【作者】 赵极瀚；

【导师】 杨细平； 张保青；

【作者基本信息】 广西大学 ， 农艺与种业（专业学位）， 2023， 硕士

【摘要】 多倍体甘蔗是基因组最复杂的物种之一。全球蔗糖产量的主要来源是现代商业杂交种,解析杂交种高糖积累的因素对蔗糖产业发展具有重要意义。目前可用的甘蔗杂交种参考基因组完整度不高,制约了相关组学研究。现代甘蔗杂交种主要起源于两个甘蔗原始种:热带种和割手密,两者的参考基因组相对完整,有望应用于解析杂交种的组学特征。本研究采用Pac Bio长片段测序技术和RNA-seq短片段测序技术生成转录组数据,组合利用热带种和割手密参考基因组,在等位基因水平引导构建甘蔗杂交种全长转录组数据集,提供了46,416个新基因,263,378个等位基因水平的转录本和139,405个可变剪接事件,对基因结构注释进行了有效的补充。PCR和RT-PCR实验结果验证了部分新基因和可变剪接事件的真实性,证明构建全长转录组结果的准确性。进一步研究显示亚基因组表达偏倚基因未表现组织特异性,同一组织中热带种亚基因组和割手密亚基因组的表达偏倚基因主要在不同的通路中执行功能。割手密亚基因组的部分表达偏倚基因在光合作用、碳固定途径富集,可能是祖先亲本割手密的基因渗入甘蔗杂交种的结果。比较高糖与低糖甘蔗杂交种,筛选与蔗糖积累相关的差异基因。其中差异表达基因反映两者之间存在固碳能力差异和关键酶调控差异,同时差异可变剪接基因反映两者之间存在转录后调控差异。部分差异基因来源于割手密亚基因组,表明割手密亚基因组对于蔗糖积累具有不可忽略的作用。此外,在一些基因模型中,同一基因的等位基因表现不同甚至相反的表达模式,反映了这些等位基因在多倍体甘蔗中存在向新功能的潜在进化。加权共表达网络分析进一步鉴定到与蔗糖积累相关的关键基因,它们分布在光合作用、碳固定、碳代谢通路。本研究的甘蔗全长转录组数据集以网页形式在线公开,用户可通过BLAST功能快速搜索数据库中的目标全长转录本,或者直接下载相关数据文件,该数据库为多倍体甘蔗杂交种提供了更加详细的转录水平的参考信息。更多还原

【Abstract】 Polyploid sugarcane is one of the most complex species in terms of genome.The main source of global sucrose production is modern commercial cultivar,and it is important to analyse the influence factors of its high sugar accumulation for the development of sugarcane industry.The currently available reference genomes of sugarcane hybrids are incomplete,limiting relevant genomic studies.Since modern sugarcane hybrids are mainly inherited from two original sugarcane species: Saccharum officinarum and Saccharum spontaneum,their relatively complete reference genomes are expected to be applied to resolve the genomic information of the hybrids.In this study,Pac Bio long-read and RNA-seq short-read sequencing were used to generate transcriptome data and a combination of the S.officinarum and S.spontaneum reference genomes was used to guide the construction of a fulllength transcriptome dataset of sugarcane hybrids at the allelic level,providing46,416 novel genes,263,378 allele-defined transcript isoforms and 139,405 alternative splicing events,which effectively complemented the gene structure annotation.PCR and RT-PCR experiment results verified the authenticity of some novel genes and alternative splicing events,demonstrating the accuracy of the process for constructing full-length transcriptome.Further research showed that the subgenomic expression-biased genes did not exhibit tissue specificity,while the expression-biased genes of the S.officinarum subgenome and the S.spontaneum subgenome in the same tissue mainly performed functions in different pathways.Some expression-biased genes in the S.spontaneum subgenome were enriched in photosynthesis and carbon fixation pathways,which might be the result of introgression from the ancestral parent S.spontaneum into the sugarcane hybrids.High-sugar and low-sugar sugarcane hybrids were compared to screen for differential genes associated with sucrose accumulation.The differentially expressed(DE)genes reflected the differences in carbon fixation capacity and key enzyme regulation between them,while the differentially alternative splice(DA)genes reflected the differences in post-transcriptional regulation between them.Some of the differential genes were derived from the S.spontaneum subgenome,indicating that the S.spontaneum subgenome has a non-negligible role in sucrose accumulation.In addition,the different or even opposite expression patterns of alleles in some gene models reflected the potential evolution of these alleles toward novel functions in polyploid sugarcane.Weighted co-expression network analysis further identified key genes associated with sucrose accumulation,these key genes were distributed in photosynthesis,carbon fixation,and carbon metabolism pathways.The sugarcane full-length transcriptomic data was available online in the form of a website,and users can quickly search for target full-length transcripts in the sequence library through the BLAST function or directly download the relevant data files.The dataset provided more comprehensive transcriptomic reference information for polyploid sugarcane hybrids.更多还原