Gene annotations for greater hornwrack bryozoan (Flustra foliacea) and repeat annotations for selected species

Here we provide the gene annotations for greater hornwrack bryozoan (Flustra foliacea). We provide these for both convenience and because some of the functional annotations of genes/proteins are removed when we prepare these for uploading to ENA. We also provide the FASTA files for the assemblies we have made.

We annotated the genome assemblies using a pre-release version of the EBP-Nor genome annotation pipeline (https://github.com/ebp-nor/GenomeAnnotation). Predicted proteins from Bugulina stolonifera were downloaded from https://datadryad.org/dataset/doi:10.5061/dryad.76hdr7t3f and miniprot (Li 2023) was used to align the proteins to the curated assemblies. UniProtKB/Swiss-Prot (UniProt Consortium 2023) release 2023_03 in addition to the metazoa part of OrthoDB v11 (Kuznetsov et al. 2023) were also aligned separately to the assemblies. Red (Girgis 2015) was run via redmask (https://github.com/nextgenusfs/redmask) on the assemblies to mask repetitive areas. GALBA (Brůna et al. 2023; Buchfink, Xie, and Huson 2015; Hoff and Stanke 2019; Li 2023; Stanke et al. 2006) was run with the B. stolonifera proteins using the miniprot mode on the masked assemblies. The funannotate-runEVM.py script from Funannotate was used to run EvidenceModeler (Haas et al. 2008) on the alignments of GRCh38 proteins, UniProtKB/Swiss-Prot proteins, vertebrata proteins and the predicted genes from GALBA. The resulting predicted proteins were compared to the protein repeats that Funannotate distributes using DIAMOND blastp and the predicted genes were filtered based on this comparison using AGAT. The filtered proteins were compared to the UniProtKB/Swiss-Prot release 2023_03 using DIAMOND (Buchfink, Xie, and Huson 2015) blastp to find gene names and InterProScan (Jones et al. 2014) was used to discover functional domains. AGATs agat_sp_manage_functional_annotation.pl was used to attach the gene names and functional annotations to the predicted genes. 

We also ran EarlGrey (Baril, Galbraith, and Hayward 2024; https://github.com/TobyBaril/EarlGrey) on all species investigated and provide the summary files folder here. These species were included: Bugulina stolonifera (Bryozoa, Gymnolaemata, Cheilostomatida; GCA_935421135.1), Cristatella mucedo (Bryozoa, Phylactolaemata, Plumatellida; GSM5182733), Cryptosula pallasiana (Bryozoa, Gymnolaemata, Cheilostomatida, GCA_945261195.1), Membranipora membranacea (Bryozoa, Gymnolaemata, Cheilostomatida; GCA_914767715.1), and Waterispora subatra (Bryozoa, Gymnolaemata, Cheilostomatida; GCF_963576615.1). We also included two outgroup species, Pecten maximus (Mollusca; GCF_902652985.1) and Lineus longissimus (Nemertea; GCF_910592395.1).

List of files provided here and their description:

tzFluFoli1.1.hap1.fa.gz - genome assembly of greater hornwrack bryozoan (hap1)

tzFluFoli1.1.hap1.proteins.fa.gz - predicted proteins greater hornwrack bryozoan (hap1)

tzFluFoli1.1.hap1.gff.gz - genome annotation of greater hornwrack bryozoan (hap1)

 tzFluFoli1.1.hap2.fa.gz - genome assembly of greater hornwrack bryozoan (hap2)

tzFluFoli1.1.hap2.proteins.fa.gz - predicted proteins greater hornwrack bryozoan (hap2)

tzFluFoli1.1.hap2.gff.gz - genome annotation of greater hornwrack bryozoan (hap2)

BugStol_summaryFiles.tar.gz - repeat annotation summary files from EarlGrey for Bugulina stolonifera

CryPall_summaryFiles.tar.gz - repeat annotation summary files from EarlGrey for Cryptosula pallasiana

CriMuce_summaryFiles.tar.gz - repeat annotation summary files from EarlGrey for Cristatella mucedo

FluFoli_summaryFiles.tar.gz  - repeat annotation summary files from EarlGrey for Flustra foliacea (hap1)

LinLong_summaryFiles.tar.gz - repeat annotation summary files from EarlGrey for Lineus longissimus

MemMemb_summaryFiles.tar.gz - repeat annotation summary files from EarlGrey for Membranipora membranacea

PecMax_summaryFiles.tar.gz - repeat annotation summary files from EarlGrey for Pecten maximus

WatSuba_summaryFiles.tar.gz - repeat annotation summary files from EarlGrey for Watersipora subatra