Abstract
Caragana korshinskii Kom. is widely distributed in various habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in the Asian and African deserts. To date, no previous genomic information or EST-SSR marker has been reported in Caragana Fabr. genus. In this study, more than two billion bases of high-quality sequence of C. korshinskii were generated by using illumina sequencing technology and demonstrated the de novo assembly and annotation of genes without prior genome information. These reads were assembled into 86,265 unigenes (mean length = 709 bp). The similarity search indicated that 33,955 and 21,978 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 26,232 a unigenes were separately assigned to Gene Ontology (GO) database. When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database, 5,598 unigenes were assigned to 5 main categories including 32 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (2,862, 43.7%), suggesting the active metabolic processes in the desert tree. In addition, a total of 19,150 EST-SSRs were identified from 15,484 unigenes, and the characterizations of EST-SSRs were further compared with other four species in Fabraceae. 126 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among the 9 germplasms in Caranaga Fabr. genus, PCR success rate were 93.7% and the phylogenic tree was constructed based on the genotypic data. This research generated a substantial fraction of transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding.
Highlights
Caragana is a genus comprises about 100 species in the family Fabraceae, and distributes in Asia and Eastern Europe
Partly because of the scarcity of suitable molecular markers, much remains to be learned about the genetic factors responsible for the ability of C. korshinskii to cope with various adverse environmental conditions
To elucidate the transcriptome of C. korshinskii, RNA was extracted from different tissues and sequenced with Illumina paired-end sequencing technology
Summary
Caragana is a genus comprises about 100 species in the family Fabraceae, and distributes in Asia and Eastern Europe. Most of the Caragana species are shrubs or small trees and with the character of high tolerance to several abiotic stresses including drought, salt, and cold [1]. Caragana korshinskii, which is widely distributes in sandy grassland in northwestern China and Mongolia[2], is a useful model organism for studying salt and drought resistance mechanisms in Caragana Fabr. Much of the work conducted on this species to date has focused on the physiological mechanisms responsible for its resistance to abiotic factors [4,5]. Partly because of the scarcity of suitable molecular markers, much remains to be learned about the genetic factors responsible for the ability of C. korshinskii to cope with various adverse environmental conditions
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