Ranitomeya imitator Dovetail Genome

Briefly, we provided brain, lung, eye, testes, tongue, leg muscle, ventral skin, dorsal skin, intestines, liver, and heart tissues from an adult male R. imitator (‘tarapoto’ color morph) to Dovetail Genomics for commercial genome generation, curation, and annotation using PacBio HiFi sequencing and Omni-C assembly. Following demultiplexing, all further analyses with R. imitator occurred via mapping to the current genome (GCA_032444005.1), which was reassembly and annotation by Vertebrate Genome Project/NCBI. Note that both genomes (Dovetail and Vertebrate Genome Project/NCBI) are assemblies of the same data. Comparisons between both genomes may be accessed here: https://www.genomeark.org/genomeark-all/Ranitomeya_imitator.html. In our analyses, PO2745_Ranitomeya_imitator.RepeatMasked.fasta.gz was the genome used. Additional processing notes by Dovetail: Repeat families found in the genome assemblies of Ranitomeya imitator were identified de novo and classified using the software package RepeatModeler (version 2.0.1). RepeatModeler depends on the programs RECON (version 1.08) and RepeatScout (version 1.0.6) for the de novo identification of repeats within the genome. The custom repeat library obtained from RepeatModeler were used to discover, identify and mask the repeats in the assembly file using RepeatMasker (Version 4.1.0). Coding sequences from Leptobrachium leishanense, Nanorana parkeri, Rhinella marina and Xenopus tropicalis were used to train the initial ab initio model for Ranitomeya imitator using the AUGUSTUS software (version 2.5.5). Six rounds of prediction optimisation were done with the software package provided by AUGUSTUS. The same coding sequences were also used to train a separate ab initio model for Ranitomeya imitator using SNAP (version 2006-07-28). RNAseq reads were mapped onto the genome using the STAR aligner software (version 2.7) and intron hints generated with the bam2hints tools within the AUGUSTUS software. MAKER, SNAP and AUGUSTUS (with intron-exon boundary hints provided from RNA-Seq) were then used to predict for genes in the repeat-masked reference genome. To help guide the prediction process, Swiss-Prot peptide sequences from the UniProt database were downloaded and used in conjunction with the protein sequences from Leptobrachium leishanense, Nanorana parkeri, Rhinella marina and Xenopus tropicalis to generate peptide evidence in the Maker pipeline. Only genes that were predicted by both SNAP and AUGUSTUS softwares were retained in the final gene sets. To help assess the quality of the gene prediction, AED scores were generated for each of the predicted genes as part of the MAKER pipeline. Genes were further characterised for their putative function by performing a BLAST search of the peptide sequences against the UniProt database. tRNA were predicted using the software tRNAscan-SE (version 2.05).