New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences

doi:10.1016/j.pld.2025.04.009

Plant Diversity ›› 2025, Vol. 47 ›› Issue (04): 561-575.DOI: 10.1016/j.pld.2025.04.009

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New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences

Ibrokhimjon Ergashov^a,b,c,d,e,f, Ziyoviddin Yusupov^a,b,d, Alireza Dolatyari^g, Mina Khorasani^h, İsmail Ekerⁱ, Nazgul Turdumatova^j, Georgy Lazkov^k, Farruhbek Rasulov^l, Hang Sun^a,b, Tao Deng^b, Komiljon Tojibaev^b,e

a. State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b. Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
c. University of Chinese Academy of Sciences, Beijing 100049, China;
d. International Joint Lab for Molecular Phylogeny and Biogeography, Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan;
e. Flora of Uzbekistan Laboratory, Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan, 32 Durmon Yuli St., Tashkent 100125, Uzbekistan;
f. Faculty of Natural Sciences, Fergana State University, Fergana 150100, Uzbekistan;
g. Plant Bank, Iranian Biological Resource Center (IBRC), Iranian Academic Center for Education, Culture & Research (ACECR), Tehran, Iran;
h. Department of Biology Education, Farhangian University, P. O. Box 14665_889, Tehran, Iran;
i. Bolu Abant İzzet Baysal University, Faculty of Science & Literature, Department of Biology, Bolu 14280, Türkiye;
j. Institute of Biology, National Academy of Sciences, Bishkek 720071, Kyrgyzstan;
k. Research Centre for Ecology and Environment of Central Asia, Bishkek 720040, Kyrgyzstan;
l. Andijan State Medical Institute, Department of Pharmaceutical Sciences, Andijan, Uzbekistan

Received:2025-01-24 Revised:2025-04-14 Online:2025-08-13 Published:2025-08-13
Contact: Hang Sun,E-mail:sunhang@mail.kib.ac.cn;Tao Deng,E-mail:dengtao@mail.kib.ac.cn;Komiljon Tojibaev,E-mail:ktojibaev@mail.ru
Supported by:
This study was supported by grants from the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0502), the state research project ‘Taxonomic Revision of Polymorphic Plant Families of the Flora of Uzbekistan’ (FZ-20200929321) and the State Programs for 2021–2025 ‘Grid mapping of the flora of Uzbekistan’ and the ‘Digital Nature. Development of a digital platform for the flora of Central Uzbekistan’, implemented by the Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan for the period 2025–2029; National Natural Science Foundation of China (32322006), the Key Projects of the Joint Fund of the National Natural Science Foundation of China (U23A20149), the R&D Program of Yunnan Province (202103AF140005). This publication has also been produced within the framework of the Grant No. PRIM 01-73 “The modernization of the Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan”, funded under the MUNIS Project, supported by the World Bank and the Government of the Republic of Uzbekistan.

New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences

a. State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b. Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
c. University of Chinese Academy of Sciences, Beijing 100049, China;
d. International Joint Lab for Molecular Phylogeny and Biogeography, Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan;
e. Flora of Uzbekistan Laboratory, Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan, 32 Durmon Yuli St., Tashkent 100125, Uzbekistan;
f. Faculty of Natural Sciences, Fergana State University, Fergana 150100, Uzbekistan;
g. Plant Bank, Iranian Biological Resource Center (IBRC), Iranian Academic Center for Education, Culture & Research (ACECR), Tehran, Iran;
h. Department of Biology Education, Farhangian University, P. O. Box 14665_889, Tehran, Iran;
i. Bolu Abant İzzet Baysal University, Faculty of Science & Literature, Department of Biology, Bolu 14280, Türkiye;
j. Institute of Biology, National Academy of Sciences, Bishkek 720071, Kyrgyzstan;
k. Research Centre for Ecology and Environment of Central Asia, Bishkek 720040, Kyrgyzstan;
l. Andijan State Medical Institute, Department of Pharmaceutical Sciences, Andijan, Uzbekistan

通讯作者: Hang Sun,E-mail:sunhang@mail.kib.ac.cn;Tao Deng,E-mail:dengtao@mail.kib.ac.cn;Komiljon Tojibaev,E-mail:ktojibaev@mail.ru
基金资助:
This study was supported by grants from the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0502), the state research project ‘Taxonomic Revision of Polymorphic Plant Families of the Flora of Uzbekistan’ (FZ-20200929321) and the State Programs for 2021–2025 ‘Grid mapping of the flora of Uzbekistan’ and the ‘Digital Nature. Development of a digital platform for the flora of Central Uzbekistan’, implemented by the Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan for the period 2025–2029; National Natural Science Foundation of China (32322006), the Key Projects of the Joint Fund of the National Natural Science Foundation of China (U23A20149), the R&D Program of Yunnan Province (202103AF140005). This publication has also been produced within the framework of the Grant No. PRIM 01-73 “The modernization of the Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan”, funded under the MUNIS Project, supported by the World Bank and the Government of the Republic of Uzbekistan.

Abstract

Abstract: Subgenus Melanocrommyum is the second largest subgenus of Allium, with a wide distribution ranging from the Canary Islands to northwestern India. This study investigates the phylogeny, biogeographic patterns, and morphological character evolution of the subgenus using 117 accessions representing 107 taxa across the 19 currently recognized sections within Allium subgenus Melanocrommyum. Although the subgenus is monophyletic, significant incongruence exists between morphological and molecular data. Our plastome-based phylogenetic analysis identified five distinct lineages (A–E), corresponding to the geographic distributions of the species. However, plastome lineages (A–E) and ITS clusters (A–G) were incongruent. Biogeographic and molecular dating analyses suggest that Melanocrommyum evolved in association with tectonic uplift events in Central Asia during the Late Miocene or Oligocene. Our finding that Melanocrommyum plastomes have lost infA and one copy rps19 gene indicate that the subgenus has undergone a relatively recent diversification. We also found that narrow leaves and fasciculate to semi-globose inflorescences may represent ancestral traits within the subgenus. This study provides new insights into the biogeographic history and trait evolution of Melanocrommyum, suggesting recent diversification influenced by tectonic events and climate change, while highlighting the complexity of molecular and morphological data integration.

Key words: Biogeography, Complete chloroplast genome, Infra-subgeneric grouping, Phylogeny, Allium, Melanocrommyum

摘要： Subgenus Melanocrommyum is the second largest subgenus of Allium, with a wide distribution ranging from the Canary Islands to northwestern India. This study investigates the phylogeny, biogeographic patterns, and morphological character evolution of the subgenus using 117 accessions representing 107 taxa across the 19 currently recognized sections within Allium subgenus Melanocrommyum. Although the subgenus is monophyletic, significant incongruence exists between morphological and molecular data. Our plastome-based phylogenetic analysis identified five distinct lineages (A–E), corresponding to the geographic distributions of the species. However, plastome lineages (A–E) and ITS clusters (A–G) were incongruent. Biogeographic and molecular dating analyses suggest that Melanocrommyum evolved in association with tectonic uplift events in Central Asia during the Late Miocene or Oligocene. Our finding that Melanocrommyum plastomes have lost infA and one copy rps19 gene indicate that the subgenus has undergone a relatively recent diversification. We also found that narrow leaves and fasciculate to semi-globose inflorescences may represent ancestral traits within the subgenus. This study provides new insights into the biogeographic history and trait evolution of Melanocrommyum, suggesting recent diversification influenced by tectonic events and climate change, while highlighting the complexity of molecular and morphological data integration.

关键词: Biogeography, Complete chloroplast genome, Infra-subgeneric grouping, Phylogeny, Allium, Melanocrommyum

Ibrokhimjon Ergashov, Ziyoviddin Yusupov, Alireza Dolatyari, Mina Khorasani, İsmail Eker, Nazgul Turdumatova, Georgy Lazkov, Farruhbek Rasulov, Hang Sun, Tao Deng, Komiljon Tojibaev. New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences[J]. Plant Diversity, 2025, 47(04): 561-575.

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New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences

New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences

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