利用大规模核基因重建薄囊蕨基部类群深层系统发育关系

The fern phylogenetic framework at the order level is increasingly clear and stable, but there are still some conflicting nodes unresolved, such as the early split pattern of the leptosporangiate ferns. In our previous work, we have reconstructed the backbone of ferns at the family level. Meanwhile, a well-supported but unexpected phylogenetic relationship of the basal leptosporangiate ferns was obtained, based on RNA-seq technique and large-scale nuclear genes. In order to elucidate the fidings furthermore, we will conduct a phylogenomic study on the basis of previous study, aimed to ascertain the defining boundary for the main orders in basal leptosporangiate ferns, and determine the phylogenetic relationship of these clades. The main research contents are including: 1) We will further extend the sampling range, screening for large-scale orthologous gene set based on transcriptome data; 2) In order to reconstruct a robust phylogenetic tree, we will emphasis on dealing with the systematic artifacts, via eliminating confounding phylogenetic signals and selecting better evolutionary models; 3) The impact of systematic error on phylogenetic reconstruction will be investigated, such as long-branch attraction and incomplete lineage sorting. The effective approach to reduce these systematic error will also be discussed. The expect research results will provide molecular phylogenetic evidences for clarification of ferns phylogenetic framework, will also shed light on the methodology advances in deep relationship reconstruction using large datasets.

蕨类植物在目级水平的系统发育框架已基本确立，但部分节点还存在争议。其中，薄囊蕨的早期分支式样一直未得到有效解决。申请者在前期工作中利用转录组数据以及大规模核基因对蕨类植物科级系统发育框架进行重建，初步解析了薄囊蕨基部类群的系统发育关系。为了进一步澄清薄囊蕨基部类群目级分类阶元的界定范围，并明确各个目之间的相对系统发育关系，本项目拟开展以下研究：1）在前期工作的基础上进一步扩大取样范围，基于转录组数据筛选得到大规模的直系同源基因集；2）通过去掉信号噪音以及选择正确的建树模型，排除系统发育假象，重建得到可靠的系统发育树；3）探讨长枝吸引、基因不完全谱系分选等因素对系统树的影响，以及排除这些系统误差的有效方法。研究结果可为完善蕨类植物系统发育框架提供分子证据，并为大尺度分类阶元间的系统发育重建提供方法借鉴。

本项目对薄囊蕨基部类群开展了基于一手活体材料的系统发育基因组学研究。采集获得了薄囊蕨基部类群科级全覆盖样本及外类群活体材料33份，获得转录组序列数据101.43G，组装获得1,522,221条Unigenes，N50平均值达到1,225bp；利用系统树法分析得到1125个薄囊蕨基部类群直系同源基因。重建获得薄囊蕨基部类群系统发育树，估算得到了薄囊蕨各支系的起源与分化时间。这些结果为进一步澄清薄囊蕨基部类群目级分类阶元的界定范围，以及明确各个目之间的相对系统发育关系提供了理论支持。另外，对薄囊蕨特殊类群展开了分子进化分析，为理解其独特的适应性进化机理提供了线索。J基于本项目的研究成果，已有两篇研究论文在线发表于SCI期刊，另有一篇研究成果在投稿过程中。