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Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition

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A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 30 April 2024 | Viewed by 2861

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Special Issue Editors

Prof. Dr. Quan Zou

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Guest Editor

Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
Interests: bioinformatics; machine learning; parallel computing
Special Issues, Collections and Topics in MDPI journals

Dr. Ran Su

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Guest Editor

School of Computer Software, Tianjin University, Tianjin 300350, China
Interests: biomedical image analysis; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since the first plant genome, that of Arabidopsis thaliana, was published in December 2000, over 1000 plant genomes representing different plant species and subspecies have been sequenced and published. With the development of sequencing technology, an increasing number of omics datasets have been released, such as pan-genomics, proteomics, transcriptomics and metabolomics. It is important to highlight that the rapid accumulation of omics datasets has greatly promoted the development of plant science, especially crop genetics and breeding. In recent years, even many bioinformatic tools have been developed for omics analyses, but there are still many challenges remaining, from the construction of complex plant genomes to multi-omics analyses. Hence, more advanced algorithms, more powerful pan-genome analysis tools and more comprehensive databases still need to be developed.

Polyploidy, heterozygosity and large genomes in plants are still the main obstacles to plant genome sequencing and assembly; we believe that future studies about omics analyses in plants can make progress by incorporating more advanced technologies. Therefore, we organized this Special Issue on “Comparative Genomics and Functional Genomics Analyses in Plants, 2nd Edition” to help us better understand the plant genome and gene function and evolution and provide a resource for decoding the molecular mechanisms of complex agronomic traits.

I am pleased to invite you to participate in this Special Issue, “Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition”. Research papers, up-to-date review articles, and commentaries are all welcome.

We also thank to Dr. Yansu Wang for her contribution and support of this Special Issue.

Prof. Dr. Quan Zou
Dr. Ran Su
Guest Editors

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Keywords

de novo genome sequencing
pan-genomic analyses
genome re-sequencing
GWAS analyses
RNA-seq
metabolomics
gene family analyses
plant evolutionary analyses
bioinformatics
database

Published Papers (3 papers)

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Research

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14 pages, 4610 KiB

Open AccessArticle

Global Analysis of the WOX Transcription Factor Family in Akebia trifoliata

by Shengpeng Chen, Huai Yang, Yongle Zhang, Chen Chen, Tianheng Ren, Feiquan Tan and Peigao Luo

Curr. Issues Mol. Biol. 2024, 46(1), 11-24; https://0-doi-org.brum.beds.ac.uk/10.3390/cimb46010002 - 19 Dec 2023

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Abstract

Akebia trifoliata is an economically important, self-incompatible fruit tree in the Lardizabalaceae family. Asexual propagation is the main strategy used to maintain excellent agronomic traits. However, the generation of adventitious roots during asexual propagation is very difficult. To study the important role of the WUSCHEL-related homeobox (WOX) transcription factor in adventitious root growth and development, we characterized this transcription factor family in the whole genome of A. trifoliata. A total of 10 AktWOXs were identified, with the following characteristics: length (657~11,328 bp), exon number (2~5), isoelectric point (5.65~9.03), amino acid number (176~361 AA) and molecular weight (20.500~40.173 kDa), and their corresponding expression sequence could also be detectable in the public transcriptomic data for A. trifoliata fruit. A total of 10 AktWOXs were classified into modern (6), intermediate (2) and ancient clades (2) and all AktWOXs had undergone strong purifying selection during evolution. The expression profile of AktWOXs during A. trifoliata adventitious root formation indicated that AktWOXs play an important role in the regulation of adventitious root development. Overall, this is the first study to identify and characterize the WOX family in A. trifoliata and will be helpful for further research on A. trifoliata adventitious root formation. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition)

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18 pages, 3213 KiB

Open AccessArticle

Enhanced UV-B Radiation in Potato Stems and Leaves Promotes the Accumulation of Anthocyanins in Tubers

by Lingyan Cui, Maoxing Li, Xing Zhang, Zongming Guo, Kaifeng Li, Yuhan Shi, Qiong Wang and Huachun Guo

Curr. Issues Mol. Biol. 2023, 45(12), 9943-9960; https://0-doi-org.brum.beds.ac.uk/10.3390/cimb45120621 - 11 Dec 2023

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Abstract

Enhanced ultraviolet-B (UV-B) radiation promotes anthocyanin biosynthesis in leaves, flowers and fruits of plants. However, the effects and underlying mechanisms of enhanced UV-B radiation on the accumulation of anthocyanins in the tubers of potatoes (Solanum tuberosum L.) remain unclear. Herein, reciprocal grafting experiments were first conducted using colored and uncolored potatoes, demonstrating that the anthocyanins in potato tubers were synthesized in situ, and not transported from the leaves to the tubers. Furthermore, the enhanced UV-B radiation (2.5 kJ·m⁻²·d⁻¹) on potato stems and leaves significantly increased the contents of total anthocyanin and monomeric pelargonidin and peonidin in the red-fleshed potato ‘21-1’ tubers, compared to the untreated control. A comparative transcriptomic analysis showed that there were 2139 differentially expressed genes (DEGs) under UV-B treatment in comparison to the control, including 1724 up-regulated and 415 down-regulated genes. The anthocyanin-related enzymatic genes in the tubers such as PAL, C4H, 4CL, CHS, CHI, F3H, F3’5’H, ANS, UFGTs, and GSTs were up-regulated under UV-B treatment, except for a down-regulated F3’H. A known anthocyanin-related transcription factor StbHLH1 also showed a significantly higher expression level under UV-B treatment. Moreover, six differentially expressed MYB transcription factors were remarkably correlated to almost all anthocyanin-related enzymatic genes. Additionally, a DEGs enrichment analysis suggested that jasmonic acid might be a potential UV-B signaling molecule involved in the UV-B-induced tuber biosynthesis of anthocyanin. These results indicated that enhanced UV-B radiation in potato stems and leaves induced anthocyanin accumulation in the tubers by regulating the enzymatic genes and transcription factors involved in anthocyanin biosynthesis. This study provides novel insights into the mechanisms of enhanced UV-B radiation that regulate the anthocyanin biosynthesis in potato tubers. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition)

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Review

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12 pages, 808 KiB

Open AccessReview

Advances in Genome Sequencing and Natural Rubber Biosynthesis in Rubber-Producing Plants

by Yingchao Tan, Jie Cao, Chaorong Tang and Kaiye Liu

Curr. Issues Mol. Biol. 2023, 45(12), 9342-9353; https://0-doi-org.brum.beds.ac.uk/10.3390/cimb45120585 - 21 Nov 2023

Viewed by 971

Abstract

Natural rubber (cis-1,4-polyisoprene, NR) is an important raw material utilized widely in the manufacturing of medical, agricultural, and industrial products. Rubber tree (Hevea brasiliensis) and several alternative rubber-producing plants (Taraxacum kok-saghyz, Lactuca sativa, and Parthenium argentatum) have the capability to produce high-quality NR. With the progress of genome sequencing, similar rubber biosynthesis pathways have been discovered among different rubber-producing plant species. NR is synthesized and stored in rubber particles, which are specialized organelles comprising a hydrophobic NR core surrounded by a lipid monolayer and membrane-bound proteins. The rubber transferase complex is considered to be the pivotal enzyme involved in catalyzing NR biosynthesis. However, the exact compositions of the RT complex in rubber-producing plants remain elusive and poorly understood. Here, we review the progress of genome sequencing, natural rubber biosynthesis, and the components of the RT complex in rubber-producing plants. We emphasize that identifying the detailed components of the RT complex holds great significance for exploring the mechanism of NR biosynthesis and accelerating molecular breeding in rubber-producing plants. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 2nd Edition)

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