基于系统发育基因组学方法探讨适应不同宿主的肉苁蓉属植物水平基因转移

Recently, horizontal gene transfer (HGT) between parasitic plants and host has been a new hotspot for evolutionary biology. For a long time, due to the lack of comparative genomics data between widely parasitic plant taxa and their different hosts which belongs to different families or genera, however, how do the parasitic species from same monophyletic group capture genes from different hosts, and what do these genes share the common or obtain the specific differences have not been fully understood. Cistanche (Orobanchaceae) is the ideal material for studying horizontal transfer of genes and their adaptive evolution in different host plants. Based on the previous study on horizontal gene transfer of parasitic plants and their host, in this study, RNA and genomic DNA of Cistanche species and their different hosts will be isolated, cDNA and gDNA library will be build and be sequenced using next-generation sequencing technology. Combined with genomic data available, horizontally transferred genes will be identified using comparative phylogenomic analyses. Their magnitude, type, variation patterns of horizontally transferred genes and possible mechanisms will be involved. The hypotheses for host shift will be tested by timing the HGT events. The occurrence of horizontally transferred genes to adapt the processes of host shift at the genomic level, the impact of the involvement of fuctional genes on divergent evolution of parasitic plants, and the factors lead to gain or loss of these genes at different times, different lineages will be inferred from comparative genomic data. Our results can facilitate our understanding the process of adaptive evolution and the genetic mechanisms of horizontal gene transfer during host shift of parasite plants. The transcriptome data of parasite and their hosts from this study can be used to carry out genomic annotation of these species in the future.

寄生植物和宿主之间的水平基因转移，是进化生物学研究的热点问题。由于缺乏对广寄生植物类群及其宿主的比较基因组学的系统研究，隶属于同一单系类群的寄生植物如何从不同科、属的宿主中捕获的水平转移基因一直不被了解。肉苁蓉属是探讨植物水平转移基因在不同宿主中适应性进化的理想材料，本研究在已有水平基因转移研究基础上，选择该属植物及其不同宿主为研究对象，通过构建文库和新一代测序技术测定转录组序列，结合已获得的基因组数据，应用系统发育基因组学方法，检测发生水平转移的基因在数量、类别、发生方式和变异式样的差别，通过时间推导检验宿主转变的不同假设，揭示水平转移基因对不同宿主选择性适应的发生规律，探讨外源功能基因的介入对寄生植物趋异进化的影响，解析在宿主转变的不同时间、不同谱系上导致水平转移基因获得和丢失的可能因素。研究结果有助于深入理解不同宿主条件下寄生物种的适应性进化过程和水平基因转移的遗传学机制。

越来越多的研究证据表明在寄生植物和宿主之间存在潜在的水平转移，然而长期以来，隶属于同一单系类群的寄生植物如何从不同科、属的宿主中捕获的水平转移基因，却一直不被了解。本课题选择列当科肉苁蓉属植物及其不同宿主为研究对象，采用新一代测序技术进行相关类群的系统发育基因组学研究，检测发生水平转移的基因在数量、类别、发生方式和变异式样的差别，探讨了水平转移基因对不同宿主选择性适应的发生规律。研究发现：1）列当科的系统发育重建证实了该科仅有3次全寄生起源，且发生不同步，可能和宿主转换有关。2）肉苁蓉属的核基因有高达3%的转录本会发生水平基因转移，绝大多数不含有完整CDS的基因，而那些极少数具有完整CDS的编码基因的进化分析显示它们与植物适应寄生习性密切相关。3）只有少数质体来源的线粒体基因发生水平基因转移，不同于先前大花草属植物的研究结果。4）针对rpoC2基因的系统发育分析表明富含信息位点的水平转移基因能够记录过去的宿主转换，这一发现有助于拓宽有用寄生植物保护过程中的历史宿主选择。上述发现加深了宿主转换对寄生物种适应性进化过程的理解，为进一步揭示水平基因转移的遗传学机制奠定了基础。