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基于蜡梅（Chimonanthus praecox）及相关植物物种的基因组数据，进行基因家族聚类，估算物种分化时间，并开展有关物种的共线性分析，计算不同类别代表性物种内旁系同源及物种间的直系同源同义替换率（synonymous substitution rate,Ks），同时基于核苷酸和氨基酸序列的串联法及并联法等多种策略，进行木兰类植物系统进化分析。结果表明，蜡梅科（Calycanthaceae）植物共享了两次全基因组复制（whole-genome duplication,WGD）事件，樟目（Laurales）的共同祖先经历了二倍化事件，木兰类植物未共享WGD事件。长枝吸引（long branch attraction,LBA）会影响系统发育的准确性，消除LBA可使用1以及0和1相位点构建系统发育树。以往对木兰类植物系统发育位置的研究结果不一致，可能是由于系统发育树的构建方法不同、不完全谱系分选（incomplete lineage sorting, ILS）的存在、分类单元取样的局限性，以及木兰类植物在进化早期的快速分化等原因。在充分考虑多种可能影响木兰类植物进化位置多种因素的基础上，二叉树或不能完全代表被子植物的早期多样化，木兰类植物更可能是真双子叶植物的姐妹，这一观点得到了较多系统发育树的支持。研究对于了解物种系统进化分歧时间、揭示WGD事件与物种分化关系以及对进一步深入研究木兰类植物进化具有重要意义。
Abstract：Based on the genome data of Chimonanthus praecox and related plant species, the gene family clustering was carried out to estimate the time of species differentiation, and the synteny analysis of related species was carried out, and the value of Ks of paralogs and orthologous within the species between species were calculated. At the same time, the phylogenetic analysis of magnoliids were carried out based on the concatenated methods and coalescent methods using nucleotide and amino acid sequences. The results showed that Calycanthaceae shared two whole-genome duplication(WGD) events, the common ancestor of Laurales experienced diploidization events, and magnoliids did not share WGD events. Long branch attraction(LBA) will affect the accuracy of phylogeny, and the concatenated trees constructed with phase 0, 1 loci and 1 loci can be used to eliminate LBA. Previous studies of the evolutionary position of magnoliids showed inconsistent results possibly due to different methods for constructing phylogenetic trees, the existence of incomplete lineage sorting(ILS), the limitation of taxon sampling, and the rapid differentiation of magnoliids in the early stages of evolution. This study fully considered various factors that may have caused errors in the evolutionary positioning of the magnoliids. A bifurcating tree might not be able to fully demonstrate the early diversification of the angiosperms. We suggest that magnoliids are most likely sister to eudicots, which was supported by the results from several phylogenetic trees. The research is of great significance for understanding the divergence time of species phylogeny, revealing the relationship between WGD events and species differentiation,and further studying the evolution of magnoliids.
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基本信息:
DOI：10.13417/j.gab.042.000791
中图分类号:Q941
引用信息:
[1]沈植国.蜡梅比较基因组学及木兰类植物系统进化分析[J].基因组学与应用生物学,2023,42(08):791-807.DOI:10.13417/j.gab.042.000791.
基金信息:
河南省农业科学院科技创新团队项目（2023TD35）; 河南省重点研发专项（221111110700）; 河南省科技兴林项目（豫财环资[2022]28号）共同资助
2023-08-14
2023-08-14
2023-08-14