RNA-Seq Blog Transcriptome Research & Industry News
Veratrilla baillonii Franch is an important Chinese medicinal herb for treating liver-related diseases, which has been over-collected in the recent decades. However, the effective conservation and related population genetic study has been hindered because of the lack of genome sequences and genetic markers in the natural population.
Now, researchers at Yunnan Normal University have conducted RNA-seq on V. baillonii and performed de novo assembly of these data to characterize the V. baillonii transcriptome, resulting in 133,019 contigs with size >200 bp. These contigs were annotated using the NCBI nonredundant database and Gene Ontology (GO) terms. From these contigs, they developed novel microsatellite simple sequence repeat (SSR) markers, identifying a total of 40,885 SSRs. SSRs with repeat motifs of 1-4 bp (mono-, di-, tri-, and tetranucleotides) accounted for 99.8% of all SSRs, with mononucleotide repeats most common, followed by dinucleotide (16.2%) and trinucleotide repeats (14.7%).
Summary of assembly and annotation results for V. baillonii.
| V. BAILLONII | |
|---|---|
| Total number of high quality reads | 28483317 |
| Total number of contigs | 133019 |
| Total size of contigs (bp) | 168009542 |
| Mean length of contigs | 1263 |
| N50 value of contigs | 2104 |
| Length range of contigs | 201–13830 |
| GC content | 40.6% |
| Total number of identified SSRs | 40885 |
| SSRs containing sequences with BLASTx hit | 28912 (70.7%) |
| SSRs containing sequences with annotation | 11148 (27.3%) |
The de novo transcriptome sequences and new SSR markers discovered by this study provide an initial step for understanding the population genetics of V. baillonii, and a valuable resource for effective conservation management.
