The Apostasia genome and the evolution of orchids
WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification. Orchid origins Around 10 per cent of flowerin...
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| Published in | Nature (London) Vol. 549; no. 7672; pp. 379 - 383 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
21.09.2017
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | WebComparing the whole genome sequence of
Apostasia shenzhenica
with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification.
Orchid origins
Around 10 per cent of flowering plant species are orchids, with a broad diversity in both morphology and lifestyle.
Apostasia
is one of the earliest-diverging genera of Orchidaceae. To study the evolution and diversity of Orchidaceae, Zhong-Jian Liu, Yves Van de Peer and colleagues sequenced the genome of
Apostasia shenzhenica
, a self-pollinating species found in southeast China. The authors also report improved genomes for two species of Epidendroideae,
Phalaenopsis equestris
and
Dendrobium catenatum
, as well as transcriptome analysis of representatives of subfamilies of Orchidaceae. Their analyses provide insights into orchid origins, genome evolution, adaptation and diversification.
Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth
1
,
2
,
3
. Here we report the draft genome sequence of
Apostasia shenzhenica
4
, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies.
A. shenzhenica
shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between
A. shenzhenica
and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms. |
|---|---|
| AbstractList | WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification. Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel thirdgeneration genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms. Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms. WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification. Around 10 per cent of flowering plant species are orchids, with a broad diversity in both morphology and lifestyle. Apostasia is one of the earliest-diverging genera of Orchidaceae. To study the evolution and diversity of Orchidaceae, Zhong-Jian Liu, Yves Van de Peer and colleagues sequenced the genome of Apostasia shenzhenica , a self-pollinating species found in southeast China. The authors also report improved genomes for two species of Epidendroideae, Phalaenopsis equestris and Dendrobium catenatum , as well as transcriptome analysis of representatives of subfamilies of Orchidaceae. Their analyses provide insights into orchid origins, genome evolution, adaptation and diversification. Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth 1 , 2 , 3 . Here we report the draft genome sequence of Apostasia shenzhenica 4 , a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms. Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms. Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth 1,2,3 . Here we report the draft genome sequence of Apostasia shenzhenica 4 , a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms. WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification. Orchid origins Around 10 per cent of flowering plant species are orchids, with a broad diversity in both morphology and lifestyle. Apostasia is one of the earliest-diverging genera of Orchidaceae. To study the evolution and diversity of Orchidaceae, Zhong-Jian Liu, Yves Van de Peer and colleagues sequenced the genome of Apostasia shenzhenica , a self-pollinating species found in southeast China. The authors also report improved genomes for two species of Epidendroideae, Phalaenopsis equestris and Dendrobium catenatum , as well as transcriptome analysis of representatives of subfamilies of Orchidaceae. Their analyses provide insights into orchid origins, genome evolution, adaptation and diversification. Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth 1 , 2 , 3 . Here we report the draft genome sequence of Apostasia shenzhenica 4 , a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms. |
| Audience | Academic |
| Author | Wang, Zhi-Wen Li, Zhen Chen, Li-Jun Chang, Song-Bin Van de Peer, Yves Wang, Meina Wang, Jie-Yu Zhang, Yong-Qiang Yoshida, Kouki Huang, Hui-Xia Xiao, Xin-Ju Zeng, Si-Jin Niu, Shan-Ce Ohme-Takagi, Masaru Shen, Ching-Yu Chen, You-Yi Yeh, Chuan-Ming Lin, Min Zhang, Guo-Qiang Sakamoto, Shingo Yagi, Masafumi Xu, Qing Liu, Zhong-Jian Mitsuda, Nobutaka Luo, Yi-Bo Lin, Yao-Cheng Pecoraro, Lorenzo Wu, Wan-Lin Wu, Xin-Yi Tsai, Wen-Chieh Fujiwara, Sumire Liu, Ke-Wei Liu, Guo-Hui Hsiao, Yu-Yun Lohaus, Rolf |
| Author_xml | – sequence: 1 givenname: Guo-Qiang surname: Zhang fullname: Zhang, Guo-Qiang organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 2 givenname: Ke-Wei surname: Liu fullname: Liu, Ke-Wei organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 3 givenname: Zhen surname: Li fullname: Li, Zhen organization: Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB Center for Plant Systems Biology – sequence: 4 givenname: Rolf surname: Lohaus fullname: Lohaus, Rolf organization: Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB Center for Plant Systems Biology – sequence: 5 givenname: Yu-Yun surname: Hsiao fullname: Hsiao, Yu-Yun organization: Orchid Research and Development Center, National Cheng Kung University, Department of Life Sciences, National Cheng Kung University – sequence: 6 givenname: Shan-Ce surname: Niu fullname: Niu, Shan-Ce organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences – sequence: 7 givenname: Jie-Yu surname: Wang fullname: Wang, Jie-Yu organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, College of Forestry, South China Agricultural University – sequence: 8 givenname: Yao-Cheng surname: Lin fullname: Lin, Yao-Cheng organization: Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB Center for Plant Systems Biology, Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica – sequence: 9 givenname: Qing surname: Xu fullname: Xu, Qing organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 10 givenname: Li-Jun surname: Chen fullname: Chen, Li-Jun organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 11 givenname: Kouki surname: Yoshida fullname: Yoshida, Kouki organization: Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku – sequence: 12 givenname: Sumire surname: Fujiwara fullname: Fujiwara, Sumire organization: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6 – sequence: 13 givenname: Zhi-Wen surname: Wang fullname: Wang, Zhi-Wen organization: PubBio-Tech Services Corporation – sequence: 14 givenname: Yong-Qiang surname: Zhang fullname: Zhang, Yong-Qiang organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 15 givenname: Nobutaka surname: Mitsuda fullname: Mitsuda, Nobutaka organization: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6 – sequence: 16 givenname: Meina surname: Wang fullname: Wang, Meina organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 17 givenname: Guo-Hui surname: Liu fullname: Liu, Guo-Hui organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 18 givenname: Lorenzo surname: Pecoraro fullname: Pecoraro, Lorenzo organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 19 givenname: Hui-Xia surname: Huang fullname: Huang, Hui-Xia organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 20 givenname: Xin-Ju surname: Xiao fullname: Xiao, Xin-Ju organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 21 givenname: Min surname: Lin fullname: Lin, Min organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 22 givenname: Xin-Yi surname: Wu fullname: Wu, Xin-Yi organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen – sequence: 23 givenname: Wan-Lin surname: Wu fullname: Wu, Wan-Lin organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Orchid Research and Development Center, National Cheng Kung University – sequence: 24 givenname: You-Yi surname: Chen fullname: Chen, You-Yi organization: Orchid Research and Development Center, National Cheng Kung University, Department of Life Sciences, National Cheng Kung University – sequence: 25 givenname: Song-Bin surname: Chang fullname: Chang, Song-Bin organization: Orchid Research and Development Center, National Cheng Kung University, Department of Life Sciences, National Cheng Kung University – sequence: 26 givenname: Shingo surname: Sakamoto fullname: Sakamoto, Shingo organization: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6 – sequence: 27 givenname: Masaru surname: Ohme-Takagi fullname: Ohme-Takagi, Masaru organization: Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Graduate School of Science and Engineering, Saitama University – sequence: 28 givenname: Masafumi surname: Yagi fullname: Yagi, Masafumi organization: NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto – sequence: 29 givenname: Si-Jin surname: Zeng fullname: Zeng, Si-Jin organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, College of Forestry, South China Agricultural University – sequence: 30 givenname: Ching-Yu surname: Shen fullname: Shen, Ching-Yu organization: Institute of Tropical Plant Sciences, National Cheng Kung University – sequence: 31 givenname: Chuan-Ming surname: Yeh fullname: Yeh, Chuan-Ming email: cmyeh@mail.saitama-u.ac.jp organization: Graduate School of Science and Engineering, Saitama University – sequence: 32 givenname: Yi-Bo surname: Luo fullname: Luo, Yi-Bo email: luoyb@ibcas.ac.cn organization: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences – sequence: 33 givenname: Wen-Chieh surname: Tsai fullname: Tsai, Wen-Chieh email: tsaiwc@mail.ncku.edu.tw organization: Orchid Research and Development Center, National Cheng Kung University, Department of Life Sciences, National Cheng Kung University, Institute of Tropical Plant Sciences, National Cheng Kung University – sequence: 34 givenname: Yves surname: Van de Peer fullname: Van de Peer, Yves email: yves.vandepeer@psb.vib-ugent.be organization: Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB Center for Plant Systems Biology, Department of Genetics, Genomics Research Institute – sequence: 35 givenname: Zhong-Jian surname: Liu fullname: Liu, Zhong-Jian email: liuzj@sinicaorchid.org organization: Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, College of Forestry, South China Agricultural University, College of Landscape Architecture, Fujian Agriculture and Forestry University, The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28902843$$D View this record in MEDLINE/PubMed |
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| Snippet | WebComparing the whole genome sequence of
Apostasia shenzhenica
with transcriptome and genome data from five orchid subfamilies permits the reconstruction of... Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in... WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of... |
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| SubjectTerms | 45/23 45/91 631/181/759 631/208/726 Angiosperms Biodiversity Biological evolution Biosynthesis Botanical research Divergence Endosperm Evolution Evolutionary genetics Flowering Flowering plants Flowers & plants Gene families Genes Genetic aspects Genomes Humanities and Social Sciences letter MADS box proteins multidisciplinary Natural history Nucleotide sequence Orchids Phylogenetics Plant species Science Seeds |
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| Title | The Apostasia genome and the evolution of orchids |
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