Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus.
Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus.
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泥鳅的全长转录组为泥鳅属的进化提供了见解
DOI：
10.1038/s41598-018-29991-6
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发表时间：
2018-08-03
影响因子：
4.6
通讯作者：
Luo S
中科院分区：
文献类型：
--
作者：
Yi S;Zhou X;Li J;Zhang M;Luo S
转录本的重建和注释，特别是对于没有参考基因组的物种，在前基因组时代的基因发现、基因组签名研究和基因组注释中起着至关重要的作用。这项研究利用PacBio SMRT测序技术产生了33,330个二倍体鳗鱼全长转录本。共鉴定出6918个具有两种或两种以上异构体的基因家族，共检测到26683个完整的ORF，平均长度为1497个碱基。总共鉴定了1,208个高可信的lncRNA，其中大多数似乎是miRNAs或snoRNAs的前体转录产物。根据1,905个单拷贝同源基因构建了泥虾属物种的系统发育树。四倍体和二倍体鳗鼠聚为一个支系，二分鼠与鳗鼠亲缘关系较近。四倍体鳗鱼的总进化率显著高于其他泥鳅。同时，在鳗鱼中鉴定出28个阳性选择基因。这些正向选择的基因可能在鳗鱼对不同栖息地环境的适应中发挥关键作用。这项研究有助于进一步探索鳗鱼的基因组特征，并为揭示四倍体泥鳅的进化史提供潜在的见解。
Reconstruction and annotation of transcripts, particularly for a species without reference genome, plays a critical role in gene discovery, investigation of genomic signatures, and genome annotation in the pre-genomic era. This study generated 33,330 full-length transcripts of diploid M. anguillicaudatus using PacBio SMRT Sequencing. A total of 6,918 gene families were identified with two or more isoforms, and 26,683 complete ORFs with an average length of 1,497 bp were detected. Totally, 1,208 high-confidence lncRNAs were identified, and most of these appeared to be precursor transcripts of miRNAs or snoRNAs. Phylogenetic tree of the Misgurnus species was inferred based on the 1,905 single copy orthologous genes. The tetraploid and diploid M. anguillicaudatus grouped into a clade, and M. bipartitus showed a closer relationship with the M. anguillicaudatus. The overall evolutionary rates of tetraploid M. anguillicaudatus were significantly higher than those of other Misgurnus species. Meanwhile, 28 positively selected genes were identified in M. anguillicaudatus clade. These positively selected genes may play critical roles in the adaptation to various habitat environments for M. anguillicaudatus. This study could facilitate further exploration of the genomic signatures of M. anguillicaudatus and provide potential insights into unveiling the evolutionary history of tetraploid loach.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
长期读取的参考基因组无基因组的重建，从阿astagalusmembranaceus揭示了参与生物活性复合生物合成的转录物变体。
影响因子：
33.5
作者：
Li J;Harata-Lee Y;Denton MD;Feng Q;Rathjen JR;Qu Z;Adelson DL
通讯作者：
Adelson DL
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
DOI：
10.1073/pnas.0911239106
发表时间：
2009-12-08
影响因子：
11.1
作者：
Goodman, Morris;Sterner, Kirstin N.;Wildman, Derek E.
通讯作者：
Wildman, Derek E.
影响因子：
3
作者：
Huang, Songqian;Cao, Xiaojuan;Tian, Xianchang
通讯作者：
Tian, Xianchang