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Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 12322

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Prof. Dr. Xiaoming Song

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Guest Editor

School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
Interests: plant genome evolution; comparative genomics; gene family; RNA-seq; expression network; non-coding RNA; database construction
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Ying Li

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Co-Guest Editor

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
Interests: genetic breeding of Brassica campestris ssp. Chinensis; downy mildew resistance; vitamin C biosynthesis and metabolism; microspore culture
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Qiusheng Kong

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Co-Guest Editor

Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
Interests: multi-omics; QTL mapping; disease resistance; fruit quality; genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Horticultural plants play critical roles in human daily life, which have important economic value, medicinal value and ornamental value. With the development of sequencing technology, genome sequencing of more and more horticultural plants has been completed. Moreover, the quality of the released genomes has been obviously improved due to the widely used of third-generation sequencing and Hi-C technology. These genomes provide rich resources for comparative and functional genomic studies in horticultural plants. Therefore, we organize this special issue to collect relevant research articles to promote the application of omics data in horticultural crops.

This special issue will mainly collect articles from the following aspects, but not limited to these aspects. (a) Gene family analysis at a large-scale level or verified experimentally; (b) Plant genome and comparative genomic analysis; (c) Population evolution and GWAS analysis; (d) Mining and verifying key genes of important agronomic traits; (e) Gene regulatory network construction; (f) Omic resource database or tool development for horticultural plants.

Prof. Dr. Xiaoming Song
Prof. Dr. Ying Li
Prof. Dr. Qiusheng Kong
Guest Editors

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Keywords

horticultural plants
gene family
comparative genomics
genome evolution
gene function
gene expression
database construction
tool development

Published Papers (9 papers)

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Research

16 pages, 4889 KiB

Open AccessArticle

Integrating Dynamic 3D Chromatin Architecture and Gene Expression Alterations Reveal Heterosis in Brassica rapa

by Liu E, Shanwu Lyu, Yaolong Wang, Dong Xiao, Tongkun Liu, Xilin Hou, Ying Li and Changwei Zhang

Int. J. Mol. Sci. 2024, 25(5), 2568; https://doi.org/10.3390/ijms25052568 - 22 Feb 2024

Viewed by 526

Abstract

Heterosis plays a significant role in enhancing variety, boosting yield, and raising economic value in crops, but the molecular mechanism is still unclear. We analyzed the transcriptomes and 3D genomes of a hybrid (F₁) and its parents (w30 and 082). The analysis of the expression revealed a total of 485 specially expressed genes (SEGs), 173 differentially expressed genes (DEGs) above the parental expression level, more actively expressed genes, and up-regulated DEGs in the F₁. Further study revealed that the DEGs detected in the F₁ and its parents were mainly involved in the response to auxin, plant hormone signal transduction, DNA metabolic process, purine metabolism, starch, and sucrose metabolism, which suggested that these biological processes may play a crucial role in the heterosis of Brassica rapa. The analysis of 3D genome data revealed that hybrid F₁ plants tend to contain more transcriptionally active A chromatin compartments after hybridization. Supplementaryly, the F₁ had a smaller TAD (topologically associated domain) genome length, but the number was the highest, and the expression change in activated TAD was higher than that of repressed TAD. More specific TAD boundaries were detected between the parents and F₁. Subsequently, 140 DEGs with genomic structural variants were selected as potential candidate genes. We found two DEGs with consistent expression changes in A/B compartments and TADs. Our findings suggested that genomic structural variants, such as TADs and A/B chromatin compartments, may affect gene expression and contribute to heterosis in Brassica rapa. This study provides further insight into the molecular mechanism of heterosis in Brassica rapa. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants)

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22 pages, 5118 KiB

Open AccessArticle

Transcriptomic Evidence of a Link between Cell Wall Biogenesis, Pathogenesis, and Vigor in Walnut Root and Trunk Diseases

by Houston J. Saxe, Sriema L. Walawage, Bipin Balan, Charles A. Leslie, Patrick J. Brown, Gregory T. Browne, Daniel A. Kluepfel, Andreas Westphal and Abhaya M. Dandekar

Int. J. Mol. Sci. 2024, 25(2), 931; https://doi.org/10.3390/ijms25020931 - 11 Jan 2024

Viewed by 1309

Abstract

Crown gall disease (Agrobacterium tumefaciens), crown/root rot disease (Phytophthora spp.), root lesion disease (Pratylenchus vulnus) and tree vigor are key traits affecting the productivity and quality of walnuts in California. Unchallenged hybrid rootstocks were analyzed by RNA-seq to examine pre-formed factors affecting these traits. Enrichment analysis of the differentially expressed genes revealed that the increased expression of cell wall biogenesis-related genes plays a key role in susceptibility to A. tumefaciens, susceptibility to Phytophthora spp. and increased vigor. Analysis of the predicted subcellular loci of the encoded proteins revealed that many gene products associated with vigor and susceptibility were targeted to the plasma membrane and extracellular space, connecting these traits to sustaining barrier function. We observed that RNA processing and splicing, along with predicted nuclear targeting, were associated with resistance to A. tumefaciens, resistance to Phytophthora spp. and low vigor. Four genes within the J. microcarpa QTL region for resistance to A. tumefaciens and Phytophthora spp. were represented among our transcripts, with two of the genes being differentially expressed in association with resistance to A. tumefaciens and decreased vigor. No differential expression related to Phytophthora spp. or P. vulnus resistance was observed in this region. Additionally, the J. microcarpa haplotype expressed more transcripts associated with resistance to A. tumefaciens, Phytophthora spp. and low vigor, but not P. vulnus, than the J. regia haplotype. We also report unique and shared hormone and defense responses associated with each trait. This research suggests a link between cell wall biogenesis, vigor and critical root diseases of walnut. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants)

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18 pages, 13306 KiB

Open AccessArticle

Polyploid Genome Assembly Provides Insights into Morphological Development and Ascorbic Acid Accumulation of Sauropus androgynus

by Fagang Xia, Bin Li, Kangkang Song, Yankun Wang, Zhuangwei Hou, Haozhen Li, Xiaohua Zhang, Fangping Li and Long Yang

Int. J. Mol. Sci. 2024, 25(1), 300; https://doi.org/10.3390/ijms25010300 - 25 Dec 2023

Cited by 1 | Viewed by 1038

Abstract

Sauropus androgynus (S. androgynus) (2n = 4x = 52) is one of the most popular functional leafy vegetables in South and Southeast Asia. With its rich nutritional and pharmaceutical values, it has traditionally had widespread use for dietary and herbal purposes. Here, the genome of S. androgynus was sequenced and assembled, revealing a genome size of 1.55 Gb with 26 pseudo-chromosomes. Phylogenetic analysis traced back the divergence of Sauropus from Phyllanthus to approximately 29.67 million years ago (Mya). Genome analysis revealed that S. androgynus polyploidized around 20.51 Mya and shared a γ event about 132.95 Mya. Gene function analysis suggested that the expansion of pathways related to phloem development, lignin biosynthesis, and photosynthesis tended to result in the morphological differences among species within the Phyllanthaceae family, characterized by varying ploidy levels. The high accumulation of ascorbic acid in S. androgynus was attributed to the high expression of genes associated with the L-galactose pathway and recycling pathway. Moreover, the expanded gene families of S. androgynus exhibited multiple biochemical pathways associated with its comprehensive pharmacological activity, geographic adaptation and distinctive pleasurable flavor. Altogether, our findings represent a crucial genomic asset for S. androgynus, casting light on the intricate ploidy within the Phyllanthaceae family. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants)

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22 pages, 6817 KiB

Open AccessArticle

Identification and Analysis of the Expression of the PIP5K Gene Family in Tomatoes

by Zepeng Wang, Zhongyu Wang, Xianguo Li, Zhaolong Chen, Yuxiang Liu, Fulin Zhang, Qi Dai, Qinghui Yu and Ning Li

Int. J. Mol. Sci. 2024, 25(1), 159; https://doi.org/10.3390/ijms25010159 - 21 Dec 2023

Viewed by 651

Abstract

To explore the function of phosphatidylinositol 4-phosphate 5-kinase (PIP5K) in tomatoes, members of the tomato PIP5K family were identified and characterized using bioinformatic methods, and their expression patterns were also analyzed under salt stress and in different tissues. Twenty-one PIP5K members—namely, SlPIP5K1–SlPIP5K21—were identified from ten chromosomes, and these were divided into three groups according to a phylogenetic analysis. Further bioinformatic analysis showed four pairs of collinear relationships and fragment replication events among the SlPIP5K family members. To understand the possible roles of the SlPIP5Ks, a cis-acting element analysis was conducted, which indicated that tomato PIP5Ks could be associated with plant growth, hormones, and stress responses. We further validated the results of the in silico analysis by integrating RNA-seq and qRT-PCR techniques for salt- and hormone-treated tomato plants. Our results showed that SlPIP5K genes exhibited tissue- and treatment-specific patterns, and some of the SlPIP5Ks exhibited significantly altered expressions after our treatments, suggesting that they might be involved in these stresses. We selected one of the SlPIP5Ks that responded to our treatments, SlPIP5K2, to further understand its subcellular localization. Our results showed that SlPIP5K2 was located on the membrane. This study lays a foundation for the analysis of the biological functions of the tomato SlPIP5K genes and can also provide a theoretical basis for the selection and breeding of new tomato varieties and germplasm innovation, especially under salt stress. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants)

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22 pages, 3357 KiB

Open AccessArticle

The Competing Endogenous RNAs Regulatory Genes Network Mediates Leaf Shape Variation and Main Effector Gene Function in Mulberry Plant (Morus alba)

by Jianbin Li, Lei Wang, Michael Ackah, Frank Kwarteng Amoako, Zijie Jiang, Yisu Shi, Haonan Li and Weiguo Zhao

Int. J. Mol. Sci. 2023, 24(23), 16860; https://doi.org/10.3390/ijms242316860 - 28 Nov 2023

Viewed by 1985

Abstract

Mulberry plants (Morus alba) have leaf shapes, ranging from unlobed to lobed, which are crucial for yield, growth, and adaptability, indicating their ability to adapt to their environment. Competing endogenous RNAs (ceRNAs) constitute a web of RNAs within the organism’s transcriptional regulatory system, including protein-coding genes (mRNAs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and others. In this study, samples for ceRNA sequencing were categorized into two groups: whole leaves and lobed leaves, each group with three replicates. In addition, we isolated, cloned, and characterized the precursor miRNA (miR156x) from the leaves of M. alba. miR156x precursor had a length of 107 base pairs and a minimum folding free energy of 50.27 kcal/mol. We constructed a pCAMBIA-35S-GUS-miR156x dual overexpression vector and established a transient transformation system for mulberry. At an optimal transformation solution (OD600 = 0.7), the GUS gene showed a higher expression in the leaves of transiently transformed mulberry with miR156x overexpression, four days after transformation, while the target genes of miR156x had decreased expression in the same leaves. Investigations into the transgenic mulberry plants uncovered various modifications to physio-chemical parameters including POD, SOD, PRO, MDA, soluble proteins and sugars, and chlorophyl content. miRNAs in the plants were found to act as negative regulators of gene expression in response to changes in leaf shape regulation, which was confirmed in vitro using dual-luciferase reporter assays. Subsequently, we cloned Maspl3 in vitro and conducted GST-Pull down assays, obtaining multiple proteins that interacted with the Maspl3 gene. This indicates that the miR156x/Maspl3/MSTRG.25812.1 regulatory module contributes to the differences in mulberry leaf shape. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants)

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14 pages, 18460 KiB

Open AccessArticle

Comparative Transcriptome Analysis between Resistant and Susceptible Pakchoi Cultivars in Response to Downy Mildew

by Yaosong Chen, Liming Miao, Xiaofeng Li, Yiwen Liu, Dandan Xi, Dingyu Zhang, Lu Gao, Yuying Zhu, Shaojun Dai and Hongfang Zhu

Int. J. Mol. Sci. 2023, 24(21), 15710; https://doi.org/10.3390/ijms242115710 - 28 Oct 2023

Viewed by 1707

Abstract

Downy mildew caused by the obligate parasite Hyaloperonospora brassicae is a devastating disease for Brassica species. Infection of Hyaloperonospora brassicae often leads to yellow spots on leaves, which significantly impacts quality and yield of pakchoi. In the present study, we conducted a comparative transcriptome between the resistant and susceptible pakchoi cultivars in response to Hyaloperonospora brassicae infection. A total of 1073 disease-resistance-related differentially expressed genes were identified using a Venn diagram. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that these genes were mainly involved in plant−pathogen interaction, plant hormone signal transduction, and other photosynthesis-related metabolic processes. Analysis of the phytohormone content revealed that salicylic acid increased significantly in the resistant material after inoculation with Hyaloperonospora brassicae, whereas the contents of jasmonic acid, abscisic acid, and 1-aminocyclopropane-1-carboxylic acid decreased. Exogenous salicylic acid treatment also significantly upregulated Hyaloperonospora brassicae-induced genes, which further confirmed a crucial role of salicylic acid during pakchoi defense against Hyaloperonospora brassicae. Based on these findings, we suggest that the salicylic-acid-mediated signal transduction contributes to the resistance of pakchoi to downy mildew, and PAL1, ICS1, NPR1, PR1, PR5, WRKY70, WRKY33, CML43, CNGC9, and CDPK15 were involved in this responsive process. Our findings evidently contribute to revealing the molecular mechanism of pakchoi defense against Hyaloperonospora brassicae. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants)

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19 pages, 5779 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the Copper Transporter (COPT/Ctr) Gene Family in Kandelia obovata, a Typical Mangrove Plant

by Quaid Hussain, Ting Ye, Sihui Li, Jackson Nkoh Nkoh, Qiao Zhou and Chenjing Shang

Int. J. Mol. Sci. 2023, 24(21), 15579; https://doi.org/10.3390/ijms242115579 - 25 Oct 2023

Cited by 3 | Viewed by 1462

Abstract

The copper transporter (COPT/Ctr) gene family plays a critical part in maintaining the balance of the metal, and many diverse species depend on COPT to move copper (Cu) across the cell membrane. In Arabidopsis thaliana, Oryza sativa, Medicago sativa, Zea mays, Populus trichocarpa, Vitis vinifera, and Solanum lycopersicum, a genome-wide study of the COPT protein family was performed. To understand the major roles of the COPT gene family in Kandelia obovata (Ko), a genome-wide study identified four COPT genes in the Kandelia obovata genome for the first time. The domain and 3D structural variation, phylogenetic tree, chromosomal distributions, gene structure, motif analysis, subcellular localization, cis-regulatory elements, synteny and duplication analysis, and expression profiles in leaves and Cu were all investigated in this research. Structural and sequence investigations show that most KoCOPTs have three transmembrane domains (TMDs). According to phylogenetic research, these KoCOPTs might be divided into two subgroups, just like Populus trichocarpa. KoCOPT gene segmental duplications and positive selection pressure were discovered by universal analysis. According to gene structure and motif analysis, most KoCOPT genes showed consistent exon–intron and motif organization within the same group. In addition, we found five hormones and four stress- and seven light-responsive cis-elements in the KoCOPTs promoters. The expression studies revealed that all four genes changed their expression levels in response to copper (CuCl₂) treatments. In summary, our study offers a thorough overview of the Kandelia obovata COPT gene family’s expression pattern and functional diversity, making it easier to characterize each KoCOPT gene’s function in the future. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants)

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20 pages, 11960 KiB

Open AccessArticle

Integrated Transcriptome and Proteome Analysis Revealed the Regulatory Mechanism of Hypocotyl Elongation in Pakchoi

by Xiaofeng Li, Dandan Xi, Lu Gao, Hongfang Zhu, Xiuke Yang, Xiaoming Song, Changwei Zhang, Liming Miao, Dingyu Zhang, Zhaohui Zhang, Xilin Hou, Yuying Zhu and Min Wei

Int. J. Mol. Sci. 2023, 24(18), 13808; https://doi.org/10.3390/ijms241813808 - 07 Sep 2023

Cited by 1 | Viewed by 892

Abstract

Hypocotyl length is a critical determinant for the efficiency of mechanical harvesting in pakchoi production, but the knowledge on the molecular regulation of hypocotyl growth is very limited. Here, we report a spontaneous mutant of pakchoi, lhy7.1, and identified its characteristics. We found that it has an elongated hypocotyl phenotype compared to the wild type caused by the longitudinal growth of hypocotyl cells. Different light quality treatments, transcriptome, and proteomic analyses were performed to reveal the molecular mechanisms of hypocotyl elongation. The data showed that the hypocotyl length of lhy7.1 was significantly longer than that of WT under red, blue, and white lights but there was no significant difference under dark conditions. Furthermore, we used transcriptome and label-free proteome analyses to investigate differences in gene and protein expression levels between lhy7.1 and WT. At the transcript level, 4568 differentially expressed genes (DEGs) were identified, which were mainly enriched in “plant hormone signal transduction”, “photosynthesis”, “photosynthesis–antenna proteins”, and “carbon fixation in photosynthetic organisms” pathways. At the protein level, 1007 differentially expressed proteins (DEPs) were identified and were mainly enriched in photosynthesis-related pathways. The comprehensive transcriptome and proteome analyses revealed a regulatory network of hypocotyl elongation involving plant hormone signal transduction and photosynthesis-related pathways. The findings of this study help elucidate the regulatory mechanisms of hypocotyl elongation in lhy7.1. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants)

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18 pages, 5709 KiB

Open AccessArticle

Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber

by Lei Xia, Han Wang, Xiaokun Zhao, Hesbon Ochieng Obel, Xiaqing Yu, Qunfeng Lou, Jinfeng Chen and Chunyan Cheng

Int. J. Mol. Sci. 2023, 24(10), 8943; https://doi.org/10.3390/ijms24108943 - 18 May 2023

Cited by 2 | Viewed by 1843

Abstract

Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, phylogenetic, haplotype, and population genetic structure analysis. Meanwhile, we explored the changes in expression of cucumber chloroplast genes under high- and low-temperature stimulation via transcriptome analysis. As a result, a total of 50 complete chloroplast genomes were successfully assembled from 121 cucumber resequencing data, ranging in size from 156,616–157,641 bp. The 50 cucumber chloroplast genomes have typical quadripartite structures, consisting of a large single copy (LSC, 86,339–86,883 bp), a small single copy (SSC, 18,069–18,363 bp), and two inverted repeats (IRs, 25,166–25,797 bp). Comparative genomic, haplotype, and population genetic structure results showed that there is more genetic variation in Indian ecotype cucumbers compared to other cucumber cultivars, which means that many genetic resources remain to be explored in Indian ecotype cucumbers. Phylogenetic analysis showed that the 50 cucumber germplasms could be classified into 3 types: East Asian, Eurasian + Indian, and Xishuangbanna + Indian. The transcriptomic analysis showed that matK were significantly up-regulated under high- and low-temperature stresses, further demonstrating that cucumber chloroplasts respond to temperature adversity by regulating lipid metabolism and ribosome metabolism. Further, accD has higher editing efficiency under high-temperature stress, which may contribute to the heat tolerance. These studies provide useful insight into genetic variation in the chloroplast genome, and established the foundation for exploring the mechanisms of temperature-stimulated chloroplast adaptation. Full article

(This article belongs to the Special Issue Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants)

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