README: Genome assembly and annotation for temperate and Antarctic icefishes

This dataset contains the genome assembly and associated annotation for two icefish species (Channichthyidae), the Antarctic mackerel icefish (Champsocephalus gunnari) and the temperate pike icefish (Champsocephalus esox), alongside a temperate outgroup, the Patagonian Blennie (Eleginops maclovinus). It is associated with the folllowing publication:

Angel G Rivera-Colón, Niraj Rayamajhi, Bushra Fazal Minhas, Giovanni Madrigal, Kevin T Bilyk, Veronica Yoon, Mathias Hüne, Susan Gregory, C H Christina Cheng, Julian M Catchen, Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish, Molecular Biology and Evolution, Volume 40, Issue 3, March 2023, msad029, https://doi.org/10.1093/molbev/msad029

Abstract

White-blooded Antarctic icefishes are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation of C. esox, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Our study presents the first whole genome characterization of a secondarily temperate notothenioid to date, providing a key resource and platform for understanding the adaptive potential of the highly vulnerable icefishes, and of cryonotothenioids in general, in face of a warming Antarctic environment.

Methods

Genomes for C. esox and C. gunnari were assembled using flye v2.5. The E. maclovinus genome was assembled with wtdbg2. All genomes were scaffolded with juicer v1.6.2. Annotation generated using BRAKER v2.1.6 and TSEBRA v1.0.1. A more in depth description is available on the README file and in the publication (Rivera-Coln et al. 2022).

Usage Notes

All 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).

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 specifications

*Does not include the gzipped compression suffix (.gz).

C. esox

Assembly and Annotation

The C. esox assembly and associated annotation have the label ceso.ftc.fv8, which denotes the species (ceso), the annotation (ftc, flye+TSEBRA Curated), and integration (fv8, flye assembly, 8th iteration).

A C. esox specimen was collected from the Puerto Natales, Chile in January 2018. For CLR sequencing, HMW DNA was extractd and sequenced using a PacBio Sequel II. After filtering for coverage and read length, raw reads were assembled with flye v2.5 (Kolgomorov et al. 2019). For scaffolding, Hi-C libraries were constructed and sequenced, after which the genome was scaffolded into super-scaffolds with juicer v1.6.2 (Durand et al. 2016). PacBio and HiC raw data is available under NCBI BioProject PRJNA857989, BioSample SAMN29660769.

For annotation, RNA was extracted from pooled C. gunnari specimens, made into a RNAseq library and sequenced. After alignment, the transcript-level evidence was used to annotate protein-coding genes using BRAKER v2.1.6 (Brna et al. 2021), which were then further processed using TSEBRA v1.0.1 (Gabriel et al. 2021). Using a custom Python script, we curated the TSEBRA 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. Manual curation was performed for the annotation of Antifreeze Glycoprotein (AFGP) coding sequences.

A conserved synteny analysis using synolog (Catchen et al. 2009; Small et al. 2016) was employed for the manual curation of the assemblies. For example, we identifying 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.

Files

C. gunnari

Assembly and Annotation

The C. gunnari assembly and associated annotation have the label cgun.ftc.fv8, which denotes the species (cgun), the annotation (ftc, flye+TSEBRA Curated), and integration (fv8, flye assembly, 8th iteration).

A male C. gunnari specimen was collected from the West Antarctic Peninsula in 2014. HMW DNA was extracted and sequenced using PacBio Sequel II and a Hi-C library, after which genome assembly, scaffolding, and annotation was performed as described above for C. esox. PacBio and HiC raw data is available under NCBI BioProject PRJNA857989, BioSample SAMN29660770.

Files

E. maclovinus

Assembly and Annotation

The E. maclovinus assembly and associated annotation have the label emac.rtc.rv5, which denotes the species (emac), the annotation (rtc, redbean+TSEBRA Curated), and integration (rv8, redbean assembly, 5th iteration).

A E. maclovinus 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 wtdgb2 (a.k.a. redbean) v2.5 (Ruan & Li 2020), and scaffolded with juicer v1.6.2. PacBio and HiC raw data is available under NCBI BioProject PRJNA857989, BioSample SAMNXXXXXXXX. For annotation, the RNA-seq data generated by Bilyk et al. (2018) was aligned to the genome, and processed using BRAKER v2.1.6 and TSEBRA v1.0.1. Both the assembly and annotations were curated as described above for C. esox.

Files

Code Availability

All the scripts and custom code used to generate these assemblies are available in a BitBucket repository.

Authors

Angel G. Rivera-Colon\
Department of Evolution, Ecology, and Behavior\
University of Illinois at Urbana-Champaign\
angelgr2@illinois.edu

Julian M. Catchen\
Department of Evolution, Ecology, and Behavior\
University of Illinois at Urbana-Champaign\
jcatchen@illinois.edu

C-H Christina Cheng\
Department of Evolution, Ecology, and Behavior\
University of Illinois at Urbana-Champaign\
c-cheng@illinois.edu