中国松基因组和甲基组揭示了针叶树进化的关键特征。

The Chinese pine genome and methylome unveil key features of conifer evolution.

机构信息

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China.

出版信息

Cell. 2022 Jan 6;185(1):204-217.e14. doi: 10.1016/j.cell.2021.12.006. Epub 2021 Dec 28.

DOI:10.1016/j.cell.2021.12.006

PMID:34965378

Abstract

Conifers dominate the world's forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers' adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.

摘要

针叶树主导着世界森林生态系统，是种植最广泛的树种。它们巨大而复杂的基因组给组装完整的参考基因组进行进化和基因组研究带来了巨大的挑战。我们呈现了一个 254 亿碱基对的中国油松（Pinus tabuliformis）染色体水平的组装，结果表明其基因组大小主要归因于巨大的基因间区和具有高转座元件（TE）含量的长内含子。具有长内含子的大基因表现出更高的表达水平。尽管缺乏最近的全基因组复制，但 91.2%的基因通过分散复制进行了复制，扩展的基因家族主要与应激反应有关，这可能支持了针叶树的适应能力，特别是在寒冷和/或干旱的条件下。与被子植物相比，其生殖调控网络明显不同。高甲基化的 TE 的缓慢去除可能导致了基因组的扩张。这项研究为针叶树的进化提供了新的见解，并为研究针叶树的适应和发育提供了资源。