Gene annotations for European grass snake (Natrix natrix natrix)

Here we provide the gene annotations for European grass snake (Natrix natrix natrix). We provide the gene anntations both for 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. To annotate the genome, we first identified repetitive regions and TEs using RepeatModeler2 and RepeatMasker as previously described. Specifically, we used the RepeatModeler2 to generate a de novo species-specific repetitive-sequence and TE library for both haplotypes and merged them. We split the library into “known” and “unknown” sets as output by RepeatModeler2. The “unknown” set was classified using DeepTE with the model designed for metazoans. To remove false-positive repetitive elements, we removed any sequence classified as “NonTE” using TERL. Then, the species-specific TE library (i.e. the “known” set and the “unknown” re-classified set) was merged to a curated TE library designed for snakes, and the final TE library was used to perform the repetitive annotation of each haplotype using RepeatMasker (https://www.repeatmasker.org/). The divergence between the individual TE copies versus their consensus sequences based on CpG-adjusted Kimura distance was estimated using RepeatMasker built-in scripts. We annotated the genome assemblies using a pre-release version of the EBP-Nor genome annotation pipeline. First, we mapped trimmed RNA-seq reads using HISAT2, retrieved transcripts using StringTie, and predicted proteins using CodAn to build a species-specific protein set. We merged this species-specific set to proteins from available and annotated snake genomes in NCBI (i.e., Natrix helvetica, Tamnophis elegans, Naja naja, and Crotalus adamanteus), proteins in the Squamata odb12 database, and toxin genes from Elapidae and Viperidae database from ToxCodAn-Genome to build a custom protein set. In addition to gene models from protein alignments, GALBA ( 1, 2, 3, 4) was run with the snake proteins using the miniprot mode on masked assemblies to generate ab initio predicted gene models. Helixer was run using the vertebrate-specific model (vertebrate_v0.3_m_0080). The funannotate-runEVM.py script from Funannotate was used to run EvidenceModeler on the alignments of snake proteins, UniProtKB/Swiss-Prot proteins, Squamata proteins from OrthoDB, and the predicted genes from GALBA and Helixer. 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 2025_03 using DIAMOND blastp to find gene names and InterProScan 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. The annotated genome assemblies can be found at ENA at GCA_990120052 (pseudo-haplotype one) and GCA_990120369 (pseudo-haplotype two). The sequencing data is at ERR18069814(PacBio) and ERR18069779 (Hi-C). All the data is collected in the umbrella project PRJEB129022. List of files provided here and their description: rNatNat1.hap1.fa.gz - genome assembly of European grass snake (hap1) rNatNat1.1.hap1.repeat.gff.gz - repeat annotation of European grass snake (hap1) rNatNat1.1.hap1.gff.gz - genome annotation of European grass snake (hap1) rNatNat11.hap1.proteins.fa.gz - predicted proteins of European grass snake (hap1) rNatNat1.1.hap2.fa.gz - genome assembly of European grass snake (hap2) rNatNat1.1.hap2.repeat.gff.gz - repeat annotation of European grass snake (hap2) rNatNat1.1.hap2.gff.gz - genome annotation of European grass snake (hap2) rNatNat1.1.hap2.proteins.fa.gz - predicted proteins of European grass snake (hap2)