Abstract
BackgroundThe 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.ResultsIn 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.ConclusionThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1908-3) contains supplementary material, which is available to authorized users.
Highlights
The Sodom apple (Calotropis gigantea), a member of the Asclepiadaceae family, is a large evergreen shrub native to continental Asia and northern Africa
The protein homology searches revealed that Sodom apple unigenes had highest similarity to Solanum lycopersicum (28.20 %) genes, implying that Sodom apple may phylogenically be closer to Solanum plants than to other eudict plants for which genome annotation has been done, such as Vitis vinifera, Populus trichocarpa and Glycine max. These results indicate that our current high throughput sequencing data and transcriptome assembly are of high quality and these data will provide a solid foundation for further gene discovery, marker development, marker-assisted selection breeding, and genetic improvement studies in Sodom apple
We found many transcripts that encode for putative proteins that are involved in fiber and secondary metabolite biosynthesis, and the fiber candidate genes were validated using the Real-Time PCR method
Summary
The Sodom apple (Calotropis gigantea), a member of the Asclepiadaceae family, is a large evergreen shrub native to continental Asia and northern Africa. Since its seed coat produces fine, silky, durable, and high-quality fiber which is used broadly in industrial applications, Sodom apple is known as Crystal Cotton [1, 2]. The genus Calotropis has two species: Calotropis gigantea (native to continental Asia and South-East Asia) and C. procera (native to northern Africa and southern Asia) [3, 4]. Due to the high-quality fiber produced with the seed coat and its characteristics of being fast-growing, drought hardy, and having wide adaptation to soil conditions, developing the cultivation of Sodom apple to provide fine and highquality fiber materials has created great interest in many countries [5]. Sodom apple has been used as a source of medicine because its milk-like latex contains various active-compounds such osmotin and lupeol, and Muriira et al BMC Genomics (2015) 16:723
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