The <it>Physalis peruviana</it> leaf transcriptome: assembly, annotation and gene model prediction
<p>Abstract</p> <p>Background</p> <p><it>Physalis peruviana</it> 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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-04-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/151 |
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| author | Garzón-Martínez Gina A Zhu Z Landsman David Barrero Luz S Mariño-Ramírez Leonardo |
| author_facet | Garzón-Martínez Gina A Zhu Z Landsman David Barrero Luz S Mariño-Ramírez Leonardo |
| author_sort | Garzón-Martínez Gina A |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Physalis peruviana</it> 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.</p> <p>Results</p> <p>We report the generation of a total of 652,614 <it>P. peruviana</it> 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. <it>De novo</it> 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 <it>P. peruviana</it> were obtained by using the genomes of <it>Solanum lycopersicum</it> (tomato) and <it>Solanum tuberosum</it> (potato). We predict 9,436 <it>P. peruviana</it> 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.</p> <p>Conclusions</p> <p>We present the first comprehensive analysis of the <it>Physalis peruviana</it> 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. <it>P. peruviana</it> was estimated to be phylogenetically branched out before the divergence of five other Solanaceae family members, <it>S. lycopersicum</it>, <it>S. tuberosum</it>, <it>Capsicum spp</it>, <it>S. melongena</it> and <it>Petunia spp</it>.</p> |
| first_indexed | 2024-12-21T20:59:25Z |
| format | Article |
| id | doaj.art-9c121b6fe95c46dfaed0f8d79f11de96 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T20:59:25Z |
| publishDate | 2012-04-01 |
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| spelling | doaj.art-9c121b6fe95c46dfaed0f8d79f11de962022-12-21T18:50:28ZengBMCBMC Genomics1471-21642012-04-0113115110.1186/1471-2164-13-151The <it>Physalis peruviana</it> leaf transcriptome: assembly, annotation and gene model predictionGarzón-Martínez Gina AZhu ZLandsman DavidBarrero Luz SMariño-Ramírez Leonardo<p>Abstract</p> <p>Background</p> <p><it>Physalis peruviana</it> 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.</p> <p>Results</p> <p>We report the generation of a total of 652,614 <it>P. peruviana</it> 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. <it>De novo</it> 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 <it>P. peruviana</it> were obtained by using the genomes of <it>Solanum lycopersicum</it> (tomato) and <it>Solanum tuberosum</it> (potato). We predict 9,436 <it>P. peruviana</it> 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.</p> <p>Conclusions</p> <p>We present the first comprehensive analysis of the <it>Physalis peruviana</it> 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. <it>P. peruviana</it> was estimated to be phylogenetically branched out before the divergence of five other Solanaceae family members, <it>S. lycopersicum</it>, <it>S. tuberosum</it>, <it>Capsicum spp</it>, <it>S. melongena</it> and <it>Petunia spp</it>.</p>http://www.biomedcentral.com/1471-2164/13/151<it>P. peruviana</it>SolanaceaeESTsFunctional annotationGene modelPhylogenetics |
| spellingShingle | Garzón-Martínez Gina A Zhu Z Landsman David Barrero Luz S Mariño-Ramírez Leonardo The <it>Physalis peruviana</it> leaf transcriptome: assembly, annotation and gene model prediction BMC Genomics <it>P. peruviana</it> Solanaceae ESTs Functional annotation Gene model Phylogenetics |
| title | The <it>Physalis peruviana</it> leaf transcriptome: assembly, annotation and gene model prediction |
| title_full | The <it>Physalis peruviana</it> leaf transcriptome: assembly, annotation and gene model prediction |
| title_fullStr | The <it>Physalis peruviana</it> leaf transcriptome: assembly, annotation and gene model prediction |
| title_full_unstemmed | The <it>Physalis peruviana</it> leaf transcriptome: assembly, annotation and gene model prediction |
| title_short | The <it>Physalis peruviana</it> leaf transcriptome: assembly, annotation and gene model prediction |
| title_sort | it physalis peruviana it leaf transcriptome assembly annotation and gene model prediction |
| topic | <it>P. peruviana</it> Solanaceae ESTs Functional annotation Gene model Phylogenetics |
| url | http://www.biomedcentral.com/1471-2164/13/151 |
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