Transcriptome sequencing of a highly salt tolerant mangrove species Sonneratia alba using Illumina platform
首发时间:2012-03-26
Abstract: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, 2,358 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, 1,266 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 (Ka/Ks >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.
keywords: mangroves1 de novo assemble codon usage bias adaptation high throughput sequencing
点击查看论文中文信息
基于Illumina平台的高耐盐红树植物杯萼海桑的转录组测序
摘要:红树植物近年来一直是受到威胁的海洋生物资源,但是基因组和转录组的数据却很少。本研究采用Illumina技术测定了一个高度耐盐的红树植物----杯萼海桑的转录组。本研究获得了大约1500万条75bp的段序列,拼接成30,628 条序列,平均长度为581 bp。从中找到了2,358 个SSR分子标记。基于20, 945 个编码基因序列的密码子偏好分析表明杯萼海桑不像一些微生物和果蝇等表现出明显的密码子偏好,其密码子使用的变异主要因为碱基组成的差异,而选择的作用相对较弱。本研究鉴定了273 耐盐相关的基因,其中一些基因的表达水平很高。通过与本属另一物种海桑的EST比较,我们发现了4个受到正选择 (Ka/Ks >1) 的基因。本研究表明Illumina测序技术完全可以应用在非模式生物的转录组测序上。所获得的大量的SSR分子标记,耐盐基因以及受到正选择的基因为进一步的遗传多样性、耐盐适应和物种形成研究奠定了基础。
基金:
论文图表:
引用
No.****
同行评议
勘误表
基于Illumina平台的高耐盐红树植物杯萼海桑的转录组测序
评论
全部评论0/1000