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...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-09-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1018029/full |
| _version_ | 1818057981999185920 |
|---|---|
| author | Cheng Song Yan Wang Muhammad Aamir Manzoor Di Mao Peipei Wei Yunpeng Cao Fucheng Zhu |
| author_facet | Cheng Song Yan Wang Muhammad Aamir Manzoor Di Mao Peipei Wei Yunpeng Cao Fucheng Zhu |
| author_sort | Cheng Song |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-10T12:53:23Z |
| format | Article |
| id | doaj.art-28e751f77ad64008b55b73623d0d086e |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-10T12:53:23Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-28e751f77ad64008b55b73623d0d086e2022-12-22T01:48:10ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-09-011310.3389/fpls.2022.10180291018029In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencingCheng Song0Yan Wang1Muhammad Aamir Manzoor2Di Mao3Peipei Wei4Yunpeng Cao5Fucheng Zhu6College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, ChinaCollege of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, ChinaSchool of Life Science, Anhui Agricultural University, Hefei, ChinaAlbrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, GermanyCollege of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, ChinaChinese Academy of Sciences (CAS) Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaCollege of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, ChinaHigh-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.https://www.frontiersin.org/articles/10.3389/fpls.2022.1018029/fullthird-generation sequencingorchidgenome assemblypolyploidyfunctional genomicsmolecular breeding |
| spellingShingle | Cheng Song Yan Wang Muhammad Aamir Manzoor Di Mao Peipei Wei Yunpeng Cao Fucheng Zhu In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing Frontiers in Plant Science third-generation sequencing orchid genome assembly polyploidy functional genomics molecular breeding |
| 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 | third-generation sequencing orchid genome assembly polyploidy functional genomics molecular breeding |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1018029/full |
| work_keys_str_mv | AT chengsong indepthanalysisofgenomesandfunctionalgenomicsoforchidusingcuttingedgehighthroughputsequencing AT yanwang indepthanalysisofgenomesandfunctionalgenomicsoforchidusingcuttingedgehighthroughputsequencing AT muhammadaamirmanzoor indepthanalysisofgenomesandfunctionalgenomicsoforchidusingcuttingedgehighthroughputsequencing AT dimao indepthanalysisofgenomesandfunctionalgenomicsoforchidusingcuttingedgehighthroughputsequencing AT peipeiwei indepthanalysisofgenomesandfunctionalgenomicsoforchidusingcuttingedgehighthroughputsequencing AT yunpengcao indepthanalysisofgenomesandfunctionalgenomicsoforchidusingcuttingedgehighthroughputsequencing AT fuchengzhu indepthanalysisofgenomesandfunctionalgenomicsoforchidusingcuttingedgehighthroughputsequencing |