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Special Issue "Recent Analysis and Applications of Comparative and Functional Genomic on Horticultural Plants"

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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
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Prof. Dr. Ying Li

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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
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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
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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

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Research

Open AccessArticle

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

and

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

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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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Open AccessArticle

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

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

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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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