Single molecule RNA sequencing uncovers trans-splicing and improves annotations in Anopheles stephensi.
Single molecule RNA sequencing uncovers trans-splicing and improves annotations in Anopheles stephensi.
复制标题
DOI：
10.1111/imb.12294
复制
发表时间：
2017-06
影响因子：
2.6
通讯作者：
Tu Z
中科院分区：
文献类型：
--
作者：
Jiang X;Hall AB;Biedler JK;Tu Z
单分子测序最近已被用来获得全长 cDNA 序列，从而改善基因组注释并揭示 RNA 亚型。在这里，我们使用了 Pacific Biosciences (PacBio) 的一种称为异构体测序 (Iso-Seq) 的方法，对亚洲疟疾蚊子史氏按蚊 (Anopheles stephensi) 的 cDNA 文库进行了测序。鉴定出超过 600,000 个全长 cDNA（称为插入片段读取）。由于 PacBio 测序固有的高错误率，我们测试了不同的纠错方法。我们发现使用 Illumina RNA-seq 进行纠错比使用默认 SMRT 管道生成更多数据。全长纠错的 PacBio 读段极大地改进了史氏按蚊的基因注释：更新了 4867 个基因模型，并在注释中添加了 1785 个选择性剪接异构体。此外，在 An 中还鉴定出了六个反式剪接事件，其中来自不同初级转录本的外显子连接在一起。斯蒂芬西。所有六个反式剪接事件似乎在蚊科动物中都是保守的，就像它们在蚊科动物中也发现的那样。冈比亚和埃及伊蚊。反式剪接事件编码的蛋白质也高度保守，并且这些蛋白质的直系同源物在外群物种中是顺式剪接的，表明反式剪接可能作为拯救进化过程中断裂的基因的机制而出现。
Single molecule sequencing has recently been used to obtain full-length cDNA sequences that improve genome annotation and reveal RNA isoforms. Here, we used one such method called isoform sequencing (Iso-Seq) from Pacific Biosciences (PacBio) to sequence a cDNA library from the Asian malaria mosquito Anopheles stephensi. More than 600,000 full length cDNAs, referred to as reads of insert, were identified. Due to the inherently high error-rate of PacBio sequencing, we tested different approaches for error-correction. We found that error-correction using Illumina RNA-seq generated more data than using the default SMRT pipeline. The full-length error-corrected PacBio reads greatly improved the gene annotation of Anopheles stephensi: 4867 gene models were updated and 1785 alternatively-spliced isoforms were added to the annotation. In addition, six trans-splicing events, where exons from different primary transcripts were joined together, were identified in An. stephensi. All six trans-splicing events appear to be conserved in Culicidae, as they are also found in An. gambiae and Aedes aegypti. The proteins encoded by trans-splicing events are also highly conserved and the orthologs of these proteins are cis-spliced in outgroup species, indicating that trans-splicing may arise as a mechanism to rescue genes that broke up during evolution.
登录
查看更多内容
影响因子：
16.6
作者：
Abdel-Ghany SE;Hamilton M;Jacobi JL;Ngam P;Devitt N;Schilkey F;Ben-Hur A;Reddy AS
通讯作者：
Reddy AS
影响因子：
14.9
作者：
Wang K;Singh D;Zeng Z;Coleman SJ;Huang Y;Savich GL;He X;Mieczkowski P;Grimm SA;Perou CM;MacLeod JN;Chiang DY;Prins JF;Liu J
通讯作者：
Liu J
保守的内含子 U1 snRNP 结合序列促进果蝇中的反式剪接
影响因子：
10.5
作者：
Gao JL;Fan YJ;Wang XY;Zhang Y;Pu J;Li L;Shao W;Zhan S;Hao J;Xu YZ
通讯作者：
Xu YZ
DOI：
10.1073/pnas.151268698
发表时间：
2001-08-14
影响因子：
11.1
作者：
Dorn, R;Reuter, G;Loewendorf, A
通讯作者：
Loewendorf, A
影响因子：
6.5
作者：
Wally, Verena;Murauer, Eva M.;Bauer, Johann W.
通讯作者：
Bauer, Johann W.