Transcriptome Sequenced – Veratrilla baillonii Franch

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.

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.

Wang L, Wang Z, Chen J, Liu C, Zhu W, Wang L, Meng L. (2015) De Novo Transcriptome Assembly and Development of Novel Microsatellite Markers for the Traditional Chinese Medicinal Herb, Veratrilla baillonii Franch (Gentianaceae). Evol Bioinform Online 11(Suppl 1):39-45. [article]

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