Dataset Information

De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea).

ABSTRACT: 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.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.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.

SUBMITTER: Muriira NG

PROVIDER: S-EPMC4580217 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea).

Muriira Nkatha G NG Xu Wei W Muchugi Alice A Xu Jianchu J Liu Aizhong A

BMC genomics 20150922

<h4>Background</h4>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.<h4>Results</h4>In this study, using the Illumina high throughput sequencing technique we obtained about 45 million paired end sequencing reads, De nov ...[more]

PMID: 26395839

Similar Datasets

Project description:Venturia inaequalis is the causal agent of apple scab, one of the most devastating diseases of apple. Due to several distinct features, it has emerged as a model fungal pathogen to study various aspects of hemibiotrophic plant pathogen interactions. The present study reports de novo assembling, annotation and characterization of the transcriptome of V. inaequalis. Venturia transcripts expressed during its growth on laboratory medium and that expressed during its biotrophic stage of infection on apple were sequenced using Illumina RNAseq technology. A total of 94,350,055 reads (50 bp read length) specific to Venturia were obtained after filtering. The reads were assembled into 62,061 contigs representing 24,571 unique genes. GO analysis suggested prevalence of genes associated with biological process categories like metabolism, transport and response to stimulus. Genes associated with molecular function like binding, catalytic activities and transferase activities were found in majority. EC and KEGG pathway analyses suggested prevalence of genes encoding kinases, proteases, glycoside hydrolases, cutinases, cytochrome P450 and transcription factors. The study has identified several putative pathogenicity determinants and candidate effectors in V. inaequalis. A large number of transcripts encoding membrane transporters were identified and comparative analysis revealed that the number of transporters encoded by Venturia is significantly more as compared to that encoded by several other important plant fungal pathogens. Phylogenomics analysis indicated that V. inaequalis is closely related to Pyrenophora tritici-repentis (the causal organism of tan spot of wheat). In conclusion, the findings from this study provide a better understanding of the biology of the apple scab pathogen and have identified candidate genes/functions required for its pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction.

Dataset Information

De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea).

Publications

De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets