DOI: 10.5061/dryad.sqv9s4n9t
title: Annotated genome assemblies for Geoscapheus dilatatus, Panesthia cribrata and Neogeoscapheus hanni

description: Genetic changes that enabled the evolution of eusociality have long
 captivated biologists. More recently, attention has focussed on the
 consequences of eusociality on genome evolution. Studies have reported
 higher molecular evolutionary rates in eusocial hymenopteran insects
 compared with their solitary relatives. To investigate the genomic
 consequences of eusociality in termites, we analysed nine genomes,
 including newly sequenced genomes from three non-eusocial cockroaches.
 Using a phylogenomic approach, we found that termite genomes have
 experienced lower rates of synonymous substitutions than those of
 cockroaches, possibly as a result of longer generation times. We
 identified higher rates of non-synonymous substitutions in termite genomes
 than in cockroach genomes, and identified pervasive relaxed selection in
 the former (24–31% of the genes analysed) compared with the latter (2–4%).
 We infer that this is due to reductions in effective population size,
 rather than gene-specific effects (e.g. indirect selection of caste-biased
 genes). We found no obvious signature of increased genetic load in
 termites, and postulate efficient purging of deleterious alleles at the
 colony level. Additionally, we identified genomic adaptations that may
 underpin caste differentiation, such as genes involved in
 post-translational modifications. Our results provide insights into the
 evolution of termites and the genomic consequences of eusociality more
 broadly.
description: Three Blaberidae genomes (<em>Geoscapheus dilatatus,
 Panesthia cribrata</em> and <em>Neogeoscapheus
 hanni</em>) were sequenced and assembled to investigate the
 evolution of this group, and to provide genomic resources for studies on
 Blattodea. These genomes were assembled using a combination of
 linked-read, long-read and Hi-C data (the raw seqeunce data are avalable
 on the SRA database under BioSample accessions SAMN39450771, SAMN39450772
 and SAMN39450773 for Geoscapheus dilatatus, Neogeoscapheus hanni and
 Panesthia cribrata respectively). Assembly methods are outlined in the
 associated manuscript. Briefly, an initial de novo <em>Geoscapheus
 dilatatus</em> genome assembly was generated using the program
 Supernova with linked-read stLFR data. Gaps were filled using the program
 TGS-GapCloser with low-coverage long-read PacBio HiFi data, and the
 assembly was subsequently scaffolded using the SALSA2 with Hi-C
 reads. An initial <em>Panesthia
 cribrata</em> genome assembly was generated using the program
 Supernova with linked-read TELL-Seq data. A second de novo assmembly was 
 generated using the program IPA with long-read PacBio Hifi data. The two
 assemblies were then merged using the program QuickMerge.
 The <em>Neogeoscapheus hanni</em> genome assembly was
 generated using the program Supernova with linked-read stLFR
 data. All three genomes were annotated using
 FGENESH++.
description: # De novo assemblies of Blaberidae genomes
 This repository contains
 genome assemblies and associated annotations for three Blaberidae species:
 *Geoscapheus dilatatus*, *Neogeoscapheus hanni* and *Panesthia cribrata*.
 The genome were assembled using a combination of linked-read, long-read
 and Hi-C data. An initial *Geoscapheus dilatatus* genome assembly was
 generated using linked-read data, then gaps were filled using low-coverage
 long-read data, and the assembly was subsequently scaffolded using Hi-C
 reads. ## Description of the data and file structure Five files are
 available for each of the three species: * Full genome assembly (fasta
 file) * *Geoscapheus dilatatus* genome assembly:
 'Geoscapheus-dilatatus_genome-assembly.fa' * *Neogeoscapheus
 hanni* genome assembly:
 'Neogeoscapheus-hanni_genome-assembly.fa' * *Panesthia cribrata*
 genome assembly: 'Panesthia-cribrata_genome-assembly.fa' *
 Genome annotation (gff3) * *Geoscapheus dilatatus* genome annotation:
 'Geoscapheus-dilatatus_fgenesh-annotation.gff3' *
 *Neogeoscapheus hanni* genome assembly:
 'Neogeoscapheus-hanni_fgenesh-annotation.gff3' * *Panesthia
 cribrata* genome assembly:
 'Panesthia-cribrata_fgenesh-annotation.gff3' * Protein sequences
 derived from the annotation (fasta) * *Geoscapheus dilatatus* protein
 sequences:
 'Geoscapheus-dilatatus_fgenesh-annotation_proteins.fa' *
 *Neogeoscapheus hanni* protein sequences:
 'Neogeoscapheus-hanni_fgenesh-annotation_proteins.fa' *
 *Panesthia cribrata* protein sequences:
 'Panesthia-cribrata_fgenesh-annotation_proteins.fa' * mRNA
 sequences derived from the annotation (fasta) * *Geoscapheus dilatatus*
 mRNA sequences:
 'Geoscapheus-dilatatus_fgenesh-annotation_mrna.fa' *
 *Neogeoscapheus hanni* mRNA sequences:
 'Neogeoscapheus-hanni_fgenesh-annotation_mrna.fa' * *Panesthia
 cribrata* mRNA sequences:
 'Panesthia-cribrata_fgenesh-annotation_mrna.fa' * Coding
 sequences (CDS) derived from the annotation (fasta) * *Geoscapheus
 dilatatus* CDS sequences:
 'Geoscapheus-dilatatus_fgenesh-annotation_cds.fa' *
 *Neogeoscapheus hanni* CDS sequences:
 'Neogeoscapheus-hanni_fgenesh-annotation_cds.fa' * *Panesthia
 cribrata* CDS sequences:
 'Panesthia-cribrata_fgenesh-annotation_cds.fa' The sequence
 names in the genome assembly files were produced by the assembly software
 used to generate the assemblies. The final assembly step of each genome
 assembly (in which the final sequence names were produced) were as
 follows: the *Geoscapheus dilatatus* genome was scaffolded using the
 program SALSA2 with Hi-C reads; the *Neogeoscapheus hanni* genome was
 produced using the program Supernova with linked-reads; the *Panesthia
 cribrata* linked-read de novo assembly (produced using the program
 Supernova) and long-read de novo assembly (produced using the program IPA)
 were merged inot a single assembly using the program QuickMerge. The
 annotation files were produced using FGENESH++ v7.2.2. The tab-delimited
 'General Feature Format' annotation files (i.e. the
 'gff3' files) represent a standard file format for genome
 assemblies; they contains information for every feature in the associated
 reference genome. The contig/scaffold sequence names in the gff3 files
 correspond to the sequence names in the associated genome assembly files.
 The protein, mRNA and CDS fasta files are based on the annotations
 detailed in the gff3 files. ## Sharing/Access information All sequence
 data that were utilised to generate these three genomes are available on
 NCBI under BioProject PRJNA1065107, with BioSample accessions
 SAMN39450771, SAMN39450772 and SAMN39450773 for *Geoscapheus dilatatus*,
 *Neogeoscapheus hanni* and *Panesthia cribrata* respectively.