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.

天麻是一种中草药，对各种神经和脑血管疾病具有良好的治疗作用。在本研究中，我们产生20611556原料从年轻块茎转录读取天麻杂交体（天麻BI.f.elata  × 天麻BI.f.pilifera）使用Illumina HiSeq™4000测序平台。从头开始的汇编和生物信息学分析显示，共有20,237,474例纯读，包括2,529,684,250 bp，它们被组装成34,323个单基因，平均长度为695.19 bp。其中，至少有Nr，Swiss-Prot，COG和KEGG数据库之一注释了24,698（71.96％）个单基因。共有4236个（12.34％）单基因被鉴定为候选转录因子，并且发现2007年（5.85％）单基因包含至少一个单序列重复（SSR）。在这些SSR中，AG / CT重复基序最常见，总计498（21.67％）。这项研究将增进我们对G. elata生理代谢，生长发育的分子机制的了解。，特别是丰富的SSR标记将为分子遗传学，分子育种和关联分析的进一步研究提供大量替代工具。