中华猕猴桃基因组可变剪接事件鉴定及分析

Genome-Wide Survey of Alternative Splicing in Actinidia chinensis

可变剪接使一个基因能产生多种m RNA成熟体,极大地增加蛋白多样性.采用中华猕猴桃基因组数据做参考数据,利用中华猕猴桃叶片和果实3个不同发育时期(未成熟、半成熟和成熟期)的转录组数据,从中华猕猴桃基因组(39040个基因)中共鉴定出11651个基因(占总基因数的29%)对应的32180个可变剪接事件.在可变剪接不同类型中,内含子保留类型的发生频率最高,占50%以上;3′可变位点类型频率约为5′端可变类型的2倍.GO富集分析结果表明,可变剪接的基因主要富集于酶调控及核苷酸结合相关功能的GO类别中,而组织特有可变剪接基因功能富集热点与组织的重要功能关联,叶片多为肌动蛋白及微管相关;未成熟果实与双组分信号系统相关;半成熟果实多与磷脂合成过程相关;成熟果实多与信号传递过程相关.另外,55.6%的维生素合成相关基因发生可变剪接事件,显著高于基因组水平的29.6%,暗示着可变剪接参与维生素合成相关基因代谢过程中的重要作用.通过对中华猕猴桃全基因组可变剪接的分析,为解析中华猕猴桃基因组及进一步开展相关分子育种工作提供依据.

Alternative splicing can increase the diversity and complexity of proteome greatly through creating multiple mRNA transcripts from a single gene. RNA-seq data from different organs （leaf, immature fruit, half-ripe fruit and mature fruit） ofActinidia chinensis had been used to identify the alternative splicing events using the A. chinensis genome as reference, and totally 32180 alternative splicing events were discovered from the A. chinensis genome （39040 genes） corresponding to 11651 genes （29% of the total genome）. Intron retention events showed the highest frequency （more than 50%） among all the different alternative splicing events. The frequency of events with alternative 3＇ splice sites was twice than the alternative 5＇ splice sites. GO enrichment analysis result showed that the alternative splicing gene was mainly enriched in enzyme regulation and nucleotide binding related GO categories. The alternative splicing events in different organs of A. chinensis seemed to preferentially occur in genes with important function. The genes of leaf were associated with the function of actin and microtubule. The genes of immature fruit decided the function of two-component signal system. The genes of half-ripe fruit were connected with phospholipid synthesis process. The genes in mature fruit were associated with signal transduction. In addition, 55.6% of vitamin related genes had been found to have alternative splicing changes, which were significantly higher than the average changes of the genome （the average splicing change level was 29.6%）. Those explained that alternative splicing events played an important role in the process of vitamin synthesis. In this paper, through the genome-wide analysis of alternative splicing in A. chinensis, a powerful resource for understanding the complex genome of A. chinensis was provided. The result was also useful to molecular breeding in kiwifruit.