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

Hannah E. Marx, Stacy A. Jorgensen, Eldridge Wisely, Zheng Li, Katrina M. Dlugosch, Michael S. Barker

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Article numbere11409
JournalApplications in Plant Sciences
Volume9
Issue number2
DOIs
StatePublished - Feb 2021

Keywords

  • NEON
  • RNA-seq
  • community transcriptomics
  • polyploidy
  • transcriptome assembly

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Plant Science

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