Enriching Genomic Resources and Marker Development from Transcript Sequences of Jatropha curcas for Microgravity Studies
Joint Authors
Tian, Wenlan
Paudel, Dev
Vendrame, Wagner
Wang, Jianping
Source
International Journal of Genomics
Issue
Vol. 2017, Issue 2017 (31 Dec. 2017), pp.1-14, 14 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2017-01-05
Country of Publication
Egypt
No. of Pages
14
Main Subjects
Abstract EN
Jatropha (Jatropha curcas L.) is an economically important species with a great potential for biodiesel production.
To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences.
In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated.
De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences.
The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors.
From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type.
Further 38,693 SNPs were detected and 7,584 remained after filtering.
This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies.
American Psychological Association (APA)
Tian, Wenlan& Paudel, Dev& Vendrame, Wagner& Wang, Jianping. 2017. Enriching Genomic Resources and Marker Development from Transcript Sequences of Jatropha curcas for Microgravity Studies. International Journal of Genomics،Vol. 2017, no. 2017, pp.1-14.
https://search.emarefa.net/detail/BIM-1167247
Modern Language Association (MLA)
Tian, Wenlan…[et al.]. Enriching Genomic Resources and Marker Development from Transcript Sequences of Jatropha curcas for Microgravity Studies. International Journal of Genomics No. 2017 (2017), pp.1-14.
https://search.emarefa.net/detail/BIM-1167247
American Medical Association (AMA)
Tian, Wenlan& Paudel, Dev& Vendrame, Wagner& Wang, Jianping. Enriching Genomic Resources and Marker Development from Transcript Sequences of Jatropha curcas for Microgravity Studies. International Journal of Genomics. 2017. Vol. 2017, no. 2017, pp.1-14.
https://search.emarefa.net/detail/BIM-1167247
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1167247