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Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)(1)

PREMISE OF THE STUDY: Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesn...

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Autores principales: Serrano-Serrano, Martha L., Marcionetti, Anna, Perret, Mathieu, Salamin, Nicolas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Botanical Society of America 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400431/
https://www.ncbi.nlm.nih.gov/pubmed/28439475
http://dx.doi.org/10.3732/apps.1600135
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author Serrano-Serrano, Martha L.
Marcionetti, Anna
Perret, Mathieu
Salamin, Nicolas
author_facet Serrano-Serrano, Martha L.
Marcionetti, Anna
Perret, Mathieu
Salamin, Nicolas
author_sort Serrano-Serrano, Martha L.
collection PubMed
description PREMISE OF THE STUDY: Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. METHODS AND RESULTS: Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S. magnifica, two species endemic to the Brazilian Atlantic Forest. A total of 300 million reads were used to assemble the transcriptomes, with an average of 92,038 transcripts and 43,506 genes per species. The transcriptomes showed good quality metrics, with the presence of all eukaryotic core genes, and an equal representation of clusters of orthologous groups (COG) classifications between species. The orthologous search produced 8602 groups, with 15–20% of them annotated using BLAST tools. DISCUSSION: This study provides the first step toward a comprehensive multispecies transcriptome characterization of the Gesneriaceae family. These resources are the basis for comparative analyses in this species-rich Neotropical plant group; they will also allow the investigation of the evolutionary importance of multiple metabolic pathways and phenotypic diversity, as well as developmental programs in these nonmodel species.
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spelling pubmed-54004312017-04-24 Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)(1) Serrano-Serrano, Martha L. Marcionetti, Anna Perret, Mathieu Salamin, Nicolas Appl Plant Sci Genomic Resources Note PREMISE OF THE STUDY: Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. METHODS AND RESULTS: Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S. magnifica, two species endemic to the Brazilian Atlantic Forest. A total of 300 million reads were used to assemble the transcriptomes, with an average of 92,038 transcripts and 43,506 genes per species. The transcriptomes showed good quality metrics, with the presence of all eukaryotic core genes, and an equal representation of clusters of orthologous groups (COG) classifications between species. The orthologous search produced 8602 groups, with 15–20% of them annotated using BLAST tools. DISCUSSION: This study provides the first step toward a comprehensive multispecies transcriptome characterization of the Gesneriaceae family. These resources are the basis for comparative analyses in this species-rich Neotropical plant group; they will also allow the investigation of the evolutionary importance of multiple metabolic pathways and phenotypic diversity, as well as developmental programs in these nonmodel species. Botanical Society of America 2017-04-12 /pmc/articles/PMC5400431/ /pubmed/28439475 http://dx.doi.org/10.3732/apps.1600135 Text en © 2017 Serrano-Serrano et al. Published by the Botanical Society of America https://creativecommons.org/licenses/by-nc-sa/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (CC-BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/) ), which permits unrestricted noncommercial use and redistribution provided that the original author and source are credited and the new work is distributed under the same license as the original.
spellingShingle Genomic Resources Note
Serrano-Serrano, Martha L.
Marcionetti, Anna
Perret, Mathieu
Salamin, Nicolas
Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)(1)
title Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)(1)
title_full Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)(1)
title_fullStr Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)(1)
title_full_unstemmed Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)(1)
title_short Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae)(1)
title_sort transcriptomic resources for an endemic neotropical plant lineage (gesneriaceae)(1)
topic Genomic Resources Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400431/
https://www.ncbi.nlm.nih.gov/pubmed/28439475
http://dx.doi.org/10.3732/apps.1600135
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