Transcriptome sequencing of a highly salt tolerant mangrove species Sonneratia alba using Illumina platform
Transcriptome sequencing of a highly salt tolerant mangrove species Sonneratia alba using Illumina platform
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使用 Illumina 平台对高耐盐红树品种 Sonneratia alba 进行转录组测序。
DOI：
10.1016/j.margen.2011.03.005
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发表时间：
2011-06-01
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：
Chen, Sufang;Zhou, Renchao;Shi, Suhua
红树林是关键和受威胁的海洋资源，但公共数据库中提供的转录组和基因组数据很少。本研究利用Illumina基因组分析仪对高耐盐性红树植物白海桑的转录组进行了测序。超过1500万个75bp的成对末端阅读片段被组装成30,628个独特的序列，平均长度为581bp。共检测到2358个SSR，其中二核苷酸重复(59.2%)和三核苷酸重复(37.7%)最为常见。基于20,945个编码序列的密码子使用偏向分析表明，白链霉菌的密码子使用偏向比一些微生物和果蝇的基因偏向要小，密码子使用的变异主要是由于组成突变偏向，而翻译选择的影响相对较弱。全基因组基因本体论(GO)分配表明，阿尔巴拟南芥与拟南芥具有相似的GO-SLIM分类。高比例的GO纤细类‘线粒体’序列和四条KEGG途径，如碳水化合物和次生代谢物代谢，可能有助于白纹伊蚊对盐的适应。此外，还筛选出了1266个与其他物种中已知的273个盐响应基因(基因家族)相匹配的独特序列作为耐盐性的候选基因，其中一些基因具有较高的覆盖深度。最后，通过将白链霉菌的转录组序列与其同源的249条已知EST序列进行比较，确定了4个具有较强选择信号的基因(K-a/K-S>；1)。这项研究证明了Illumina平台成功地应用于非模式生物转录组的从头组装。白链霉菌丰富的SSR标记、盐敏基因和4个具有自然选择特征的基因为今后的遗传多样性、盐分适应性和物种形成研究提供了丰富的序列来源。(C)2011爱思唯尔B.V.保留所有权利。
Mangroves are critical and threatened marine resources, yet few transcriptomic and genomic data are available in public databases. The transcriptome of a highly salt tolerant mangrove species, Sonneratia alba, was sequenced using the Illumina Genome Analyzer in this study. Over 15 million 75-bp paired-end reads were assembled into 30,628 unique sequences with an average length of 581 bp. Of them, 2358 SSRs were detected, with di-nucleotide repeats (59.2%) and tri-nucleotide repeats (37.7%) being the most common. Analysis of codon usage bias based on 20,945 coding sequences indicated that genes of S. alba were less biased than those of some microorganisms and Drosophila and that codon usage variation in S. alba was due primarily to compositional mutation bias, while translational selection has a relatively weak effect. Genome-wide gene ontology (GO) assignments showed that S. alba shared a similar GO slim classification with Arabidopsis thaliana. High percentages of sequences assigned to GO slim category 'mitochondrion' and four KEGG pathways, such as carbohydrates and secondary metabolites metabolism, may contribute to salt adaptation of S. alba. In addition, 1266 unique sequences matched to 273 known salt responsive genes (gene families) in other species were screened as candidates for salt tolerance of S. alba, and some of these genes showed fairly high coverage depth. At last, we identified four genes with signals of strong diversifying selection (K-a/K-s>1) by comparing the transcriptome sequences of S. alba with 249 known ESTs from its congener S. caseolaris. This study demonstrated a successful application of the Illumina platform to de novo assembly of the transcriptome of a non-model organism. Abundant SSR markers, salt responsive genes and four genes with signature of natural selection obtained from S. alba provide abundant sequence sources for future genetic diversity, salt adaptation and speciation studies. (C) 2011 Elsevier B.V. All rights reserved.