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

Abstract

BackgroundPhysalis 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.ResultsWe 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.ConclusionsWe 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.

Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling

“…The average G + C content of unigenes in P. alkekengi and P. peruviana was 39.8 and 40.5%, respectively. The G + C content in P. peruviana is consistent with what has been reported previously (Garzon-Martinez et al, 2012). …”

“…RNA sequencing (RNA-seq) on NGSs can be used for both model and non-model plants (Gongora-Castillo and Buell, 2013; Fukushima and Kusano, 2014; Weber, 2015). Successful transcriptome studies on non-model plants, e.g., crop plants such as the eggplant (Ramesh et al, 2016), pepper (Gordo et al, 2012) and tobacco (Lei et al, 2014) and medicinal plants, e.g., Withania somnifera (Gupta et al, 2013; Senthil et al, 2015) and P. peruviana (Garzon-Martinez et al, 2012) from the Solanaceae family have been published. Resources for transcriptome data from medicinal plants, e.g., the Medicinal Plant Genomics Resource (MPGR 1 ) and the Medicinal Plants Transcriptomics (Medplants 2 ; Gongora-Castillo et al, 2012a,b; Yeo et al, 2013) are available.…”

Citogenética de genotipos de uchuva, Physalis peruviana L., y Physalis floridana Rydb., con respuesta diferencial a Fusarium oxysporum

“…El país también ha avanzado en el conocimiento de la variabilidad genética de la uchuva, incluyendo la caracterización de germoplasma a escala morfo-agronómica para atributos vegetativos y de fruto (Trillos et al, 2008;Herrera et al, 2012) y molecular (Bonilla et al, 2008;Simbaqueba et al, 2011;Garzón et al, 2012). En citogenética, el conocimiento es todavía escaso; se destacan los estudios de Rodríguez y Bueno (2006) y Lagos (2006), quienes reportan variación en el número de cromosomas en algunos ecotipos de la especie, desde 2n = 24 hasta 2n = 48 con un número básico probable de X = 12.…”

VARIABILIDAD GENÉTICA DE PARENTALES Y POBLACIONES F1 INTER E INTRAESPECÍFICAS DE Physalis peruviana L. Y P. floridana Rydb.

“…Por ejemplo, se han generado marcadores moleculares procedentes de Genes Relacionados con Inmunidad vegetal (IRGs) y de microsatétiles (SRRs) a partir de la secuencia y anotación del trascriptoma foliar de la especie (ENCISO-RODRÍGUEZ et al, 2013;GARZÓN-MARTÍNEZ et al, 2012;SIMBAQUEBA et al, 2011). Adicionalmente, se han realizado caracterizaciones morfo-agronómicas y moleculares de colecciones de germoplasma (BONILLA et al, 2008;TRILLOS et al, 2008;HERRERA et al, 2012) y se ha avanzado en el conocimiento del comportamiento híbrido de la especie en cuanto a aptitud combinatoria a nivel morfo-agronómico y de características de fruto (LAGOS et al, 2007;LEIVA-BRONDO et al, 2001).…”