De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae)

Particle and Fibre Toxicology

Yanfei Che¹  Wenbo Fu¹  Zhentian Yan¹  Liang Qiao¹  Qiyi He¹  Yao Tang¹  Fengling Si¹  Wanshun Li²  Zhengbo He¹  Yu-Juan Zhang¹  Bin Chen¹ 

[1] Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, P R, China;BGI-Shenzhen, Shenzhen, P R, China

关键词: Vector control;    Malaria;    Simple sequence repeat;    Codon usage bias;    RNA-Seq;    Transcriptome;    Anopheles sinensis;   

Others  :  1183565
DOI  :  10.1186/1756-3305-7-314

 received in 2014-02-15, accepted in 2014-06-23,  发布年份 2014

【 摘 要 】

Background

Anopheles sinensis is the major malaria vector in China and Southeast Asia. Vector control is one of the most effective measures to prevent malaria transmission. However, there is little transcriptome information available for the malaria vector. To better understand the biological basis of malaria transmission and to develop novel and effective means of vector control, there is a need to build a transcriptome dataset for functional genomics analysis by large-scale RNA sequencing (RNA-seq).

Methods

To provide a more comprehensive and complete transcriptome of An. sinensis, eggs, larvae, pupae, male adults and female adults RNA were pooled together for cDNA preparation, sequenced using the Illumina paired-end sequencing technology and assembled into unigenes. These unigenes were then analyzed in their genome mapping, functional annotation, homology, codon usage bias and simple sequence repeats (SSRs).

Results

Approximately 51.6 million clean reads were obtained, trimmed, and assembled into 38,504 unigenes with an average length of 571 bp, an N50 of 711 bp, and an average GC content 51.26%. Among them, 98.4% of unigenes could be mapped onto the reference genome, and 69% of unigenes could be annotated with known biological functions. Homology analysis identified certain numbers of An. sinensis unigenes that showed homology or being putative 1:1 orthologues with genomes of other Dipteran species. Codon usage bias was analyzed and 1,904 SSRs were detected, which will provide effective molecular markers for the population genetics of this species.

Conclusions

Our data and analysis provide the most comprehensive transcriptomic resource and characteristics currently available for An. sinensis, and will facilitate genetic, genomic studies, and further vector control of An. sinensis.

【 授权许可】

   
2014 Chen et al.; licensee BioMed Central Ltd.

【 图 表 】

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