Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld 33501, Germany.
Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld 33501, Germany.
G3 (Bethesda). 2024 Nov 6;14(11). doi: 10.1093/g3journal/jkae179.
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 Universal Single-Copy Orthologs score raised from 84.7% to 95.2%. We furthermore included the new genome in a reference-free alignment of the genomes of 11 pinniped species to characterize evolutionary conservation across the Pinnipedia using genome-wide Genomic Evolutionary Rate Profiling. We then implemented Gene Ontology enrichment analyses to identify biological processes associated with those genes showing the highest levels of either conservation or differentiation between the 2 major pinniped families, the Otariidae and Phocidae. We show that processes linked to neuronal development, the circulatory system, and osmoregulation are overrepresented both in conserved as well as in differentiated regions of the genome.
南极软毛海豹（Arctocephalus gazella）是一种重要的顶级掠食者，也是南大洋生态系统健康的指示物种。尽管数量丰富，但由于历史上的海豹捕猎，该物种曾濒临灭绝，目前正由于气候变化而减少。基因组工具对于理解这些人为影响和预测长期生存能力至关重要。然而，当前的参考基因组（“arcGaz3”）在完整性和连续性方面都有很大的改进空间。因此，我们结合了 PacBio 测序、单倍型感知 HiRise 组装以及基于 Hi-C 信息的支架构建，生成了南极软毛海豹参考基因组的精细组装（“arcGaz4_h1”）。新的组装体长 2.53Gb，支架 N50 为 55.6Mb，包含 18 个染色体大小的支架，与 otariids 中预期的 18 条染色体相对应。基因组完整性得到了极大的提高，包含了 23408 个注释基因，Benchmarking Universal Single-Copy Orthologs 评分从 84.7%提高到 95.2%。此外，我们将新基因组纳入了 11 种鳍足类物种的无参考基因组比对中，使用全基因组基因组进化率分析（Genomic Evolutionary Rate Profiling）来描述鳍足类动物中的进化保守性。然后，我们实施了基因本体论富集分析，以确定与那些在 2 个主要鳍足类家族（Otariidae 和 Phocidae）之间表现出最高保守性或分化程度的基因相关的生物学过程。我们发现，与神经元发育、循环系统和渗透压调节相关的过程在基因组的保守和分化区域都有较高的代表性。
