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Open Access Highly Accessed Research article

The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction

Gina A Garzón-Martínez1, Z Iris Zhu2, David Landsman2, Luz S Barrero13 and Leonardo Mariño-Ramírez123*

Author Affiliations

1 Plant Molecular Genetics Laboratory, Center of Biotechnology and Bioindustry (CBB), Colombian Corporation for Agricultural Research (CORPOICA), Bogota, Colombia

2 Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, United States of America, Bethesda, MD, USA

3 PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia

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BMC Genomics 2012, 13:151  doi:10.1186/1471-2164-13-151

Published: 25 April 2012

Abstract

Background

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.

Results

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.

Conclusions

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.

Keywords:
P. peruviana; Solanaceae; ESTs; Functional annotation; Gene model; Phylogenetics