De novo assembly and characterization of the transcriptome and development of microsatellite markers in a Chinese endemic Euphorbia kansui
2020
Xueyan Zhao | Meng Wang | Jia Chai | Qian Li | Yafu Zhou | Yan Li | Xia Cai
Euphorbia kansui Liou is an endemic and traditional medicinal plant in China. Despite its value, the genomic and transcriptomic information of E. kansui is limited. In the present study, a total of 43,211,690 high-quality reads were generated using Illumina paired-end sequencing technology. After assembly, 58,362 unigenes were recovered with an N50 length of 1,683 bp. 36,396 (62.36%) of these unigenes had at least one blast hit against the multiple public databases. Based on KEGG pathway analyses, unigenes were discovered to encode known enzymes that catalyze the formation of the terpenoid backone and diterpenoid. In addition, the unigenes related to casbene synthase, which catalyzes the formation of the major active constituents (diterpenoids) in E. kansui, were identified. For functional marker development, 7,016 candidate simple sequence repeats (SSR, microsatellites) were identified from 6,150 unigenes, and 40 SSR loci were selected randomly and amplified in two populations of E. kansui. A total of 28 loci were amplified successfully and 23 loci exhibited polymorphisms. The number of alleles of each locus ranged from 2 to 8 alleles and the mean number of alleles per locus was 3.391. The observed heterozygosity and expected heterozygosity varied from 0.100 to 1.000 and 0.099 to 0.809, respectively. The microsatellite markers developed here will be useful for studies on population genetics of this endemic species. Moreover, the information of the transcriptome will provide a useful resource for the future research on metabolism, regulation of the terpenoid biosynthesis, genetic and proteome studies of E. kansui.
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