Nadiya F, Anjali N, Thomas Jinu, Gangaprasad A, Sabu K K
Biotechnology and Bioinformatics Division, Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram 695562, India.
Department of Botany, University of Kerala, Thiruvananthapuram 695581, India.
Genom Data. 2016 Dec 31;11:102-103. doi: 10.1016/j.gdata.2016.12.013. eCollection 2017 Mar.
(L.) Maton, known as 'queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base) and 24,889,197 (75 base) raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild) and SRX1141276 (cultivars). The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.
小豆蔻（L.），被誉为“香料女王”，是姜科多年生草本单子叶植物，原产于印度南部。小豆蔻是一种具有经济价值的香料作物，广泛用于烹饪和药用。在本研究中，我们使用Ion Proton RNA测序技术对野生型和五个小豆蔻栽培品种基因型进行了转录组测序和转录组组装。RNA测序分别为小豆蔻野生型和栽培品种基因型生成了总计22,811,983条（92碱基）和24,889,197条（75碱基）的原始读数，分别占约8.21GB和7.65GB的序列数据。原始数据已提交至NCBI的SRA数据库，登录号分别为SRX1141272（野生型）和SRX1141276（栽培品种）。对原始读数进行质量过滤，并使用MIRA组装器进行组装，野生型和栽培品种小豆蔻分别得到112,208条和264,161条重叠群，N50值分别为616和664。使用包括PlantCyc在内的多个数据库对组装的单基因进行功能注释以进行途径注释。这项工作代表了关于小豆蔻转录组测序的首次报道。为了生成一个全面的参考转录组，我们进一步组装了野生型和栽培品种基因型的原始读数，这可能会丰富植物转录组数据库并引发小豆蔻基因组学的深入研究。
