Camponotus fellah cDNA lists for: Social isolation shortens lifespan through oxidative stress in ants
Data files
Aug 04, 2023 version files 32.31 MB
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Cfel_transcriptome.fasta
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README.md
Oct 04, 2023 version files 58.94 MB
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Cfel_transcriptome.fasta
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evmodPasaWccl.gtf
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README.md
Abstract
Social isolation negatively affects health, induces detrimental behaviors, and shortens lifespan in social species. Little is known about the mechanisms underpinning these effects because model species are typically short-lived and non-social. Using colonies of carpenter ant Camponotus fellah, we show that social isolation induces hyperactivity, alters space-use, and reduces lifespan via changes in the expression of genes with key roles in oxidation-reduction and an associated accumulation of reactive oxygen species. These physiological effects are localized to the fat body and oenocytes, which perform liver-like functions in insects. We use pharmacological manipulations to demonstrate that the oxidation-reduction pathway causally underpins the detrimental effects of social isolation on behavior and lifespan. These findings have important implications for our understanding of how social isolation affects behavior and lifespan in general.
README: Camponotus fellah transcriptome for: Social isolation shortens lifespan through oxidative stress in ants
Three Oxford Nanopore sequencing libraries were prepared from high molecular weight genomic DNA using the RAD002 kit and sequenced on a MinION Mark1-B on three rev D R9.4.1 flowcells. Reads were basecalled using Guppy v2.1.3 (Oxford Nanopore Technologies) and assembled using wtdbg2. The assembly was then polished with Nanopore long reads using Medaka v0.6 (https://github.com/nanoporetech/medaka), then with Illumina reads first using Pilon , and then using variants called by freebayes (https://github.com/ekg/freebayes) with variant quality scores greater than 30. Candidate annotations were generated using the hint-guided gene predictors Augustus and SNAP, genome-guided RNA-seq assembly from the Trinity assembler and PASA refinement tool, and liftover of NCBI RefSeq protein annotations from Camponotus floridanus using GenomeThreader . Augustus and SNAP were run through the MAKER pipeline with protein homology evidence from the NCBI RefSeq Nasonia vitripennis, Apis mellifera, Camponotus floridanus, and Ooceraea biroi proteomes and RNA-seq alignments. MAKER was run first using pre-packaged ab-initio models from Nasonia vitripennis for Augustus and from Apis mellifera for SNAP, then again with the same evidence but with ab-initio models retrained from the first round. All candidate gene models were then combined using EvidenceModeler with the above-described transcript and homologous protein alignments used as evidence.
Description of the data and file structure
A transcriptome file (fasta) and an annotation file (gtf).