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Power Up Plant Genetic Research with Genomic Data 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 September 2024 | Viewed by 7181

Special Issue Editors


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Guest Editor
Lab of Plant Genetics and Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
Interests: molecular genetics; breeding, whole genome sequencing; digital phenotyping
Special Issues, Collections and Topics in MDPI journals
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
Interests: genome; domestication; quantitative trait locus; flowering; agriculture; soybean
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Developments in plant genetics and genomics research usually lags behind those in mammals and human due to the complexity of the plant genome and the limitations of research resources. Regardless, with the advances in sequencing technology, the building of high-quality genomes and the sequencing of huge populations of plants are no longer technologically challenging, nor resource intensive. Epigenomics, transcriptomics, proteomics, metabolomics, and phenomics have also made significant advances in recently years, creating more opportunities in plant genomic research. Although the generation of genome sequencing data is no longer a limitation, there are a vast volume of genomic data deposited in public databases. Diving into the sea of genomic data to generate new knowledge has become the next challenge in the genomic era. Each plant genome is made up of hundreds of millions to trillions of bases, which each contain tens of thousands of genes and numerous non-coding elements. Currently, only a tiny fraction of the plant genome is being characterized, even in the model plant Arabidopsis. In this Special Issue, we would like to invite dedicated scientists to submit their recent research and review articles on plant genomics and genetics with the support of molecular biology and biotechnology.

Prof. Dr. Hon-Ming Lam
Dr. Sachiko Isobe
Dr. Man-Wah Li
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genome sequencing
  • optical mapping
  • genome editing
  • population genomics
  • genome-wide
  • association mapping
  • functional genomics
  • epigenomics
  • genetic interaction
  • chromatin
  • biodiversity

Published Papers (7 papers)

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Research

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16 pages, 30973 KiB  
Article
Genome-Wide Identification and Expression Analysis of YTH Gene Family for Abiotic Stress Regulation in Camellia chekiangoleosa
by Xiang Cheng, Sheng Yao, Jingjing Zhang, Dengbao Wang, Shaojun Xu, Qiong Yu and Kongshu Ji
Int. J. Mol. Sci. 2024, 25(7), 3996; https://doi.org/10.3390/ijms25073996 - 03 Apr 2024
Viewed by 498
Abstract
N6-methyladenosine (m6A) is essential for RNA metabolism in cells. The YTH domain, conserved in the kingdom of Eukaryotes, acts as an m6A reader that binds m6A-containing RNA. In plants, the YTH domain is involved in [...] Read more.
N6-methyladenosine (m6A) is essential for RNA metabolism in cells. The YTH domain, conserved in the kingdom of Eukaryotes, acts as an m6A reader that binds m6A-containing RNA. In plants, the YTH domain is involved in plant hormone signaling, stress response regulation, RNA stability, translation, and differentiation. However, little is known about the YTH genes in tea-oil tree, which can produce edible oil with high nutritional value. This study aims to identify and characterize the YTH domains within the tea-oil tree (Camellia chekiangoleosa Hu) genome to predict their potential role in development and stress regulation. In this study, 10 members of the YTH family containing the YTH domain named CchYTH1-10 were identified from C. chekiangoleosa. Through analysis of their physical and chemical properties and prediction of subcellular localization, it is known that most family members are located in the nucleus and may have liquid–liquid phase separation. Analysis of cis-acting elements in the CchYTH promoter region revealed that these genes could be closely related to abiotic stress and hormones. The results of expression profiling show that the CchYTH genes were differentially expressed in different tissues, and their expression levels change under drought stress. Overall, these findings could provide a foundation for future research regarding CchYTHs in C. chekiangoleosa and enrich the world in terms of epigenetic mark m6A in forest trees. Full article
(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data 2.0)
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14 pages, 2458 KiB  
Article
Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications
by Tao Wu, Yong-Kang Sima, Shao-Yu Chen, Yu-Pin Fu, Hui-Fen Ma, Jia-Bo Hao and Yun-Feng Zhu
Int. J. Mol. Sci. 2024, 25(6), 3506; https://doi.org/10.3390/ijms25063506 - 20 Mar 2024
Viewed by 491
Abstract
Based on Sima and Lu’s system of the family Magnoliaceae, the genus Lirianthe Spach s. l. includes approximately 25 species, each with exceptional landscaping and horticultural or medical worth. Many of these plants are considered rare and are protected due to their endangered [...] Read more.
Based on Sima and Lu’s system of the family Magnoliaceae, the genus Lirianthe Spach s. l. includes approximately 25 species, each with exceptional landscaping and horticultural or medical worth. Many of these plants are considered rare and are protected due to their endangered status. The limited knowledge of species within this genus and the absence of research on its chloroplast genome have greatly impeded studies on the relationship between its evolution and systematics. In this study, the chloroplast genomes of eight species from the genus Lirianthe were sequenced and analyzed, and their phylogenetic relationships with other genera of the family Magnoliaceae were also elucidated. The results showed that the chloroplast genome sizes of the eight Lirianthe species ranged from 159,548 to 159,833 bp. The genomes consisted of a large single-copy region, a small single-copy region, and a pair of inverted repeat sequences. The GC content was very similar across species. Gene annotation revealed that the chloroplast genomes contained 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, totaling 130 genes. Codon usage analysis indicated that codon usage was highly conserved among the eight Lirianthe species. Repeat sequence analysis identified 42–49 microsatellite sequences, 16–18 tandem repeats, and 50 dispersed repeats, with microsatellite sequences being predominantly single-nucleotide repeats. DNA polymorphism analysis revealed 10 highly variable regions located in the large single-copy and small single-copy regions, among which rpl32-trnL, petA-psbJ, and trnH-psbA were the recommended candidate DNA barcodes for the genus Lirianthe species. The inverted repeat boundary regions show little variation between species and are generally conserved. The result of phylogenetic analysis confirmed that the genus Lirianthe s. l. is a monophyletic taxon and the most affinal to the genera, Talauma and Dugandiodendron, in Sima and Lu’s system and revealed that the genus Lirianthe s. s. is paraphyletic and the genus Talauma s. l. polyphyletic in Xia’s system, while Magnolia subsection Gwillimia is paraphyletic and subsection Blumiana polyphyletic in Figlar and Nooteboom’s system. Morphological studies found noticeable differences between Lirianthe species in aspects including leaf indumentum, stipule scars, floral orientation, tepal number, tepal texture, and fruit dehiscence. In summary, this study elucidated the chloroplast genome evolution within Lirianthe and laid a foundation for further systematic and taxonomic research on this genus. Full article
(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data 2.0)
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22 pages, 8094 KiB  
Article
Distribution and Location of BEVs in Different Genotypes of Bananas Reveal the Coevolution of BSVs and Bananas
by Xueqin Rao, Huazhou Chen, Yongsi Lu, Runpei Liu and Huaping Li
Int. J. Mol. Sci. 2023, 24(23), 17064; https://doi.org/10.3390/ijms242317064 - 02 Dec 2023
Viewed by 647
Abstract
Members of the family Caulimoviridae contain abundant endogenous pararetroviral sequences (EPRVs) integrated into the host genome. Banana streak virus (BSV), a member of the genus Badnavirus in this family, has two distinct badnaviral integrated sequences, endogenous BSV (eBSV) and banana endogenous badnavirus sequences [...] Read more.
Members of the family Caulimoviridae contain abundant endogenous pararetroviral sequences (EPRVs) integrated into the host genome. Banana streak virus (BSV), a member of the genus Badnavirus in this family, has two distinct badnaviral integrated sequences, endogenous BSV (eBSV) and banana endogenous badnavirus sequences (BEVs). BEVs are distributed widely across the genomes of different genotypes of bananas. To clarify the distribution and location of BEVs in different genotypes of bananas and their coevolutionary relationship with bananas and BSVs, BEVs and BSVs were identified in 102 collected banana samples, and a total of 327 BEVs were obtained and categorized into 26 BEVs species with different detection rates. However, the majority of BEVs were found in Clade II, and a few were clustered in Clade I. Additionally, BEVs and BSVs shared five common conserved motifs. However, BEVs had two unique amino acids, methionine and lysine, which differed from BSVs. BEVs were distributed unequally on most of chromosomes and formed hotspots. Interestingly, a colinear relationship of BEVs was found between AA and BB, as well as AA and SS genotypes of bananas. Notably, the chromosome integration time of different BEVs varied. Based on our findings, we propose that the coevolution of bananas and BSVs is driven by BSV Driving Force (BDF), a complex interaction between BSVs, eBSVs, and BEVs. This study provides the first clarification of the relationship between BEVs and the coevolution of BSVs and bananas in China. Full article
(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data 2.0)
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23 pages, 6085 KiB  
Article
Co-Expression Network Analysis of the Transcriptome Identified Hub Genes and Pathways Responding to Saline–Alkaline Stress in Sorghum bicolor L.
by Hongcheng Wang, Lvlan Ye, Lizhou Zhou, Junxing Yu, Biao Pang, Dan Zuo, Lei Gu, Bin Zhu, Xuye Du and Huinan Wang
Int. J. Mol. Sci. 2023, 24(23), 16831; https://doi.org/10.3390/ijms242316831 - 27 Nov 2023
Viewed by 741
Abstract
Soil salinization, an intractable problem, is becoming increasingly serious and threatening fragile natural ecosystems and even the security of human food supplies. Sorghum (Sorghum bicolor L.) is one of the main crops growing in salinized soil. However, the tolerance mechanisms of sorghum [...] Read more.
Soil salinization, an intractable problem, is becoming increasingly serious and threatening fragile natural ecosystems and even the security of human food supplies. Sorghum (Sorghum bicolor L.) is one of the main crops growing in salinized soil. However, the tolerance mechanisms of sorghum to saline–alkaline soil are still ambiguous. In this study, RNA sequencing was carried out to explore the gene expression profiles of sorghum treated with sodium bicarbonate (150 mM, pH = 8.0, treated for 0, 6, 12 and 24 h). The results show that 6045, 5122, 6804, 7978, 8080 and 12,899 differentially expressed genes (DEGs) were detected in shoots and roots after 6, 12 and 24 h treatments, respectively. GO, KEGG and weighted gene co-expression analyses indicate that the DEGs generated by saline–alkaline stress were primarily enriched in plant hormone signal transduction, the MAPK signaling pathway, starch and sucrose metabolism, glutathione metabolism and phenylpropanoid biosynthesis. Key pathway and hub genes (TPP1, WRKY61, YSL1 and NHX7) are mainly related to intracellular ion transport and lignin synthesis. The molecular and physiological regulation processes of saline–alkali-tolerant sorghum are shown by these results, which also provide useful knowledge for improving sorghum yield and quality under saline–alkaline conditions. Full article
(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data 2.0)
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17 pages, 6385 KiB  
Article
MicroRNA2871b of Dongxiang Wild Rice (Oryza rufipogon Griff.) Negatively Regulates Cold and Salt Stress Tolerance in Transgenic Rice Plants
by Wanling Yang, Yong Chen, Rifang Gao, Yaling Chen, Yi Zhou, Jiankun Xie and Fantao Zhang
Int. J. Mol. Sci. 2023, 24(19), 14502; https://doi.org/10.3390/ijms241914502 - 25 Sep 2023
Viewed by 986
Abstract
Cold and salt stresses are major environmental factors that constrain rice production. Understanding their mechanisms is important to enhance cold and salt stress tolerance in rice. MicroRNAs (miRNAs) are a class of non-coding RNAs with only 21–24 nucleotides that are gene regulators in [...] Read more.
Cold and salt stresses are major environmental factors that constrain rice production. Understanding their mechanisms is important to enhance cold and salt stress tolerance in rice. MicroRNAs (miRNAs) are a class of non-coding RNAs with only 21–24 nucleotides that are gene regulators in plants and animals. Previously, miR2871b expression was suppressed by cold stress in Dongxiang wild rice (DXWR, Oryza rufipogon Griff.). However, its biological functions in abiotic stress responses remain elusive. In the present study, miR2871b of DWXR was overexpressed to investigate its function under stress conditions. When miR2871b of DWXR was introduced into rice plants, the transgenic lines were more sensitive to cold and salt stresses, and their tolerance to cold and salt stress decreased. The increased expression of miR2871b in rice plants also increased the levels of reactive oxygen species (ROS) and malondialdehyde (MDA); however, it markedly decreased the activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) and the contents of proline (Pro) and soluble sugar (SS). These data suggested that miR2871b of DXWR has negative regulatory effects on cold and salt stress tolerance. Meanwhile, 412 differentially expressed genes (DEGs) were found in rice transgenic plants using transcriptome sequencing, among which 266 genes were up-regulated and 146 genes were down-regulated. Furthermore, the upstream cis-acting elements and downstream targets of miR2871b were predicted and analyzed, and several critical acting elements (ABRE and TC-rich repeats) and potential target genes (LOC_Os03g41200, LOC_Os07g47620, and LOC_Os04g30260) were obtained. Collectively, these results generated herein further elucidate the vital roles of miR2871b in regulating cold and salt responses of DXWR. Full article
(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data 2.0)
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16 pages, 6504 KiB  
Article
Towards the Investigation of the Adaptive Divergence in a Species of Exceptional Ecological Plasticity: Chromosome-Scale Genome Assembly of Chouardia litardierei (Hyacinthaceae)
by Ivan Radosavljević, Krešimir Križanović, Sara Laura Šarančić and Jernej Jakše
Int. J. Mol. Sci. 2023, 24(13), 10755; https://doi.org/10.3390/ijms241310755 - 28 Jun 2023
Viewed by 1208
Abstract
One of the central goals of evolutionary biology is to understand the genomic basis of adaptive divergence. Different aspects of evolutionary processes should be studied through genome-wide approaches, therefore maximizing the investigated genomic space. However, in-depth genome-scale analyses often are restricted to a [...] Read more.
One of the central goals of evolutionary biology is to understand the genomic basis of adaptive divergence. Different aspects of evolutionary processes should be studied through genome-wide approaches, therefore maximizing the investigated genomic space. However, in-depth genome-scale analyses often are restricted to a model or economically important species and their closely related wild congeners with available reference genomes. Here, we present the high-quality chromosome-level genome assembly of Chouardia litardierei, a plant species with exceptional ecological plasticity. By combining PacBio and Hi-C sequencing technologies, we generated a 3.7 Gbp genome with a scaffold N50 size of 210 Mbp. Over 80% of the genome comprised repetitive elements, among which the LTR retrotransposons prevailed. Approximately 86% of the 27,257 predicted genes were functionally annotated using public databases. For the comparative analysis of different ecotypes’ genomes, the whole-genome sequencing of two individuals, each from a distinct ecotype, was performed. The detected above-average SNP density within coding regions suggests increased adaptive divergence-related mutation rates, therefore confirming the assumed divergence processes within the group. The constructed genome presents an invaluable resource for future research activities oriented toward the investigation of the genetics underlying the adaptive divergence that is likely unfolding among the studied species’ ecotypes. Full article
(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data 2.0)
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Review

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38 pages, 1164 KiB  
Review
Genetic Basis of Grain Size and Weight in Rice, Wheat, and Barley
by Sebastian Gasparis and Michał Miłosz Miłoszewski
Int. J. Mol. Sci. 2023, 24(23), 16921; https://doi.org/10.3390/ijms242316921 - 29 Nov 2023
Cited by 2 | Viewed by 1522
Abstract
Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during [...] Read more.
Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during the pre-anthesis phase, up to grain filling and maturation. Understanding the genetic and molecular mechanisms that control grain size is a prerequisite for improving grain yield potential. The last decade has brought significant progress in genomic studies of grain size control. Several genes underlying grain size and weight were identified and characterized in rice, which is a model plant for cereal crops. A molecular function analysis revealed most genes are involved in different cell signaling pathways, including phytohormone signaling, transcriptional regulation, ubiquitin–proteasome pathway, and other physiological processes. Compared to rice, the genetic background of grain size in other important cereal crops, such as wheat and barley, remains largely unexplored. However, the high level of conservation of genomic structure and sequences between closely related cereal crops should facilitate the identification of functional orthologs in other species. This review provides a comprehensive overview of the genetic and molecular bases of grain size and weight in wheat, barley, and rice, focusing on the latest discoveries in the field. We also present possibly the most updated list of experimentally validated genes that have a strong effect on grain size and discuss their molecular function. Full article
(This article belongs to the Special Issue Power Up Plant Genetic Research with Genomic Data 2.0)
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