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PremiseTagSeq is a cost‐effective approach for gene expression studies requiring a large number of samples. To date, TagSeq studies in plants have been limited to those with a high‐quality reference genome. We tested the suitability of reference transcriptomes for TagSeq in non‐model plants, as part of a study of natural gene expression variation at the Santa Rita Experimental Range National Ecological Observatory Network (NEON) core site. MethodsTissue for TagSeq was sampled from multiple individuals of four species (Bouteloua aristidoidesandEragrostis lehmanniana[Poaceae],Tidestromia lanuginosa[Amaranthaceae], andParkinsonia florida[Fabaceae]) at two locations on three dates (56 samples total). One sample per species was used to create a reference transcriptome via standard RNA‐seq. TagSeq performance was assessed by recovery of reference loci, specificity of tag alignments, and variation among samples. ResultsA high fraction of tags aligned to each reference and mapped uniquely. Expression patterns were quantifiable for tens of thousands of loci, which revealed consistent spatial differentiation in expression for all species. DiscussionTagSeq using de novo reference transcriptomes was an effective approach to quantifying gene expression in this study. Tags were highly locus specific and generated biologically informative profiles for four non‐model plant species.
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De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes
Abstract This study presents eight new high-qualityde novotranscriptomes from six co-occurring species of calanoid copepods, the first published forNeocalanus plumchrus,N. cristatus, Eucalanus bungiiandMetridia pacificaand additional ones forN. flemingeriandCalanus marshallae. They are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. ‘Omics data for this diverse and numerous taxonomic group are sparse and difficult to obtain. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Quality filtered reads were assembled with Trinity software and validated using multiple criteria. The study’s primary purpose is to provide a resource for gene expression studies. The integrated database can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes. An example of an additional use is provided for discovering novel and evolutionarily-significant proteins within the Calanoida. A workflow was designed to find and characterize unannotated transcripts with homologies acrossde novoassemblies that have also been shown to be eco-responsive.
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- PAR ID:
- 10409495
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Scientific Data
- Volume:
- 10
- Issue:
- 1
- ISSN:
- 2052-4463
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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