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

Autor: Marx HE; Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona 85721 USA.; Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan 48109-1048 USA., Jorgensen SA; Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona 85721 USA., Wisely E; Genetics Graduate Interdisciplinary Program University of Arizona Tucson Arizona 85721 USA., Li Z; Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona 85721 USA., Dlugosch KM; Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona 85721 USA., Barker MS; Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona 85721 USA.
Jazyk: angličtina
Zdroj: Applications in plant sciences [Appl Plant Sci] 2021 Feb 14; Vol. 9 (2), pp. e11409. Date of Electronic Publication: 2021 Feb 14 (Print Publication: 2021).
DOI: 10.1002/aps3.11409
Abstrakt: 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.
(© 2021 Marx et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.)
Databáze: MEDLINE
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