基于联合测序分析技术挖掘红苞凤梨lncRNA信息

lncRNA identification of Ananas comosus var. bracteatus by hybrid sequencing

关键词:  红苞凤梨, Hiseq2500测序, SMRT全长转录组测序, lncRNA鉴定

Key words:   Ananas comosus var. bracteatus, Hiseq2500, SMRT full length transcriptome sequence, lncRNA identification

摘要:

为了揭示lncRNA在红苞凤梨嵌合叶片形成和生长发育过程中的调控作用机制,该文以金边红苞凤梨为材料,采用Hiseq2500测序和SMRT三代全长转录组测序联合测序分析技术,分析挖掘红苞凤梨lncRNA信息。结果表明:(1)鉴定得到6 018条lncRNA,包含3 298个基因间lncRNA,870个反义lncRNA,717个内含子lncRNA和1 109个正义lncRNA,数据量较二代测序有了极大的提高。(2)结构分析表明,红苞凤梨lncRNA的总体表达丰度低于mRNA; 序列长度在 400～1 200 nt区间比例高于mRNA,而在>1 600 nt区间,lncRNA分布的比例显著小于mRNA; lncRNA中的外显子数量总体少于mRNA,开放阅读框长度总体上也短于mRNA。(3)差异表达分析表明,在全绿、全白叶片发育过程中鉴定到1 710个差异表达lncRNA。(4)靶基因预测结果表明,5 441个lncRNA通过cis作用方式预测到靶基因,1 544个lncRNA通过trans方式预测到靶基因。(5)靶基因的功能注释和富集分析显示,差异表达lncRNA的靶基因主要作为酶蛋白参与调节叶片代谢活动和信号转导等方面,与叶片的颜色形成、光合作用和生长发育密切相关。该文鉴定出的lncRNA信息以及对其结构和功能的分析,为红苞凤梨以及凤梨科其他植物的lncRNA表观遗传调控机理研究提供了数据基础,筛选出的差异表达lncRNA在金边红苞凤梨叶片嵌合性状的形成和生长发育中具有重要的调控作用。

Abstract:

In order to reveal the regulation function of lncRNA on the chimeric character formation and development of the leaf of Ananas comosus var. bracteatus, Hiseq2500 sequencing and SMRT the third-generation full-length transcriptome sequencing were applyed to identify lncRNA of Ananas comosus var. bracteatus. The results were as follows:(1)A total of 6 018 lncRNA were identified, containing 3 298 intergenic lncRNA, 870 antisense lncRNA, 717 intron lncRNA and 1 109 sense lncRNA, which were greatly improved compared with the second-generation information.(2)Structural analysis showed that the overall expression level of lncRNA was lower than that of mRNA. The transcript length distribution of lncRNA in the range of 400-1 200 nt was higher than that of mRNA, while in the range > 1 600 nt, the proportion of lncRNA distribution was significantly lower than that of mRNA. The number of exons in lncRNA was generally less than that of mRNA, and the open reading frame was also shorter in length than that of mRNA.(3)For analysis of differential expression, 1 710 differentially expressed lncRNA were identified during the development of complete green and complete white leaves.(4)Target gene prediction results showed that 5 441 lncRNA were predicted target genes by Cis action, and 1 544 lncRNA were predicted target genes by Trans action.(5)Functional annotation and enrichment analysis of target genes revealed that the target genes of differentially expressed lncRNA mainly act on metabolic activities and signal transduction of leaves as enzyme proteins, and were closely related to leaf color formation, photosynthesis and leaf growth. The lncRNA information identified in this paper and, as well as the analysis of its structure and functions, provide the data basis for the study of the epigenetic regulation mechanism of lncRNA in Ananas comosus var. bracteatus and other plants in Bromeliaceae. The identified differentially expression of lncRNA plays an important role in the chimeric character formation and development of leaf of Ananas comosus var. bracteatus.