title: De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea).
abstract: BACKGROUND
  The Sodom apple (Calotropis gigantea), a member of the Asclepiadaceae family, is a large evergreen shrub native to continental Asia and northern Africa. As an important medicinal shrub and a fiber resource plant, there is an urgent need for developing molecular markers to facilitate breeding and genetic improvement of varieties.
  
  
  RESULTS
  In this study, using the Illumina high throughput sequencing technique we obtained about 45 million paired end sequencing reads, De novo assembled and generated a total of 133,634 transcripts with a mean of 1837.47 bp in length. Based on protein homology searches against available databases, a total of 21,851 unigenes were functionally annotated. In particular, many transcripts that encode for putative proteins involved in fiber and secondary metabolite biosynthesis were identified and analyzed. Key fiber genes identified were validated experimentally through Real-Time PCR technique. Various transcription factors involved in regulating plant response to abiotic stress were also identified. In addition, based on the unigene sequences assembled, 11,623 microsatellites loci were detected, which provide very useful resources for developing microsatellite molecular markers.
  
  
  CONCLUSIONS
  This study is the first report on transcriptome information in the Calotropis species and provides rich gene transcript resources for conducting further studies on understanding the molecular basis of fiber and secondary metabolite biosynthesis, serving the genetic improvement and resource utilization in Calotropis plants.
authors.affiliation: Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. muriira@mail.kib.ac.cn.|University of Chinese Academy of Sciences, Beijing, 100049, China. muriira@mail.kib.ac.cn.|World Agroforestry Centre, East and Central Asia Office, 132 Lanhei Road, Kunming, 650201, China. muriira@mail.kib.ac.cn.|World Agroforestry Centre (ICRAF), P.O. Box 30677-00100, Nairobi, Kenya. muriira@mail.kib.ac.cn.
authors.forename: Nkatha G
authors.initials: NG
authors.lastname: Muriira
authors.affiliation: Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. xuwei@mail.kib.ac.cn.|University of Chinese Academy of Sciences, Beijing, 100049, China. xuwei@mail.kib.ac.cn.
authors.forename: Wei
authors.initials: W
authors.lastname: Xu
authors.affiliation: World Agroforestry Centre (ICRAF), P.O. Box 30677-00100, Nairobi, Kenya. a.muchugi@cgiar.org.
authors.forename: Alice
authors.initials: A
authors.lastname: Muchugi
authors.affiliation: Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. j.c.xu@cgiar.org.|World Agroforestry Centre, East and Central Asia Office, 132 Lanhei Road, Kunming, 650201, China. j.c.xu@cgiar.org.
authors.forename: Jianchu
authors.initials: J
authors.lastname: Xu
authors.affiliation: Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. liuaizhong@mail.kib.ac.cn.
authors.forename: Aizhong
authors.initials: A
authors.lastname: Liu
mesh_terms: D031107:Calotropis / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA; D015398:Signal Transduction; D013312:Stress, Physiological / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
chemical_list: D014157:Transcription Factors