De novo assembly of the transcriptome of Aegiceras corniculatum, a mangrove species in the Indo-West Pacific region
De novo assembly of the transcriptome of Aegiceras corniculatum, a mangrove species in the Indo-West Pacific region
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印度-西太平洋地区红树林树种桐花树转录组的从头组装
DOI：
10.1016/j.margen.2016.05.004
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发表时间：
2016-08-01
期刊：
影响因子：
1.9
通讯作者：
Shi, Suhua
中科院分区：
文献类型：
--
作者：
Fang, Lu;Yang, Yuchen;Shi, Suhua
桐花树Aegiceras corniculatum（L.）布兰科是最耐盐的红树林物种之一，可以在红树林的向海边缘在3%的盐度中茁壮成长。我们对A. Corniculatum利用Illumina GA平台开发其基因组资源，用于生态学和进化研究。我们获得了约5000万个长度为75 bp的高质量双端读段。使用短读段组装程序Velvet，我们产生了49，437个重叠群，平均长度为625 bp。共有32，744个（66.23%）重叠群与GenBank非冗余（NR）蛋白质数据库显示出显着相似性。这些序列中的30，911和18，004被分配到基因本体和真核生物蛋白质组（KOG）。从我们的组件中，共有4942个转录本与KEGG直系同源物具有显著的相似性，并参与144个KEGG途径，而9899个unigenes具有酶委员会（EC）编号。此外，从7342个序列中鉴定出9792个转录组衍生的SSR。根据我们严格的标准，从2058个重叠群中也鉴定出4165个候选SNP。这些SNP中的一些通过桑格测序进一步验证。本研究所获得的基因组资源对该红树林的生态学、进化和功能基因组学研究具有重要价值。(C)2016爱思唯尔B.V.保留所有权利。
Aegiceras corniculatum (L.) Blanco is one of the most salt tolerant mangrove species and can thrive in 3% salinity at the seaward edge of mangrove forests. Here we sequenced the transcriptome of A. corniculatum used Illumina GA platform to develop its genomic resources for ecological and evolutionary studies. We obtained about 50 million high-quality paired-end reads with 75 bp in length. Using the short read assembler Velvet, we yielded 49,437 contigs with the average length of 625 bp. A total of 32,744 (66.23%) contigs showed significant similarity to the GenBank non-redundant (NR) protein database. 30,911 and 18,004 of these sequences were assigned to Gene Ontology and eukaryotic orthologous groups of proteins (KOG). A total of 4942 transcripts from our assemblies had significant similarity with KEGG Orthologs and were involved in 144 KEGG pathways, while 9899 unigenes had enzyme commission (EC) numbers. In addition, 9792 transcriptome-derived SSRs were identified from 7342 sequences. With our strict criteria, 4165 candidate SNPs were also identified from 2058 contigs. Some of these SNPs were further validated by Sanger sequencing. Genomic resources generated in this study should be valuable in ecological, evolutionary, and functional genomics studies for this mangrove species. (C) 2016 Elsevier B.V. All rights reserved.