Ramesh Kumar Ramagoni, Hemalatha R, Vijayendra Chary Anchoju, Arshi Uz Zaman Syed, Dushyant Singh Baghel, Dinesh Kumar Bharadwaj
Department of Microbiology & Immunology, National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, Telangana State 500 007, India.
Nucleome Informatics Pvt. Ltd., Hyderabad, Telangana State 500 049, India.
Gene. 2016 Jan 15;576(1 Pt 1):64-71. doi: 10.1016/j.gene.2015.09.064. Epub 2015 Sep 28.
Eggplant is the third most important Solanaceae crop after tomato and potato, particularly in India and China. A transcriptome analysis of eggplant's fruit was performed to study genes involved in medicinal importance and allergies. Illumina HiSeq 2000 system generated 89,763,638 raw reads (~18 Gb) from eggplant. High quality reads (59,039,694) obtained after trimming process, were assembled into a total of 149,224 non redundant set of transcripts. Out of 80,482 annotated sequences of eggplant fruit (BLASTx results against nr-green plant database), 40,752 transcripts showed significant similarity with predicted proteins of Solanum tuberosum (51%) followed by Solanum lycopersicum (34%) and other sequenced plant genomes. With BLASTx top hit analysis against existing allergens, a total of 1986 homologous allergen sequences were found, which had >37% similarity with 48 different allergens existing in the database. From the 48 putative allergens, 526 B-cell linear epitopes were identified using BepiPred linear epitope prediction tool. Transcript sequences generated from this study can be used to map epitopes of monoclonal antibodies and polyclonal sera from patients. With the support of this whole transcriptome catalogue of eggplant fruit, complete list of genes can be predicted based on which secondary structures of proteins may be modeled.
茄子是继番茄和马铃薯之后第三重要的茄科作物，在印度和中国尤为如此。对茄子果实进行了转录组分析，以研究与药用价值和过敏相关的基因。Illumina HiSeq 2000系统从茄子中生成了89,763,638条原始读数（约18 Gb）。经过修剪过程后获得的高质量读数（59,039,694条）被组装成总共149,224个非冗余转录本集合。在茄子果实的80,482条注释序列（与nr-绿色植物数据库的BLASTx结果）中，40,752个转录本与马铃薯（51%）、其次是番茄（34%）以及其他已测序植物基因组的预测蛋白具有显著相似性。通过对现有过敏原进行BLASTx最佳匹配分析，共发现1986条同源过敏原序列，它们与数据库中存在的48种不同过敏原的相似度>37%。利用BepiPred线性表位预测工具从这48种假定过敏原中鉴定出526个B细胞线性表位。本研究生成的转录本序列可用于绘制患者单克隆抗体和多克隆血清的表位图谱。在茄子果实的这个完整转录组目录的支持下，可以预测基因的完整列表，据此可以对蛋白质的二级结构进行建模。
