De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies

Simple item page
dc.citation.issue1
dc.citation.volume50
dc.contributor.authorThunders MC
dc.contributor.authorCavanagh J
dc.contributor.authorLi Y
dc.coverage.spatialEngland
dc.date.available2017-02-27
dc.date.available2017-02-20
dc.date.issued17/02/2017
dc.description.abstractBACKGROUND: Earthworms are sensitive to toxic chemicals present in the soil and so are useful indicator organisms for soil health. Eisenia fetida are commonly used in ecotoxicological studies; therefore the assembly of a baseline transcriptome is important for subsequent analyses exploring the impact of toxin exposure on genome wide gene expression. RESULTS: This paper reports on the de novo transcriptome assembly of E. fetida using Trinity, a freely available software tool. Trinotate was used to carry out functional annotation of the Trinity generated transcriptome file and the transdecoder generated peptide sequence file along with BLASTX, BLASTP and HMMER searches and were loaded into a Sqlite3 database. To identify differentially expressed transcripts; each of the original sequence files were aligned to the de novo assembled transcriptome using Bowtie and then RSEM was used to estimate expression values based on the alignment. EdgeR was used to calculate differential expression between the two conditions, with an FDR corrected P value cut off of 0.001, this returned six significantly differentially expressed genes. Initial BLASTX hits of these putative genes included hits with annelid ferritin and lysozyme proteins, as well as fungal NADH cytochrome b5 reductase and senescence associated proteins. At a cut off of P = 0.01 there were a further 26 differentially expressed genes. CONCLUSION: These data have been made publicly available, and to our knowledge represent the most comprehensive available transcriptome for E. fetida assembled from RNA sequencing data. This provides important groundwork for subsequent ecotoxicogenomic studies exploring the impact of the environment on global gene expression in E. fetida and other earthworm species.
dc.description.publication-statusPublished online
dc.format.extent7 - ?
dc.identifierhttps://www.ncbi.nlm.nih.gov/pubmed/28241869
dc.identifier10.1186/s40659-017-0114-y
dc.identifier.citationBiol Res, 2017, 50 (1), pp. 7 - ?
dc.identifier.doi10.1186/s40659-017-0114-y
dc.identifier.eissn0717-6287
dc.identifier.elements-id338160
dc.identifier.harvestedMassey_Dark
dc.identifier.urihttps://hdl.handle.net/10179/10625
dc.languageeng
dc.publisherSociedad de Biología de Chile
dc.relation.isPartOfBiol Res
dc.relation.urihttp://biolres.biomedcentral.com/articles/10.1186/s40659-017-0114-y
dc.subjectE. fetida
dc.subjectEarthworm
dc.subjectEcotoxicology
dc.subjectGene expression
dc.subjectRNA
dc.subjectSequence
dc.subjectTranscriptome
dc.subjectTrinity
dc.subjectAnimals
dc.subjectEcotoxicology
dc.subjectEnvironmental Exposure
dc.subjectGene Expression Profiling
dc.subjectGene Ontology
dc.subjectOligochaeta
dc.subjectSequence Analysis, RNA
dc.subjectSoftware
dc.subjectSoil Pollutants
dc.subjectToxicogenetics
dc.subjectTranscriptome
dc.subject.anzsrc06 Biological Sciences
dc.titleDe novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies
dc.typeJournal article
pubs.notesNot known
pubs.organisational-group/Massey University
pubs.organisational-group/Massey University/College of Health
Files
Collections
Journal Articles