Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion

doi:10.1016/j.pld.2020.07.008

Plant Diversity ›› 2021, Vol. 43 ›› Issue (02): 102-110.DOI: 10.1016/j.pld.2020.07.008

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Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion

Ziyoviddin Yusupov^a,b,c, Tao Deng^a, Sergei Volis^a, Furkat Khassanov^b, Dilmurod Makhmudjanov^a,b,c, Komiljon Tojibaev^b, Hang Sun^a

a CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
b International Joint Lab for Molecular Phylogeny and Biogeography, Institute of Botany, Academy Sciences of Uzbekistan, Tashkent, 100125, Uzbekistan
c University of Chinese Academy of Sciences, Beijing, China

Received:2020-04-21 Revised:2020-07-29 Online:2021-05-20 Published:2021-04-25
Contact: Komiljon Tojibaev, Hang Sun
Supported by:
We are grateful to two anonymous reviewers for comments on the manuscript. The manuscript has greatly improved due to these invaluable comments. The authors in particular wish to thank Dr. David E. Boufford for editing the English. This study was supported by the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0502), the International Partnership Program of Chinese Academy of Sciences (151853KYSB20180009) and the Strategic Priority Research Program of Chinese Academy of Sciences (XDA20050203) to H.S., and the Youth Innovation Promotion Association of Chinese Academy of Sciences (2019382), the Young Academic and Technical Leader Raising Foundation of Yunnan Province (2019HB039), the Chinese Academy of Sciences “Light of West China” Program and the Biodiversity Survey, Monitoring and Assessment (2019HB2096001006) to T. D, and the the Belt and Road Project of West Light Foundation of the Chinese Academy of Sciences.

Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion

Ziyoviddin Yusupov^a,b,c, Tao Deng^a, Sergei Volis^a, Furkat Khassanov^b, Dilmurod Makhmudjanov^a,b,c, Komiljon Tojibaev^b, Hang Sun^a

a CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
b International Joint Lab for Molecular Phylogeny and Biogeography, Institute of Botany, Academy Sciences of Uzbekistan, Tashkent, 100125, Uzbekistan
c University of Chinese Academy of Sciences, Beijing, China

通讯作者: Komiljon Tojibaev, Hang Sun
基金资助:
We are grateful to two anonymous reviewers for comments on the manuscript. The manuscript has greatly improved due to these invaluable comments. The authors in particular wish to thank Dr. David E. Boufford for editing the English. This study was supported by the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0502), the International Partnership Program of Chinese Academy of Sciences (151853KYSB20180009) and the Strategic Priority Research Program of Chinese Academy of Sciences (XDA20050203) to H.S., and the Youth Innovation Promotion Association of Chinese Academy of Sciences (2019382), the Young Academic and Technical Leader Raising Foundation of Yunnan Province (2019HB039), the Chinese Academy of Sciences “Light of West China” Program and the Biodiversity Survey, Monitoring and Assessment (2019HB2096001006) to T. D, and the the Belt and Road Project of West Light Foundation of the Chinese Academy of Sciences.

Abstract

Abstract: Allium sect. Cepa (Amaryllidaceae) comprises economically important plants, yet resolving the phylogenetic relationships within the section has been difficult as nuclear and chloroplast-based phylogenetic trees have been incongruent. Until now, phylogenetic studies of the section have been based on a few genes. In this study, we sequenced the complete chloroplast genome (plastomes) of four central Asian species of sect. Cepa: Allium oschaninii, A. praemixtum, A. pskemense and A. galanthum. Their chloroplast (cp) genomes included 114 unique genes of which 80 coded proteins. Seven protein-coding genes were highly variable and therefore promising for future phylogenetic and phylogeographic studies. Our plastome-based phylogenetic tree of Allium sect. Cepa revealed two separate clades: one comprising the central Asian species A. oschaninii, A. praemixtum, and A. pskemense, and another comprising A. galanthum, A. altaicum, and two cultivated species, A. cepa and A. fistulosum. These findings contradict previously reported phylogenies that relied on ITS and morphology. Possible explanations for this discrepancy are related to interspecific hybridization of species ancestral to A. galanthum and A. cepa followed by chloroplast capture; however, this is impossible to prove without additional data. Our results suggest that the central Asian Allium species did not play a role in the domestication of the common onion. Among the chloroplast genes, rpoC2 was identified as a gene of choice in further phylogeographical studies of the genus Allium.

Key words: Chloroplast genome, SNP, Phylogeny, Chloroplast capture

摘要： Allium sect. Cepa (Amaryllidaceae) comprises economically important plants, yet resolving the phylogenetic relationships within the section has been difficult as nuclear and chloroplast-based phylogenetic trees have been incongruent. Until now, phylogenetic studies of the section have been based on a few genes. In this study, we sequenced the complete chloroplast genome (plastomes) of four central Asian species of sect. Cepa: Allium oschaninii, A. praemixtum, A. pskemense and A. galanthum. Their chloroplast (cp) genomes included 114 unique genes of which 80 coded proteins. Seven protein-coding genes were highly variable and therefore promising for future phylogenetic and phylogeographic studies. Our plastome-based phylogenetic tree of Allium sect. Cepa revealed two separate clades: one comprising the central Asian species A. oschaninii, A. praemixtum, and A. pskemense, and another comprising A. galanthum, A. altaicum, and two cultivated species, A. cepa and A. fistulosum. These findings contradict previously reported phylogenies that relied on ITS and morphology. Possible explanations for this discrepancy are related to interspecific hybridization of species ancestral to A. galanthum and A. cepa followed by chloroplast capture; however, this is impossible to prove without additional data. Our results suggest that the central Asian Allium species did not play a role in the domestication of the common onion. Among the chloroplast genes, rpoC2 was identified as a gene of choice in further phylogeographical studies of the genus Allium.

关键词: Chloroplast genome, SNP, Phylogeny, Chloroplast capture

Ziyoviddin Yusupov, Tao Deng, Sergei Volis, Furkat Khassanov, Dilmurod Makhmudjanov, Komiljon Tojibaev, Hang Sun. Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion[J]. Plant Diversity, 2021, 43(02): 102-110.

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Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion

Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion

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