The Metasequoia genome and evolutionary relationships among redwoods

作者：Fangfang Fu, Chi Song, Chengjin Wen, Lulu Yang, Ying Guo, Xiaoming Yang, Ziqiang Shu, Xiaodong Li, Yangfan Feng, Bingshuang Liu, Mingsheng Sun, Yinxiao Zhong, Li Chen, Yan Niu, Jie Chen, Guibin Wang, Tongming Yin, Shilin Chen, Liang‐Jiao Xue, Fuliang Cao · 发表于：Plant Communications · 年份：2023 · DOI：10.1016/j.xplc.2023.100643 · 被引用次数：29 · 研究领域：Plant Pathogens and Fungal Diseases、Genomics and Phylogenetic Studies、Plant responses to water stress

Redwood trees (Sequoioideae), including Metasequoia glyptostroboides (dawn redwood), Sequoiadendron giganteum (giant sequoia), and Sequoia sempervirens (coast redwood), are threatened and widely recognized iconic tree species. Genomic resources for redwood trees could provide clues to their evolutionary relationships. Here, we report the 8-Gb reference genome of M. glyptostroboides and a comparative analysis with two related species. More than 62% of the M. glyptostroboides genome is composed of repetitive sequences. Clade-specific bursts of long terminal repeat retrotransposons may have contributed to genomic differentiation in the three species. The chromosomal synteny between M. glyptostroboides and S. giganteum is extremely high, whereas there has been significant chromosome reorganization in S. sempervirens. Phylogenetic analysis of marker genes indicates that S. sempervirens is an autopolyploid, and more than 48% of the gene trees are incongruent with the species tree. Results of multiple analyses suggest that incomplete lineage sorting (ILS) rather than hybridization explains the inconsistent phylogeny, indicating that genetic variation among redwoods may be due to random retention of polymorphisms in ancestral populations. Functional analysis of ortholog groups indicates that gene families of ion channels, tannin biosynthesis enzymes, and transcription factors for meristem maintenance have expanded in S. giganteum and S. sempervirens, which is consistent with their ex...