Supplementary data for: Genomics of secondarily temperate adaptation in the only non-Antarctic icefish

White-blooded Antarctic icefishes are an example of extreme biological specialization both to the chronic cold of the Southern Ocean and to life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Despite these constraints, a single icefish species, the pike icefish Champsocephalus esox, is presently found in temperate South American waters. To study the genetic mechanisms underlying temperate adaptation in this species, 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 Antarctic icefishes. However, we observe evidence of chromosomal rearrangements, some of which coincide with regions of elevated genetic divergence in pike icefish populations. Our results show several key biological pathways under selection, including genes related to the mitochondria, iron tr..., 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-Colón et al. 2022)., 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, and GTF, and AGP file formats.
File format specifications

File Suffix*
Description

*.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

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

携白血特征的南极冰鱼（Antarctic icefishes）是极端生物特化的典型代表：它们既适配南大洋常年低温的环境，同时演化出了不依赖血红蛋白的生存模式。因此，冰鱼演化出的特化生理结构使其仅能存活于低温且高溶氧的南极水域中。尽管存在这类生理限制，目前仍有一种冰鱼——矛冰鱼（*Champsocephalus esox*）——在温带的南美水域中被发现。为探究该物种适应温带环境的遗传机制，本研究构建了矛冰鱼及其南极近缘种——南极鲱冰鱼（*Champsocephalus gunnari*）的染色体级基因组组装结果。矛冰鱼的基因组结构与组织形式与南极冰鱼高度相似，但研究团队检测到了染色体重排现象，其中部分重排区域与矛冰鱼种群中遗传分化程度较高的区段相重合。本研究结果揭示了数类受选择作用的核心生物学通路，包括与线粒体、铁代谢相关的基因（原文截断为iron tr...）。

矛冰鱼与南极鲱冰鱼的基因组组装采用flye v2.5软件完成，巴塔哥尼亚线纹鳚（*Eleginops maclovinus*）的基因组组装则使用wtdbg2软件完成；所有基因组均通过juicer v1.6.2进行支架构建，基因组注释则依托BRAKER v2.1.6与TSEBRA v1.0.1软件生成。更详细的描述可参见README文件及相关论文（Rivera-Colón等，2022）。

所有文件均已进行gzip压缩，但文件格式均为标准生物信息学格式：基因组组装及编码/氨基酸序列采用FASTA（FASTA）格式，基因组注释采用GTF（GTF）格式，基因组支架信息采用AGP（AGP）格式。FASTA、GTF及AGP的文件格式说明可参见对应链接。

文件格式规范

文件后缀* 描述

*.fa 核苷酸FASTA格式的基因组组装序列

*.agp AGP格式的基因组组装结构信息

*.gtf GTF格式的基因组注释信息

*.cds.fa 所有注释蛋白编码基因的核苷酸FASTA格式基因组序列

*.protein.fa 所有注释蛋白编码基因的氨基酸FASTA格式蛋白质序列

*注：文件后缀未包含gzip压缩后缀（.gz）。

# 温带与南极冰鱼的基因组组装及注释

本数据集包含两种冰鱼科（Channichthyidae）物种的基因组组装结果与配套注释信息，分别为南极鲱冰鱼（*Champsocephalus gunnari*）与温带矛冰鱼（*Champsocephalus esox*），同时附带温带外类群物种巴塔哥尼亚线纹鳚（*Eleginops maclovinus*）的基因组数据。本数据集关联以下学术论文：

> 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. 《仅有的非南极冰鱼的次生温带适应基因组学》. *Molecular Biology and Evolution*，第40卷，第3期，2023年3月，msad029，DOI: 10.1093/molbev/msad029

## 摘要

携白血特征的南极冰鱼是极端生物特化的典型范例，它们既适配南大洋常年低温的环境，同时演化出了不依赖血红蛋白的生存模式……