Enriching Genomic Resources and Marker Development from Transcript Sequences ofJatropha curcasfor Microgravity Studies.
Jatropha (Jatropha curcasL.) 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.
Environmental Horticulture Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL 32610, USA.
Wenlan
W
Tian
Agronomy Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL 32610, USA.
Dev
D
Paudel
Environmental Horticulture Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL 32610, USA; Tropical Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 18905 SW 280th Street, Homestead, FL 33031-3314, USA.
Wagner
0000-0001-6391-7623
W
Vendrame
Agronomy Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL 32610, USA; Agronomy Department, Genetics Institute, Plant Molecular and Cellular Biology Program, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL 32610, USA; Center for Genomics and Biotechnology, Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
Jianping
0000-0002-0259-1508
J
Wang