Genomic analyses of the southern and eastern yellowjacket wasps (Hymenoptera: Vespidae) reveal evolutionary signatures of social life
Data files
Aug 21, 2024 version files 525.60 MB
Abstract
The evolution of sociality in insects represented a remarkable development in biological history. Social wasps are particularly noteworthy because they display gradations in social behaviors. Here, we sequence the genomes of two highly diverged Vespula wasps to gain greater insight into the evolution of sociality. Both V. squamosa and V. maculifrons Buysson (Hymenoptera: Vespidae) are highly social wasps and live in large colonies characterized by distinct caste systems. However, V. squamosa is a facultative social parasite, and V. maculifrons is its frequent host. We found that the genomes of both species were ~200 Mbp in size, similar to the sizes of congeneric species. Analyses of gene expression from members of different castes and developmental stages revealed similarities in expression patterns among immature life stages. Next, we found evidence of DNA methylation within the genome of both species directly from PacBio HiFi DNA sequence reads. Patterns of gene expression were correlated with DNA methylation levels within genes; genes that were highly and uniformly expressed were also relatively highly methylated. Finally, we uncovered evidence of differences in patterns of molecular evolution in the two taxa, consistent with V. squamosa showing changes in selective constraint associated with its facultatively parasitic or polygyne life history. Moreover, rates of gene evolution were correlated with variation in gene expression between castes and developmental stages, as expected if more highly expressed genes were subject to stronger levels of selection. Overall, this study expands our understanding of genomic consequences of social evolution in insects. Keywords: Social Insects, Genetics, Behavior, Population Genetics, Vespidae Entomological Society of America Editorial Office: 170 Jennifer Road, Suite 230, Annapolis, MD 21401, USA. Editorial Office Phone: 1-301-731-4535.
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README: Genomic analyses of the southern and eastern yellowjacket wasps (Hymenoptera: Vespidae) reveal evolutionary signatures of social life
https://doi.org/10.5061/dryad.w6m905qxj
Description:
This repository contains the pipeline used for the study of two Vespula species. The pipeline includes scripts and tools for quality control, alignment, assembly, quantification, methylation, and differential expression analysis. Additionally, it provides scripts for genomic feature extraction and various visualizations. The transposable element (TE) files from EDTA (https://github.com/oushujun/EDTA) contain annotations of all TEs (TEanno.gff3.gz), intact TEs only (intact.gff3.gz), a library of reconstructed TEs (TElib.fa.gz), and a summary statistic of the TEs (TEanno.sum.gz). The collinearity files come from running OrthoVenn3 (https://orthovenn3.bioinfotoolkits.net) and contain orthodox comparisons between multiple species. The genome alignment files come from running D-Genies (https://dgenies.toulouse.inra.fr) and contain full genome alignments files and visualizations. The methylation files are the coverage files that can be used to count the pileup of methylated reads in the standard bed file format. Some of the file formats in this dataset include: fasta (https://www.ncbi.nlm.nih.gov/genbank/fastaformat/), newick (https://phylipweb.github.io/phylip/newicktree.html), gff (https://www.ensembl.org/info/website/upload/gff.html?redirect=no), and bed (https://grch37.ensembl.org/info/website/upload/bed.html) file formats. Files may be tar gzipped in some cases.
Repository Structures:
Please see "All_paths_and_files_list.txt" for a complete list of files. A quick summary of the files can be found below.
./Data
├── TE_files
│ ├── V.maculifrons.fasta.mod.EDTA.TEanno.gff3.gz
│ ├── V.maculifrons.fasta.mod.EDTA.TEanno.sum.gz
│ ├── V.maculifrons.fasta.mod.EDTA.TElib.fa.gz
│ ├── V.maculifrons.fasta.mod.EDTA.intact.gff3.gz
│ ├── V.squamosa.fasta.mod.EDTA.TEanno.gff3.gz
│ ├── V.squamosa.fasta.mod.EDTA.TEanno.sum.gz
│ ├── V.squamosa.fasta.mod.EDTA.TElib.fa.gz
│ ├── V.squamosa.fasta.mod.EDTA.intact.gff3.gz
│ └── ...
├── collinearity
│ ├── Alignments_collinearity.txt
│ ├── Multiple_sequence_alignment.fasta.gz
│ ├── Orthogroups.txt.gz
│ ├── Result_all_species_collinearity.txt
│ ├── Species_divergence_time_tree.nwk.gz
│ ├── Species_phylogenetic_tree.nwk.gz
│ ├── cafe5.tar.gz
│ ├── collinear.png
│ ├── gene_families.txt.gz
│ ├── orthologous.html
│ ├── single_copy.tar.gz
│ └── ...
├── genome_alignment_files
│ ├── 46818775_map_V.germanica_to_V.maculifrons.paf
│ ├── 46818778_map_V.vulgaris_to_V.maculifrons.paf
│ ├── ...
│ └── V.vulgaris_V.maculifrons_wpR0Z_20221122233916.html
├── methylation_files
│ ├── Vespula_maculifrons_methylation_coverage.bed.gz
│ └── Vespula_squamosa_methylation_coverage.bed.gz
./Software
├── 1_globus
│ ├── 1_globus_maculifrons_download.slurm
│ └── 1_globus_squamosa_download.slurm
├── 1_illumina
│ └── 1_illumina_download.slurm
├── 2_SMRT
│ ├── 2_pbmarkdup_v.maculifrons.slurm
│ └── 2_pbmarkdup_v.squamosa.slurm
├── ...
├── 45_InterProScan
│ ├── 45_InterProScan.slurm
│ └── 45_InterProScan_2.slurm
├── 46_counts
│ ├── 46_counts.slurm
│ ├── TE_fa_list.txt
│ └── prot_fa_list.txt
└── 49_seqtk
│ └── 49_seqtk.slurm
Methods
Vespula squamosa and Vespula maculifrons transposable elements and methylation coverage files. Transposable element annotation generated from EDTA v2.1.0 and methylation analysis conducted in SeqMonk v1.48.1.