Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness

The Antarctic fur seal (Arctocephalus gazella) is an important top predator and indicator of the health of the Southern Ocean ecosystem. Although abundant, this species narrowly escaped extinction due to historical sealing and is currently declining as a consequence of climate change. Genomic tools are essential for understanding these anthropogenic impacts and for predicting long-term viability. However, the current reference genome (“arcGaz3”) shows considerable room for improvement in terms of both completeness and contiguity. We therefore combined PacBio sequencing, haplotype aware HiRise assembly and scaffolding based on Hi-C information to generate a refined assembly of the Antarctic fur seal reference genome (“arcGaz4_h1”). The new assembly is 2.53 Gb long, has a scaffold N50 of 55.6 Mb and includes 18 chromosome-sized scaffolds, which correspond to the 18 chromosomes expected in otariids. Genome completeness is greatly improved, with 23,408 annotated genes and a Benchmarking Uni..., , , # Data from \"Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness\"

[https://doi.org/10.5061/dryad.g1jwstqzn](https://doi.org/10.5061/dryad.g1jwstqzn)

## Overview:

This repository contains the data used in the study \"Refinement of the Antarctic fur seal (*Arctocephalus gazella*) reference genome increases continuity and completeness\" by Hench et. al., which introduces the Antarctic fur seal reference genome version arcGaz4_h1.

The data set includes:

* the two initial *de novo* haplotype assemblies by Dovetail genomics (`de_novo_genomes.tar.gz`)
* the genome annotation of the final assembly for the first haplotype in two formats (\"arcGaz4_h1\", `arcGaz4_h1_annotation.gff3.gz` and `arcGaz4_h1_annotation.gtf.gz`)
* a multi-species whole genome alignment of eleven pinniped species (`pinniped_set.hal`)
* the inferred neutral tree for the eleven aligned species (`rerooted.tree`)
* a one-on-one whole genome alignment of the Anta...