De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis

BMC Research Notes

Andrew J Wood²  Honglan Yang¹  Xiaoshuang Li²  Daoyuan Zhang¹  Bei Gao³ 

[1] Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China;Department of Plant Biology, Southern Illinois University-Carbondale, Carbondale 62901-6509, IL, USA;University of Chinese Academy of Sciences, Beijing 100049, China

关键词: Transcriptome;    Syntrichia;    Stress;    Physcomitrella;    Desiccation;    Biological soil crust;   

Others  :  1131750
DOI  :  10.1186/1756-0500-7-490

 received in 2014-07-15, accepted in 2014-07-24,  发布年份 2014

【 摘 要 】

Background

Syntrichia caninervis is a desiccation-tolerant moss and the dominant bryophyte of the Biological Soil Crusts (BSCs) found in the Mojave and Gurbantunggut deserts. Next generation high throughput sequencing technologies offer an efficient and economic choice for characterizing non-model organism transcriptomes with little or no prior molecular information available.

Results

In this study, we employed next generation, high-throughput, Illumina RNA-Seq to analyze the poly-(A) + mRNA from hydrated, dehydrating and desiccated S. caninervis gametophores. Approximately 58.0 million paired-end short reads were obtained and 92,240 unigenes were assembled with an average size of 493 bp, N50 value of 662 bp and a total size of 45.48 Mbp. Sequence similarity searches against five public databases (NR, Swiss-Prot, COSMOSS, KEGG and COG) found 54,125 unigenes (58.7%) with significant similarity to an existing sequence (E-value ≤ 1e-5) and could be annotated. Gene Ontology (GO) annotation assigned 24,183 unigenes to the three GO terms: Biological Process, Cellular Component or Molecular Function. GO comparison between P. patens and S. caninervis demonstrated similar sequence enrichment across all three GO categories. 29,370 deduced polypeptide sequences were assigned Pfam domain information and categorized into 4,212 Pfam domains/families. Using the PlantTFDB, 778 unigenes were predicted to be involved in the regulation of transcription and were classified into 49 transcription factor families. Annotated unigenes were mapped to the KEGG pathways and further annotated using MapMan. Comparative genomics revealed that 44% of protein families are shared in common by S. caninervis, P. patens and Arabidopsis thaliana and that 80% are shared by both moss species.

Conclusions

This study is one of the first comprehensive transcriptome analyses of the moss S. caninervis. Our data extends our knowledge of bryophyte transcriptomes, provides an insight to plants adapted to the arid regions of central Asia, and continues the development of S. caninervis as a model for understanding the molecular aspects of desiccation-tolerance.

【 授权许可】

   
2014 Gao et al.; licensee BioMed Central Ltd.

【 图 表 】

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