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

Shihui Niu, Jiang Li, Wenhao Bo, Weifei Yang, Andrea Zuccolo, Stefania Giacomello, Xi Chen, Fangxu Han, Junhe Yang, Yitong Song, Yumeng Nie, Biao Zhou (+24 others)
2021 Cell  
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
more » ... d 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.
doi:10.1016/j.cell.2021.12.006 pmid:34965378 fatcat:gxqyqsgznnaltlwm5wyqbyplr4