Plant Molecular Genetics Laboratory, Center of Biotechnology and Bioindustry (CBB), Colombian Corporation for Agricultural Research (CORPOICA), Bogota, Colombia.
BMC Genomics. 2012 Apr 25;13:151. doi: 10.1186/1471-2164-13-151.
Physalis peruviana commonly known as Cape gooseberry is a member of the Solanaceae family that has an increasing popularity due to its nutritional and medicinal values. A broad range of genomic tools is available for other Solanaceae, including tomato and potato. However, limited genomic resources are currently available for Cape gooseberry.
We report the generation of a total of 652,614 P. peruviana Expressed Sequence Tags (ESTs), using 454 GS FLX Titanium technology. ESTs, with an average length of 371 bp, were obtained from a normalized leaf cDNA library prepared using a Colombian commercial variety. De novo assembling was performed to generate a collection of 24,014 isotigs and 110,921 singletons, with an average length of 1,638 bp and 354 bp, respectively. Functional annotation was performed using NCBI's BLAST tools and Blast2GO, which identified putative functions for 21,191 assembled sequences, including gene families involved in all the major biological processes and molecular functions as well as defense response and amino acid metabolism pathways. Gene model predictions in P. peruviana were obtained by using the genomes of Solanum lycopersicum (tomato) and Solanum tuberosum (potato). We predict 9,436 P. peruviana sequences with multiple-exon models and conserved intron positions with respect to the potato and tomato genomes. Additionally, to study species diversity we developed 5,971 SSR markers from assembled ESTs.
We present the first comprehensive analysis of the Physalis peruviana leaf transcriptome, which will provide valuable resources for development of genetic tools in the species. Assembled transcripts with gene models could serve as potential candidates for marker discovery with a variety of applications including: functional diversity, conservation and improvement to increase productivity and fruit quality. P. peruviana was estimated to be phylogenetically branched out before the divergence of five other Solanaceae family members, S. lycopersicum, S. tuberosum, Capsicum spp, S. melongena and Petunia spp.
秘鲁番茄，俗称刺果番荔枝，是茄科植物的一员，由于其营养价值和药用价值，越来越受欢迎。茄科的其他物种，包括番茄和土豆，拥有广泛的基因组工具。然而，目前可用的秘鲁番茄基因组资源有限。
我们使用 454 GS FLX Titanium 技术，总共生成了 652614 个秘鲁番茄表达序列标签（EST）。这些 EST 来自用哥伦比亚商业品种制备的标准化叶片 cDNA 文库，平均长度为 371bp。进行从头组装生成了 24014 个 isogroups 和 110921 个单体，平均长度分别为 1638bp 和 354bp。使用 NCBI 的 BLAST 工具和 Blast2GO 进行功能注释，鉴定出 21191 个组装序列的可能功能，包括参与所有主要生物过程和分子功能以及防御反应和氨基酸代谢途径的基因家族。通过使用番茄（Solanum lycopersicum）和土豆（Solanum tuberosum）的基因组，在秘鲁番茄中获得基因模型预测。我们预测了 9436 个具有多外显子模型和保守内含子位置的秘鲁番茄序列，相对于土豆和番茄基因组。此外，为了研究物种多样性，我们从组装的 EST 中开发了 5971 个 SSR 标记。
我们首次对秘鲁番茄叶片转录组进行了全面分析，这将为该物种遗传工具的开发提供有价值的资源。带有基因模型的组装转录本可以作为标记发现的潜在候选者，具有多种应用，包括：功能多样性、保护和改良以提高生产力和果实质量。秘鲁番茄在其他五个茄科成员（番茄、土豆、辣椒、茄子和矮牵牛）分化之前就已经分支出来。
