De novo assembly and characterization of the transcriptome and development of microsatellite markers in a Chinese endemic Euphorbia kansui

Abstract

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.

EST-SSR markers development and application in an important medicinal plant, Schisandra chinensis (Schisandraceae)

“…The most highly represented EST-SSR type was dinucleotide (64.54%); TC/GA was the most common motif (48.46%) followed by CT/AG (39.52%), with other motif types comprising merely 12.02% of all EST-SSR dincleotides. TC/GA was revealed as the most common dinucleotide repeat unit in S. chinensis, which is identical to pigeonpea (Cajanus cajan) and tree rhododendron (Rhododendron arboreum) [26,35] but distinct from barley (Hordeum vulgare), wheat (Triticum aestivum), corn (Zea mays), sorghum (Sorghum bicolor), rice (Oryza sativa) [20], eggplant (Solanum melongena) [19], peanut (Arachis hypogaea) [24], sugarcane (Saccharum officinarum) [36], grass (Miscanthus) [18], daylily (Hemerocallis citrina) [37], Chinese gansui (Euphorbia kansui) [38], thorn pear (Rosa roxburghii) [27], and Chinese yew (Taxus chinensis) [22]. There were 30 types of trinucleotide repeat motifs among S. chinensis ESTs.…”

Identifying Terpenoid Biosynthesis Genes in Euphorbia maculata via Full-Length cDNA Sequencing

“…The PacBio SMRT system is especially useful for plants lacking reference genome sequence data because it reads full-length transcripts [ 25 , 26 , 27 ]. Plant metabolites are often biosynthesized in specific tissues; thus, tissue-specific transcriptomes can be compared to identify key genes involved in various complex metabolite biosynthesis pathways in plants [ 28 , 29 ].…”