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De Novo Assembly and Annotation of the Juvenile Tuber Transcriptome of aGastrodia elataHybrid by RNA Sequencing: Detection of SSR Markers

Authors Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia; Baloch, Faheem Shehzad

Journal BIOCHEMICAL GENETICS , DEC 2020,6:58

DOI 10.1007/s10528-020-09983-w PubMed 32632662

Abstract Gastrodia elatais 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 aG. elatahybrid (Gastrodia elata BI.f.elata x Gastrodia elata BI.f.pilifera) by using Illumina HiSeq (TM) 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 ofG. elata, particularly abundant SSR markers will offer plenty of alternative tools for further studies about molecular genetics, molecular breeding and association analysis.

Species covered 天麻(原变型) Gastrodia elata