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Nannoperca australis liver transcriptome
Nannoperca australis liver transcriptome assembled using Trinity based on RNAseq data from five individuals. Assembly contains 201,037 Trinity transcripts clustered into 96,717 Trinity \"genes\".
Trinity.fasta
ORF_counts
Raw counts data for 27,425 longest open reading frames
TMM_ORF_counts
cross sample normalized counts for 27,425 ORFs
SPP_trinotate_annotation_report
annotation information for Trinity.fasta assembly
", "type": { "id": "notes", "title": { "de": "Anmerkungen", "en": "Notes" } } } ], "creators": [ { "affiliations": [ { "name": "Flinders University" } ], "person_or_org": { "family_name": "Brauer", "given_name": "Chris J.", "name": "Brauer, Chris J.", "type": "personal" } }, { "affiliations": [ { "name": "University of Canberra" } ], "person_or_org": { "family_name": "Unmack", "given_name": "Peter J.", "name": "Unmack, Peter J.", "type": "personal" } }, { "affiliations": [ { "name": "Flinders University" } ], "person_or_org": { "family_name": "Beheregaray", "given_name": "Luciano B.", "name": "Beheregaray, Luciano B.", "type": "personal" } } ], "description": "Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in non-model species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g. dry/hot lowland; wet/cold upland) and represent opposite ends of the species' spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an ANOVA-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within-populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations.", "locations": { "features": [ { "place": "Australia" } ] }, "publication_date": "2017-11-08", "publisher": "Zenodo", "related_identifiers": [ { "identifier": "10.1111/mec.14432", "relation_type": { "id": "iscitedby", "title": { "de": "Wird zitiert von", "en": "Is cited by" } }, "scheme": "doi" } ], "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "CC0 waives copyright interest in a work you've created and dedicates it to the world-wide public domain. Use CC0 to opt out of copyright entirely and ensure your work has the widest reach." }, "icon": "cc-cc0-icon", "id": "cc0-1.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" }, "title": { "en": "Creative Commons Zero v1.0 Universal" } } ], "subjects": [ { "subject": "Nannoperca australis" }, { "subject": "conservation genomics" }, { "subject": "comparative transcriptomics" } ], "title": "Data from: Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish" }, "parent": { "access": { "owned_by": { "user": "90070" } }, "communities": { "default": "734b6452-1f40-4db0-b218-08ab1d568b7f", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_submission_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2020-02-04T14:03:17.992421+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "734b6452-1f40-4db0-b218-08ab1d568b7f", "links": {}, "metadata": { "curation_policy": "

The Dryad collection in Zenodo contains datasets mirrored from the Dryad Digital Repository. If you want your dataset to appear here, submit it through https://datadryad.org. No other datasets will be accepted.

", "description": "Dryad is an international open-access repository of research data, especially data underlying scientific and medical publications. Dryad is a curated general-purpose repository that makes data discoverable, freely reusable, and citable.", "organizations": [ { "id": "00x6h5n95" } ], "page": "

Dryad is a community-governed open data publishing and curation repository. Through Dryad and Zenodo's partnership, Zenodo hosts a preservation copy of Dryad datasets, available through this Zenodo Community. For more information or to access the original published datasets, visit https://datadryad.org.

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