De Novo Assembly and Annotation of the Juvenile Tuber Transcriptome of a Gastrodia elata Hybrid by RNA Sequencing: Detection of SSR Markers

Abstract

Gastrodia elata is a traditional Chinese herbal medicine with good therapeutic effect on various nervous and cerebrovascular diseases. In the present study, we generated 20,611,556 raw reads from the young tuber transcriptome of a G. elata hybrid (Gastrodia elata BI.f.elata × Gastrodia elata BI.f.pilifera) by using Illumina HiSeq™ 4000 sequencing platform. De novo assembly and bioinformatics analysis revealed 20,237,474 clean reads, including 2,529,684,250 bp that assembled into 34,323 unigenes with an average length of 695.19 bp. Among them, 24,698 (71.96%) unigenes were annotated by at least one of the Nr, Swiss-Prot, COG and KEGG databases. A total of 4236 (12.34%) unigenes were identified as candidate transcription factors, and 2007 (5.85%) unigenes were found to contain at least one single sequence repeat (SSR). Of these SSRs, AG/CT repeat motif was the most frequent, with a total of 498 (21.67%). This study will enhance our understanding about the molecular mechanism of physiological metabolism, growth and development of G. elata, particularly abundant SSR markers will offer plenty of alternative tools for further studies about molecular genetics, molecular breeding and association analysis.

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Acknowledgements

This work was funded by the key project of the Science Department of Guizhou Province [LH(2015)7754], Science and technology plan project of Guizhou Province [2019]4318 and “Talent team project of Guizhou Education Department [2015]70”.

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Wang, Y., Shahid, M.Q., Ghouri, F. et al. De Novo Assembly and Annotation of the Juvenile Tuber Transcriptome of a Gastrodia elata Hybrid by RNA Sequencing: Detection of SSR Markers. Biochem Genet 58, 914–934 (2020). https://doi.org/10.1007/s10528-020-09983-w

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Keywords

  • Gastrodia elata
  • Sequencing
  • SSR
  • Transcriptome
  • Unigenes