ArticleApplications in plant sciences2021
Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest.
Article in Applications in plant sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Unveiling the genetic diversity of the genera Enamovirus and Polerovirus through data-driven virus discovery.Archives of virology · 2025Article
- Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot study from an invaded alpine streambed.Ecology and evolution · 2021Article
- Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest.Applications in plant sciences · 2021Article
- GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data.Applications in plant sciencesArticle
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premiseLarge-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.
methodsWe 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.
resultsOnly modest differences in assembly quality were observed across multiple 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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