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In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing

High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them h...

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Detalles Bibliográficos
Autores principales: Song, Cheng, Wang, Yan, Manzoor, Muhammad Aamir, Mao, Di, Wei, Peipei, Cao, Yunpeng, Zhu, Fucheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9539832/
https://www.ncbi.nlm.nih.gov/pubmed/36212315
http://dx.doi.org/10.3389/fpls.2022.1018029
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author Song, Cheng
Wang, Yan
Manzoor, Muhammad Aamir
Mao, Di
Wei, Peipei
Cao, Yunpeng
Zhu, Fucheng
author_facet Song, Cheng
Wang, Yan
Manzoor, Muhammad Aamir
Mao, Di
Wei, Peipei
Cao, Yunpeng
Zhu, Fucheng
author_sort Song, Cheng
collection PubMed
description High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies.
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spelling pubmed-95398322022-10-08 In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing Song, Cheng Wang, Yan Manzoor, Muhammad Aamir Mao, Di Wei, Peipei Cao, Yunpeng Zhu, Fucheng Front Plant Sci Plant Science High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies. Frontiers Media S.A. 2022-09-23 /pmc/articles/PMC9539832/ /pubmed/36212315 http://dx.doi.org/10.3389/fpls.2022.1018029 Text en Copyright © 2022 Song, Wang, Manzoor, Mao, Wei, Cao and Zhu https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Song, Cheng
Wang, Yan
Manzoor, Muhammad Aamir
Mao, Di
Wei, Peipei
Cao, Yunpeng
Zhu, Fucheng
In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing
title In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing
title_full In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing
title_fullStr In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing
title_full_unstemmed In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing
title_short In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing
title_sort in-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9539832/
https://www.ncbi.nlm.nih.gov/pubmed/36212315
http://dx.doi.org/10.3389/fpls.2022.1018029
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