Progress Towards Plant Community Transcriptomics: Pilot RNA-Seq Data from 24 Species of Vascular Plants at Harvard Forest

BioRxiv : the Preprint Server for Biology
H. E. MarxMichael S. Barker


Premise of the study: Large scale projects such as NEON are collecting ecological data on entire biomes to track and understand plant responses to climate change. NEON provides an opportunity for researchers 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 phylogenetically diverse NEON plant communities, including species with diploid and polyploid genomes. Methods: We used Illumina NextSeq to generate >20 Gb of RNA-seq for each of 24 vascular plant species representing 12 genera and 9 families at the Harvard Forest NEON site. Each species was sampled twice, in July and August 2016. We used Transrate, BUSCO, and GO analyses to assess transcriptome quality and content. Results: We obtained nearly 650 Gb of RNA-seq data that assembled into more than 755,000 translated protein sequences across the 24 species. We observed only modest differences in assembly quality scores across a range of k-mer values. 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 genes between diploid and polyploid ...Continue Reading

Related Concepts

Biologic Segmentation
Magnetic Resonance Imaging
Projections and Predictions
Anatomic Structures
Diffusion Magnetic Resonance Imaging
Weighing Patient
Fractional Precipitation
Anatomical Space Structure

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Related Papers

Juan Zeno Sanchez-Ramos
Cardiovascular Diagnosis and Therapy
Jessica Lloyd-Jones
Nature Chemistry
Felice Grandinetti
© 2020 Meta ULC. All rights reserved