De Novo Assembly of Allotetraploid <em>Arabidopsis suecica</em> Transcriptome using Short Reads for Gene Discovery and Marker Identification

China Biotechnology

2011, Vol. 31

Issue (7): 45-53 DOI:

De Novo Assembly of Allotetraploid Arabidopsis suecica Transcriptome using Short Reads for Gene Discovery and Marker Identification

LIU Xin-xing, CHEN Chao

Resources and Bioengineering School at Central South University, Changsha 410083, China

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Abstract

To facilitate the research on Arabidopsis suecica (A.suecica), a method was presented for de novo assembly of A.suecica transcriptome using short reads produced by Illumina sequencing platform. 23 million sequencing reads were assembled into 125 953 unique sequences with the N50 length of 550 bp and mean size of 331 bp. At the protein level, a total of 96 057 (76.3%) A.suecica transcripts showed significant similarity with transcripts proteins from the other plants in the Nr database. Functional categorization revealed the conservation of genes involved in various biological processes in A.suecica. In addition, simple sequence repeats(SSRs) motifs in the A.suecica transcriptome was identified. The data provides a comprehensive sequence resource available for A.suecica study and demonstrates that the short pair-end reads sequencing allows de novo transcriptome assembly in a allotetraploid species lacking genome information. It is anticipated that the next generation sequencing(NGS) technologies significantly accelerate the research of the transcriptome in both model and non-model organisms. In addition, the strategy for de novo assembly of transcriptome data presented here will be helpful in other similar transcriptome studies.

Key words： Arabidopsis suecica Transcriptome assembly SOAPdenovo NGS(next generation sequencing)

Received: 14 March 2011 Published: 25 July 2011

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LIU Xin-xing, CHEN Chao. De Novo Assembly of Allotetraploid Arabidopsis suecica Transcriptome using Short Reads for Gene Discovery and Marker Identification. China Biotechnology, 2011, 31(7): 45-53.

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https://manu60.magtech.com.cn/biotech/ OR https://manu60.magtech.com.cn/biotech/Y2011/V31/I7/45

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