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Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest

PREMISE: Large‐scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a...

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Autores principales: Marx, Hannah E., Jorgensen, Stacy A., Wisely, Eldridge, Li, Zheng, Dlugosch, Katrina M., Barker, Michael S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7910807/
https://www.ncbi.nlm.nih.gov/pubmed/33680580
http://dx.doi.org/10.1002/aps3.11409
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author Marx, Hannah E.
Jorgensen, Stacy A.
Wisely, Eldridge
Li, Zheng
Dlugosch, Katrina M.
Barker, Michael S.
author_facet Marx, Hannah E.
Jorgensen, Stacy A.
Wisely, Eldridge
Li, Zheng
Dlugosch, Katrina M.
Barker, Michael S.
author_sort Marx, Hannah E.
collection PubMed
description PREMISE: Large‐scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA‐seq data from diverse plant communities. METHODS: We generated >650 Gbp of RNA‐seq for 24 vascular plant species representing 12 genera and nine families at the Harvard Forest NEON site. Each species was sampled twice in 2016 (July and August). We assessed transcriptome quality and content with TransRate, BUSCO, and Gene Ontology annotations. RESULTS: Only modest differences in assembly quality were observed across multiple k‐mers. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated transcripts between diploid and polyploid transcriptomes. DISCUSSION: We provide new RNA‐seq data sets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high‐quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers opportunities for large‐scale studies at the intersection of ecology and genomics.
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spelling pubmed-79108072021-03-05 Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest Marx, Hannah E. Jorgensen, Stacy A. Wisely, Eldridge Li, Zheng Dlugosch, Katrina M. Barker, Michael S. Appl Plant Sci Genomic Resources Article PREMISE: Large‐scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA‐seq data from diverse plant communities. METHODS: We generated >650 Gbp of RNA‐seq for 24 vascular plant species representing 12 genera and nine families at the Harvard Forest NEON site. Each species was sampled twice in 2016 (July and August). We assessed transcriptome quality and content with TransRate, BUSCO, and Gene Ontology annotations. RESULTS: Only modest differences in assembly quality were observed across multiple k‐mers. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated transcripts between diploid and polyploid transcriptomes. DISCUSSION: We provide new RNA‐seq data sets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high‐quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers opportunities for large‐scale studies at the intersection of ecology and genomics. John Wiley and Sons Inc. 2021-02-14 /pmc/articles/PMC7910807/ /pubmed/33680580 http://dx.doi.org/10.1002/aps3.11409 Text en © 2021 Marx et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genomic Resources Article
Marx, Hannah E.
Jorgensen, Stacy A.
Wisely, Eldridge
Li, Zheng
Dlugosch, Katrina M.
Barker, Michael S.
Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest
title Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest
title_full Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest
title_fullStr Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest
title_full_unstemmed Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest
title_short Pilot RNA‐seq data from 24 species of vascular plants at Harvard Forest
title_sort pilot rna‐seq data from 24 species of vascular plants at harvard forest
topic Genomic Resources Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7910807/
https://www.ncbi.nlm.nih.gov/pubmed/33680580
http://dx.doi.org/10.1002/aps3.11409
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