The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction.
The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction.
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DOI：
10.1186/1471-2164-13-151
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发表时间：
2012-04-25
期刊：
影响因子：
4.4
通讯作者：
Mariño-Ramírez L
中科院分区：
文献类型：
--
作者：
Garzón-Martínez GA;Zhu ZI;Landsman D;Barrero LS;Mariño-Ramírez L
秘鲁酸浆（Physalis peruviana）通常被称为海角醋栗（Cape gooseberry），是茄科（Solanaceae）家族的成员，由于其营养和药用价值而越来越受欢迎。广泛的基因组工具可用于其他茄科，包括番茄和马铃薯。然而，有限的基因组资源，目前可用于角醋栗。我们报告了使用454 GS FLX Titanium技术总共产生了652，614个秘鲁黑胫病菌表达序列标签（EST）。EST，平均长度为371 bp，从使用哥伦比亚商业品种制备的归一化叶cDNA文库中获得。进行从头组装以产生24，014个isotig和110，921个单例的集合，平均长度分别为1，638 bp和354 bp。使用NCBI的BLAST工具和Blast 2GO进行功能注释，其鉴定了21，191个组装序列的推定功能，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）（番茄）和马铃薯（Solanum tuberosum）（马铃薯）的基因组，获得秘鲁疫霉中的基因模型预测。我们预测9,436 P. peruviana序列与多外显子模型和保守的内含子位置相对于马铃薯和番茄基因组。此外，为了研究物种多样性，我们从组装的EST中开发了5，971个SSR标记。我们提出了第一个全面的分析，秘鲁酸浆叶转录组，这将提供宝贵的资源，在该物种的遗传工具的发展。组装的转录本与基因模型可以作为潜在的候选标记发现与各种应用，包括：功能多样性，保护和改善，以提高生产力和水果品质。据估计，P. peruviana在其他五个茄科成员，S.番茄S. tuberosum、Capsicum spp、S. melongena和矮牵牛属（Petunia spp.）
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.
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影响因子：
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作者：
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通讯作者：
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影响因子：
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4.4
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Tanksley, SD
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