基于二代测序技术的菊科莴苣属植物系统基因组学研究

Lactuca L. belongs to the subtribe Lactucinae, tribe Cichorieae of the family Asteraceae. The genus has been the difficult and controversial part in the phylogenetic studies of Asteraceae family for a long time, due to the complex and diverse morphological characters within the genus and the resemble features to the species from related genera. Former studies of Lactuca have been focused on the lettuce gene pool and a small amount of species, lacking a systematic study. In recent years, phylogenomics, based on Next Generation Sequencing (NGS) technologies, becomes one of the important tools to investigate the phylogenetic relationships at different levels of plant taxa. This project aims to study the phylogenomics within Lactuca and between Lactuca and representing species from related genera (as outgroups), using high throughput DNA sequencing. The chloroplast genome sequences, nuclear Conserved Ortholog Set (COS) loci and ribosomal intergenic spacer (ITS) will be assembled, annotated and used for constructing phylogenetic trees. Finally, the phylogenetic trees will be combined with some important morphological characters, as well as chromosome number and geographical distribution, to investigate their patterns on the evolutionary trees. The results of this study will contribute to the circumscription of Lactuca, its subgeneric classification and the origin of Lactuca. In the meantime, the results will also shed a new light on the phylogenetic relationships in Lactucinae, as well as new genetic resources for lettuce breeding.

莴苣属Lactuca L.隶属于菊科菊苣族莴苣亚族，该属植物性状变异较大且与其近缘属植物性状交叉严重，是菊科植物系统发育研究中的难点之一。之前莴苣属的研究仅局限于生菜基因库和少数物种中，缺乏系统性研究。基于二代测序技术的系统基因组学是近年来揭示植物类群不同等级间系统发育关系的重要手段之一。本研究拟以莴苣属物种及其近缘属代表物种（外类群）为研究对象，使用二代测序技术对莴苣属及外类群植物进行高通量测序。通过叶绿体全基因组序列、细胞核保守同源基因序列和核糖体DNA间隔序列来构建莴苣属植物分子系统发育树，结合莴苣属重要的形态学、染色体数目及地理分布等特征，探究莴苣属的界限划分，属内系统发育关系和起源等问题。研究结果也将为莴苣亚族的系统发育以及生菜新种质资源的研究提供一定的理论依据。

莴苣属Lactuca L.是菊科菊苣族莴苣亚族的中心属，也是分类学上的一个疑难属。该属包含有蔬菜莴苣和其野生种，具有较高的经济价值。本项目首次获得100个莴苣属及近缘属完整叶绿体基因组，还对35个莴苣属和近缘属类群的瘦果微形态及12个菊苣族类群的线粒体基因组进行了研究。主要研究结果包括：（1）系统发育分析表明莴苣属物种主要分为六个分支，其中五个分支仍然属于莴苣属，第六个分支则主要包含非洲种，应当转移到Melanoseris中或者成立一新属；（2）莴苣属可能的起源中心为地中海地区；（3）栽培莴苣潜在的基因库包括六个野生种；（4）选择压力分析发现栽培莴苣的叶绿体基因组中一些与能量代谢过程有关的基因，如atpF和ycf2，受到了正选择作用，这可能与人工驯化历史有关；（5）瘦果微形态研究结果表明瘦果喙的有无及长短、果柄形状、翅的有无、肋的数目、表皮细胞排列方式及瘦果表面蜡质的发育程度等特征可以作为莴苣属、假福王草属Paraprenanthes Chang及紫菊属Notoseris Shih的主要分类依据；（6）林生假福王草P. diversifolia (Vaniot) N. Kilian线粒体基因组与已发表的三个莴苣属线粒体基因组的基因排列具有较高的相似性，而与其他莴苣亚族之外的菊科物种的序列相似性较低，具有较多的基因重排现象。本项目为研究莴苣属的界限划分、属内系统发育关系及栽培莴苣的起源提供了重要数据支持，并为研究栽培莴苣的进化史及遗传育种提供了理论基础。