.22 standard deviations that tend to cluster around the mean. The most critical component based on principal component analysis (PCA) was the RSCU. These findings would help plant breeders in the development of growth habits for tomatoes during breeding programs. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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17 pages, 2566 KiB

Open AccessArticle

A Genome-Wide Scan Divulges Key Loci Involved in Resistance to Aphids (Aphis craccivora) in Cowpea (Vigna unguiculata)

by Patrick Obia Ongom, Abou Togola, Christian Fatokun and Ousmane Boukar

Genes 2022, 13(11), 2002; https://doi.org/10.3390/genes13112002 - 01 Nov 2022

Cited by 1 | Viewed by 1712

Abstract

Cowpea aphids (Aphis craccivora Koch) double as a direct damaging pest and a virus vector to cowpea, threatening the economic yield of the crop. Given the multiple ecotypes, different alleles have been implicated in aphid resistance, necessitating the identification of key genes [...] Read more.

Cowpea aphids (Aphis craccivora Koch) double as a direct damaging pest and a virus vector to cowpea, threatening the economic yield of the crop. Given the multiple ecotypes, different alleles have been implicated in aphid resistance, necessitating the identification of key genes involved. The present study implemented a genome-wide scan using 365 cowpea mini-core accessions to decipher loci involved in resistance to aphid ecotype from Kano, Nigeria. Accessions were artificially inoculated with A. craccivora in insect-proof cages and damage severity assessed at 21 days after infestation. Significant phenotypic differences based on aphid damage severity were registered among the accessions. Skewed phenotypic distributions were depicted in the population, suggesting the involvement of major genes in the control of resistance. A genome-wide scan identified three major regions on chromosomes Vu10, Vu08 and Vu02, and two minor ones on chromosomes Vu01 and Vu06, that were significantly associated with aphid resistance. These regions harbored several genes, out of which, five viz Vigun01g233100.1, Vigun02g088900.1, Vigun06g224900.1, Vigun08g030200.1 and Vigun10g031100.1 were the most proximal to the peak single nucleotide polymorphisms (SNPs) positions. These genes are expressed under stress signaling, mechanical wounding and insect feeding. The uncovered loci contribute towards establishing a marker-assisted breeding platform and building durable resistance against aphids in cowpea. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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14 pages, 2799 KiB

Open AccessArticle

Functional Study on Cytochrome P450 in Response to L(−)-Carvone Stress in Bursaphelenchus xylophilus

by Jie Chen, Xin Hao, Ruina Tan, Yang Li, Bowen Wang, Jialiang Pan, Wei Ma and Ling Ma

Genes 2022, 13(11), 1956; https://doi.org/10.3390/genes13111956 - 27 Oct 2022

Cited by 3 | Viewed by 1594

Abstract

Bursaphelenchus xylophilus (PWN) causes pine wilt disease (PWD), which is one of the most devastating pine diseases worldwide. Cytochrome P450 (CYP) catalyzes the biosynthetic metabolism of terpenoids and plays an important role in the modification of secondary metabolites in all living organisms. We [...] Read more.

Bursaphelenchus xylophilus (PWN) causes pine wilt disease (PWD), which is one of the most devastating pine diseases worldwide. Cytochrome P450 (CYP) catalyzes the biosynthetic metabolism of terpenoids and plays an important role in the modification of secondary metabolites in all living organisms. We investigated the molecular characteristics and biological functions of Bx-cyp29A3 in B. xylophilus. The bioinformatics analysis results indicated that Bx-cyp29A3 has a transmembrane domain and could dock with L(−)-carvone. The gene expression pattern indicated that Bx-cyp29A3 was expressed in 0.2, 0.4, 0.6, 0.8, and 1.0 mg/mL L(−)-carvone solutions. The Bx-cyp29A3 expression increased in a dose-dependent manner and peaked at 24 h of exposure when the L(−)-carvone solution concentration was 0.8 mg/mL. However, the gene expression peaked at 0.6 mg/mL after 36 h. Furthermore, RNA interference (RNAi) indicated that Bx-cyp29A3 played an essential role in the response to L(−)-carvone. The mortality rates of the Bx-cyp29A3 knockdown groups were higher than those of the control groups in the 0.4, 0.6, 0.8, and 1.0 mg/mL carvone solutions after 24 h of exposure or 36 h of exposure. In summary, bioinformatics provided the structural characteristics and conserved sequence properties of Bx-cyp29A3 and its encoded protein, which provided a target gene for the study of the P450 family of B. xylophilus. Gene silencing experiments clarified the function of Bx-cyp29A3 in the immune defense of B. xylophilus. This study provides a basis for the screening of new molecular targets for the prevention and management of B. xylophilus. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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19 pages, 2929 KiB

Open AccessArticle

Genome-Wide Identification of Potential mRNAs in Drought Response in Wheat (Triticum aestivum L.)

by Muhammad Aqeel, Wajya Ajmal, Quratulain Mujahid, Maryam Murtaza, Mansour Almuqbil, Shakira Ghazanfar, Muhammad Uzair, Ayesha Wadood, Syed Mohammed Basheeruddin Asdaq, Rameesha Abid, Ghulam Muhammad Ali and Muhammad Ramzan Khan

Genes 2022, 13(10), 1906; https://doi.org/10.3390/genes13101906 - 20 Oct 2022

Cited by 1 | Viewed by 2217

Abstract

Plant cell metabolism inevitably forms an important drought-responsive mechanism, which halts crop productivity. Globally, more than 30% of the total harvested area was affected by dehydration. RNA-seq technology has enabled biologists to identify stress-responsive genes in relatively quick times. However, one shortcoming of [...] Read more.

Plant cell metabolism inevitably forms an important drought-responsive mechanism, which halts crop productivity. Globally, more than 30% of the total harvested area was affected by dehydration. RNA-seq technology has enabled biologists to identify stress-responsive genes in relatively quick times. However, one shortcoming of this technology is the inconsistent data generation compared to other parts of the world. So, we have tried, here, to generate a consensus by analyzing meta-transcriptomic data available in the public microarray database GEO NCBI. In this way, the aim was set, here, to identify stress genes commonly identified as differentially expressed (p < 0.05) then followed by downstream analyses. The search term “Drought in wheat” resulted in 233 microarray experiments from the GEO NCBI database. After discarding empty datasets containing no expression data, the large-scale meta-transcriptome analytics and one sample proportional test were carried out (Bonferroni adjusted p < 0.05) to reveal a set of 11 drought-responsive genes on a global scale. The annotation of these genes revealed that the transcription factor activity of RNA polymerase II and sequence-specific DNA-binding mechanism had a significant role during the drought response in wheat. Similarly, the primary root differentiation zone annotations, controlled by TraesCS5A02G456300 and TraesCS7B02G243600 genes, were found as top-enriched terms (p < 0.05 and Q < 0.05). The resultant standard drought genes, glycosyltransferase; Arabidopsis thaliana KNOTTED-like; bHLH family protein; Probable helicase MAGATAMA 3; SBP family protein; Cytochrome c oxidase subunit 2; Trihelix family protein; Mic1 domain-containing protein; ERF family protein; HD-ZIP I protein; and ERF family protein, are important in terms of their worldwide proved link with stress. From a future perspective, this study could be important in a breeding program contributing to increased crop yield. Moreover, the wheat varieties could be identified as drought-resistant/sensitive based on the nature of gene expression levels. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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Open AccessBrief Report

The Genome of a Pigeonpea Compatible Rhizobial Strain ‘10ap3’ Appears to Lack Common Nodulation Genes

by Francina L. Bopape, Ahmed Idris Hassen, Rogerio M. Chiulele, Addmore Shonhai and Eastonce T. Gwata

Genes 2023, 14(5), 1084; https://doi.org/10.3390/genes14051084 - 14 May 2023

Cited by 1 | Viewed by 1549 | Correction

Abstract

The symbiotic fixation of atmospheric nitrogen (N) in root nodules of tropical legumes such as pigeonpea (Cajanus cajan) is a complex process, which is regulated by multiple genetic factors at the host plant genotype microsymbiont interface. The process involves multiple genes [...] Read more.

The symbiotic fixation of atmospheric nitrogen (N) in root nodules of tropical legumes such as pigeonpea (Cajanus cajan) is a complex process, which is regulated by multiple genetic factors at the host plant genotype microsymbiont interface. The process involves multiple genes with various modes of action and is accomplished only when both organisms are compatible. Therefore, it is necessary to develop tools for the genetic manipulation of the host or bacterium towards improving N fixation. In this study, we sequenced the genome of a robust rhizobial strain, Rhizobium tropici ‘10ap3’ that was compatible with pigeonpea, and we determined its genome size. The genome consisted of a large circular chromosome (6,297,373 bp) and contained 6013 genes of which 99.13% were coding sequences. However only 5833 of the genes were associated with proteins that could be assigned to specific functions. The genes for nitrogen, phosphorus and iron metabolism, stress response and the adenosine monophosphate nucleoside for purine conversion were present in the genome. However, the genome contained no common nod genes, suggesting that an alternative pathway involving a purine derivative was involved in the symbiotic association with pigeonpea. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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11 pages, 27913 KiB

Open AccessProject Report

Genome-Wide Analysis and Expression of the GRAS Transcription Factor Family in Avena sativa

by Lei Ling, Mingjing Li, Naiyu Chen, Guoling Ren, Lina Qu, Hua Yue, Xinyu Wu and Jing Zhao

Genes 2023, 14(1), 164; https://doi.org/10.3390/genes14010164 - 06 Jan 2023

Cited by 1 | Viewed by 1590

Abstract

The GRAS transcription factor is an important transcription factor in plants. In recent years, more GRAS genes have been identified in many plant species. However, the GRAS gene family has not yet been studied in Avena sativa. We identified 100 members of [...] Read more.

The GRAS transcription factor is an important transcription factor in plants. In recent years, more GRAS genes have been identified in many plant species. However, the GRAS gene family has not yet been studied in Avena sativa. We identified 100 members of the GRAS gene family in A. sativa (Avena sativa), named them AsGRAS1~AsGRAS100 according to the positions of 21 chromosomes, and classified them into 9 subfamilies. In this study, the motif and gene structures were also relatively conserved in the same subfamilies. At the same time, we found a great deal related to the stress of cis-acting promoter regulatory elements (MBS, ABRE, and TC-rich repeat elements). qRT-PCR suggested that the AsGRAS gene family (GRAS gene family in A. sativa) can regulate the response to salt, saline–alkali, and cold and freezing abiotic stresses. The current study provides original and detailed information about the AsGRAS gene family, which contributes to the functional characterization of GRAS proteins in other plants. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

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