Subgenome- aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family

• 成果类型: Article
• 署名作者: Sun, Pengchuan; Lu, Zhiqiang; Wang, Zhenyue; Wang, Shang; Zhao, Kexin; Mei, Dong; Yang, Jiao; Yang, Yongzhi; Renner, Susanne S.; Liu, Jianquan
• 署名单位: Sichuan University; Chinese Academy of Sciences; Xishuangbanna Tropical Botanical Garden, CAS; Lanzhou University; Washington University (WUSTL)
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-15178
• DOI: 10.1073/pnas.2313921121
• 发表日期: 2024-04-09
• 关键词: polyploidy; phylogeny; malvaceae; evolutionary; bombacoideae; malvales

摘要

Malvaceae comprise some 4,225 species in 243 genera and nine subfamilies and include economically important species, such as cacao, cotton, durian, and jute, with cotton an important model system for studying the domestication of polyploids. Here, we use chromosome - level genome assemblies from representatives of five or six subfamilies (depending on the placement of Ochroma) to differentiate coexisting subgenomes and their evolution during the family's deep history. The results reveal that the allohexaploid Helicteroideae partially derive from an allotetraploid Sterculioideae and also form a component of the allodecaploid Bombacoideae and Malvoideae. The ancestral Malvaceae karyotype consists of 11 protochromosomes. Four subfamilies share a unique reciprocal chromosome translocation, and two other subfamilies share a chromosome fusion. DNA alignments of single - copy nuclear genes do not yield the same relationships as inferred from chromosome structural traits, probably because of genes originating from different ancestral subgenomes. These results illustrate how chromosome- structural data can unravel the evolutionary history of groups with ancient hybrid genomes.