SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus
SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus
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SMRT 测序分析揭示了 Ananas comosus var. 的全长转录本和可变剪接模式。
DOI：
10.7717/peerj.7062
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发表时间：
2019-06-21
期刊：
影响因子：
2.7
通讯作者：
Huang, Zhuo
中科院分区：
文献类型：
--
作者：
Ma, Jun;Xiang, Yixuan;Huang, Zhuo
背景菠萝bracteatus是一种多年生草本单子叶植物，因其嵌合叶而作为观赏植物栽培。由于其基因组的复杂性，并且由于在公共GenBank数据库中没有可用的基因组信息，mRNA转录物的完整结构尚不清楚，并且对Ananas comosus var. bracteatus.Methods.构建了3个大小分级的全长cDNA文库（1-2 kb、2-3 kb和3-6 kb），并在5个单分子实时荧光（SMRT）细胞（分别为2个细胞、2个细胞和1个细胞）中进行测序。总共鉴定了19，838个转录本用于选择性剪接（AS）分析。其中，19,185个（96.7%）转录本进行了功能注释。通过将非冗余同种型映射到参考基因组，总共鉴定了9，921个基因。总共鉴定了10，649个AS事件，其中大多数是内含子保留事件。选择性剪接基因在植物的碳代谢、氨基酸合成、糖酵解等基本代谢过程中发挥作用。14个与叶绿素生物合成相关的基因被鉴定为具有AS事件。在与白化病叶表型相关的途径中分类的基因（ko 00860、ko 00195、ko 00196和ko 00710）的剪接位点的分布以及常规和非典型AS位点的百分比变化很大。结果表明，在所有基因中，有8，316个基因至少携带一个poly（A）位点，共产生21，873个poly（A）位点。这些结果表明，所获得的基因组的基因结构和功能信息的质量大大提高，这可能有助于进一步的遗传研究。具苞片的
Background. Ananas comosus var. bracteatus is an herbaceous perennial monocot cultivated as an ornamental plant for its chimeric leaves. Because of its genomic complexity, and because no genomic information is available in the public GenBank database, the complete structure of the mRNA transcript is unclear and there are limited molecular mechanism studies for Ananas comosus var. bracteatus.Methods. Three size fractionated full-length cDNA libraries (1-2 kb, 2-3 kb, and 3-6 kb) were constructed and subsequently sequenced in five single-molecule real-time (SMRT) cells (2 cells, 2 cells, and 1 cell, respectively).Results. In total, 19,838 transcripts were identified for alternative splicing (AS) analysis. Among them, 19,185 (96.7%) transcripts were functionally annotated. A total of 9,921 genes were identified by mapping the non-redundant isoforms to the reference genome. A total of 10,649 AS events were identified, the majority of which were intron retention events. The alternatively spliced genes had functions in the basic metabolism processes of the plant such as carbon metabolism, amino acid biosynthesis, and glycolysis. Fourteen genes related to chlorophyll biosynthesis were identified as having AS events. The distribution of the splicing sites and the percentage of conventional and non-canonical AS sites of the genes categorized in pathways related to the albino leaf phenotype (ko00860, ko00195, ko00196, and ko00710) varied greatly. The present results showed that there were 8,316 genes carrying at least one poly (A) site, which generated 21,873 poly (A) sites. These findings indicated that the quality of the gene structure and functional information of the obtained genome was greatly improved, which may facilitate further genetic study of Ananas comosus var. bracteatus.