DOI: 10.5061/dryad.qbzkh18nt
title: Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus

description: This dataset contains the genome assembly and associated annotation of the
 Patagonian Blennie (Eleginops maclovinus), the closest extant taxon to the
 Antarctic notothenioid radiation. In addition to the characterization of
 the E. maclovinus genome, the dataset includes a description
 of circadian rhythm orthologs for E. maclovinus, other
 notothenenioid taxa, and teleost outgroups, as well as a copy of the
 bioinformatic scripts used for the assembly, annotation, and other
 downstream analysis.
description: An <em>E. maclovinus</em> specimen was collected from
 the Puerto Natales, Chile in January 2018. HMW DNA was extracted and
 sequenced using PacBio Sequel II and a Hi-C library. A contig-level genome
 assembly was first generated using <em>wtdgb2</em> (a.k.a.
 <em>redbean</em>) v2.5 (Ruan
 & Li 2020), and scaffolded with
 <em>juicer</em> v1.6.2 (Durand et
 al. 2016). PacBio and HiC raw data is available under NCBI
 BioProject PRJNA857989. For annotation, the RNA-seq data generated by
 Bilyk et al. (2018) was aligned to the genome, and processed using <em>BRAKER</em> v2.1.6 (Brůna et al. 2021). The generated annotation was then further processed using <em>TSEBRA</em> v1.0.1 (Gabriel et al. 2021). Using a custom Python script (see scripts section), we curated the <em>TSEBRA</em> output to guarantee consistency in the naming of genes and transcripts, as well as incorporating gene names and description based on the corresponding zebrafish orthologs. A conserved synteny analysis using <em>synolog</em> (Catchen et al. 2009; Small et al. 2016) was employed for the manual curation of the assemblies. For example, we identified missasemblies in structural variants limited to contig boundaries or merged scaffolds belonging to the same chromosome sequences. We used a custom Python program to propagate these changes through the constituent assembly files. For the circadian rhythm comparative analysis, assemblies and annotations were downloaded from genomic databases (e.g., ENSEMBL, NCBI). Circadian gene orthologs were identified using <em>synolog</em> and extracted using custom Python scripts. A detailed step-by-step description of the methods is available in the associated publication (Cheng et al.).
description: All assembly and annotation files are gzipped, but are otherwise
 standard bioinformatic formats (i.e., FASTA for genome assembly and
 coding/amino acid sequences, GTF for annotation, AGP for scaffolding). In
 addition, bioinformatic scripts for data generation and analysis are in
 Python (*.py) or Bash (*.sh, but might require the installation of
 additional, open-source software (e.g., <em>wtdbg2</em>,
 <em>BRAKER</em>) See links for a
 description of the FASTA (http://www.ncbi.nlm.nih.gov/blast/fasta.shtml), and GTF (https://useast.ensembl.org/info/website/upload/gff.html), and AGP (https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/) file format specifications. File format Specification <strong>File Suffix<sup>1</sup></strong> <strong>Description</strong> *.fa Genome assembly in nucleotide FASTA format.  *.agp Assembly structure in AGP format. *.gtf Genome annotation in GTF format. *.cds.fa Genomic sequence for all annotated protein-coding genes in nucleotide FASTA format. *.protein.fa Protein sequence for all annotated protein-coding genes in amino acid FASTA format. <sup>1</sup>Does not include the gzipped compression suffix (*.gz).