长穗偃麦草和中间偃麦草基因组构成与进化研究

The Thinopyrum genus is an important wild relatives in wheat genetic improvement. Intermediate wheatgrass (Thinopyrum intermedium) and Thinopyrum ponticum are widely used in wheat breeding, but their genome constitutions had long been controversial. We previously constructed the phylogenetic relationship based on the well assembled and annotated genomes of Thinopyrum elongatum, Thinopyrum intermedium and Wheat-Thinopyrum ponticum substitution lines, and confirmed that the E genome are the donor constitution of Thinopyrum ponticum, and had the closest relationship with wheat B subgenome. One of the subgenomes of Thinopyrum intermedium is more closely related to the D genome of the Aegilops genus, probably originated from this genus; the other two subgenomes are far from the E genome, and their donor sources need to be further confirmed. Therefore, in this study we intend to further sequence and assemble the transcriptome of wheat diploid species, and analyze the genome constitution and evolutionary mechanism of Thinopyrum intermedium through comparative genome analysis. On this basis, transcriptome sequencing and assembly are carried out on multiple Wheat-Thinopyrum ponticum substitution lines. By comparing with the wheat genome, genes from the single chromosome of Thinopyrum ponticum are separated, and then compare with diploid genome data to preliminarily explore its genome constitution and evolution mechanism. This work will give more theoretical basis for the further use of the Thinopyrum genus in wheat genetic improvement.

偃麦草属物种是小麦遗传改良工作中重要的近缘野生材料。长穗偃麦草及中间偃麦草染色体组构成一直以来存在着较多的争议。本研究前期利用已经完成组装的二倍体长穗偃麦草、中间偃麦草及小麦-十倍体长穗偃麦草异代换系基因组数据，明确了E基因组是十倍体长穗偃麦草的供体来源之一，与小麦B亚基因组关系最近。而中间偃麦草其中一个亚基因组与粗山羊草D染色体组关系最为密切，很可能来源于山羊草属供体；另外两个亚基因组与E基因组关系均较远，其供体来源尚需进一步研究。因此，本研究拟进一步对小麦族二倍体种进行转录组测序及组装，通过比较基因组分析明确中间偃麦草基因组构成和进化机制。在此基础上，对多份小麦-十倍体长穗偃麦草异代换系进行转录组测序，通过与小麦基因组比较，拆分出长穗偃麦草单染色体的基因，进而与二倍体基组数据进行比较，初步探讨十倍体长穗偃麦草基因组构成及进化机制，为进一步有效利用偃麦草属改良小麦提供理论基础。

偃麦草属物种是小麦遗传改良工作中非常重要的野生近缘材料。中间偃麦草和长穗偃麦草等多倍体偃麦草染色体基组构成一直以来存在较多的争议。本项目通过对小麦族多个二倍体基组物种进行转录组测序及组装，利用比较基因组学手段来明确中间偃麦草基因组构成和演化机制。本研究选取有代表性的中间偃麦草材料（PI 440031）进行了第三代PacBio HiFi测序及基因组组装，组装基因组大小为10.89 Gb，contig N50长度为26.3 Mb。另外，通过Hi-C测序技术产生了1.6 Tb二代Illumina测序数据，构建了中间偃麦草基因组物理图谱并成功拆分出三套亚基因组序列，并对其基因组结构进行了注释及解析。进一步，完成了山羊草属（包括拟斯卑尔脱山羊草、小伞山羊草、尾状山羊草、顶芒山羊草、高大山羊草、沙融山羊草、无芒山羊草、单芒山羊草、希尔斯山羊草、二角山羊草等）、假鹅观草、新麦草、海滨大麦、鼠大麦、异形花草、簇毛麦、黑麦、旱麦草等二倍体基组物种的转录组测序及组装。最终，将注释完成的中间偃麦草基因序列与上述二倍体基组物种转录组组装序列以及二倍体长穗偃麦草、乌拉尔图小麦、二粒小麦、普通小麦、大麦等已公布基因组的注释基因序列进行聚类分析发现：中间偃麦草三个亚基组构成中，其中一个基组与山羊草属物种聚类在一起，可以认为是山羊草属的祖先物种；另外两个亚基因组则与该基组距离较远，而分别与簇毛麦和假鹅观草聚类在一起，可以认为是簇毛麦和假鹅观草的祖先种，说明其基因组构成更符合“StStVVXX”的染色体基组类型，而没有偃麦草属物种作为其直接供体，与之前文献报道中“EeEeEbEbStSt”的染色体基组类型不符。该结果明确了中间偃麦草染色体基组构成，并为进一步有效利用偃麦草属多倍体偃麦草进行小麦遗传改良提供坚实的理论基础。