竹亚科青篱竹族的线粒体基因组及其在系统发育上的应用

The tribe Arundinarieae (Poaceae: Bambusoideae) contains many economically important bamboos such as the moso bamboo, and building its phylogeny has been proved to be a difficult problem in the Bambusoideae subfamily. The Arundinarieae was divided into 10 major clades in the previous studies, and recently the phylogenetic relationships among them have only been partially resolved based on the complete chloroplast genome sequences. The utility of mitochondrial genome sequences for plant phylogenetic reconstruction was also suggested in our study. The mitochondrial genomes of plants usually have a large genome size and exhibit a number of unique features including a low rate of molecular evolution and frequent genome structure rearrangement. However, the mechanisms underlying the evolution of plant mitochondrial genomes have not yet been revealed. Now there are 8 grasses with their mitochondrial genomes sequenced but no complete mitochondrial genome sequence from a bamboo species. We will choose one representative species from each of the 8 Arundinarieae major clades which all have species distributed in China, and sequence their mitochondrial genomes by second generation sequencing technology in this project. A complete mitochondrial genome from Arundinarieae will be assembled and annotated. We will also conduct comparative genomic analysis for the mitochondrial genomes in the grass family to unveil the features and evolutionary dynamics of mitochondrial genomes of Arundinarieae. Using phylogenomic approach the phylogeny of Arundinarieae will be reconstructed based on the mitochondrial genome evidences, especially from these genome-scale characters, to shed light into the resolution of the difficult Arundinarieae phylogeny.

青篱竹族隶属于禾本科竹亚科，包括许多具有重要经济价值的竹种如毛竹等，是竹亚科系统学研究的难点。青篱竹族目前被划分成10个分支，项目申请者利用全叶绿体基因组数据解决了部分分支之间的关系，并发现线粒体基因组数据在植物系统发育分析中同样具有利用价值。植物线粒体基因组较大，具有进化速率低、结构变异频繁等特点，其内在进化机制尚不清楚。已有8种禾本科植物完成线粒体基因组的测序，但仍缺少来自竹亚科的代表。本项目从青篱竹族在我国均有分布的8个主要分支中各选取1个代表种，利用第二代测序技术开展较大规模的线粒体基因组测序，拼接组装出完整的青篱竹族线粒体基因组序列，完成基因组注释。在禾本科内开展比较基因组学研究，全面阐明青篱竹族线粒体基因组结构与进化模式，揭示其进化机制。基于线粒体基因组证据，尤其是结构上的变异，以系统发育基因组学的手段构建青篱竹族系统发育关系，为解决这一困难类群的系统发育关系提供新思路。

温带木本竹类即青篱竹族，包括20余属600多种，包括了我国经济价值最大的竹种如毛竹等重要竹类，以东亚地区为其现代分布和多样化中心。青篱竹族种类数目多，形态性状十分多样化，在经典分类上存在着很多问题和争论，也是禾本科系统学研究的难点。目前，青篱竹族的系统发育构建主要运用叶绿体基因组序列，将其划分成了十二个主要分支。相比于叶绿体基因组，植物的线粒体基因组较大，具有进化速率低、结构变异频繁等特点，较少应用于植物系统发育重建上。然而，线粒体基因组本身包含了大量序列信息，是否同样可以提供系统发育信息这一问题悬而未决。在第二代测序技术快速发展的情况下，本项目提出测序青篱竹族的线粒体基因组，解析其进化模式，构建该类群的系统发育关系并评判其潜在应用价值。通过两种测序方式，即高盐低pH值差速离心分离较高纯度的细胞器DNA和总DNA测序，完成了25种竹类线粒体基因组的测序拼接及基因组注释，代表了青篱竹族十一个主要分支。通过比较基因组学分析揭示了青篱竹族线粒体基因组在序列进化上的保守性和在基因组结构上的大量重排，并在竹类中发现了线粒体DNA序列水平转移到叶绿体基因组的现象。基于共有的34个线粒体蛋白质编码基因和从线粒体基因组中随机挑选的50 kb序列构建系统发育树，编码基因序列包含的信息位点不足，难以用来构建系统发育关系，而50 kb的比对序列包含了大量信息位点，所构建的系统树具有较高的分辨率。虽然基于线粒体DNA序列的青篱竹族系统发育树同已有的叶绿体系统发育关系存在极大冲突，需要进一步的深入研究，本项目的研究结果展示了线粒体DNA序列在植物系统发育重建上的巨大潜在应用价值，为其它困难植物类群系统发育关系的解决提供了新思路。