芭蕉基因组草图揭示其进化轨迹和环境适应性

Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation.

机构信息

Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.

Noblis, Inc., Washington, DC, USA.

出版信息

Nat Commun. 2024 Oct 12;15(1):8833. doi: 10.1038/s41467-024-53157-w.

DOI:10.1038/s41467-024-53157-w

PMID:39396056

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11470940/

Abstract

Baobab (Adansonia digitata) is a long-lived tree endemic to Africa with economic, ecological, and cultural importance, yet its genomic features are underexplored. Here, we report a chromosome-level reference genome anchored to 42 chromosomes for A. digitata, alongside draft assemblies for a sibling tree, two trees from distinct locations in Africa, and A. za from Madagascar. The baobab genome is uniquely rich in DNA transposons, which make up 33%, while LTR retrotransposons account for 10%. A. digitata experienced whole genome multiplication (WGM) around 30 million years ago (MYA), followed by a second WGM event 3-11 MYA, likely linked to autotetraploidy. Resequencing of 25 trees identify three subpopulations, with gene flow across West Africa distinct from East Africa. Gene enrichment and fixation index (Fst) analyses show baobab retained multiple circadian, flowering, and light-responsive genes, which likely support longevity through the UV RESISTANCE LOCUS 8 (UVR8) pathway. In sum, we provide genomic resources and insights for baobab breeding and conservation.

摘要

猴面包树（Adansonia digitata）是一种原产于非洲的长寿树种，具有经济、生态和文化重要性，但它的基因组特征尚未得到充分探索。在这里，我们报告了一个基于 42 条染色体的猴面包树染色体水平参考基因组，以及来自非洲两个不同地点的另外两株亲缘树和来自马达加斯加的 A. za 的草图组装。猴面包树基因组富含独特的 DNA 转座子，占 33%，而 LTR 逆转录转座子占 10%。约 3000 万年前（MYA），猴面包树经历了全基因组倍增（WGM），随后在 3-11 MYA 发生了第二次 WGM 事件，可能与同源四倍体有关。对 25 棵树进行重测序，确定了三个亚群，西非的基因流与东非不同。基因富集和固定指数（Fst）分析表明，猴面包树保留了多个生物钟、开花和光响应基因，这些基因可能通过 UV 抗性基因 8（UVR8）途径支持其长寿。总之，我们为猴面包树的繁殖和保护提供了基因组资源和见解。