The Genome Assembly and Annotation of the Southern Elephant Seal Mirounga leonina

Bo-Mi Kim,Jeong-Hoon Kim,Hyun Park,Euna Jo,Young Min Chi,Seung Jae Lee,Seunghyun Kang,Jin-Hyoung Kim,Yoon Jin Lee,Jun Hyuck Lee

doi:10.3390/genes11020160

Abstract

The southern elephant seal Mirounga leonina is the largest phocid seal and one of the two species of elephant seals. They are listed as ‘least concern’ by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species 2015. Here, we have assembled the reference genome for M. leonina using the 10× chromium sequencing platform. The final genome assembly of M. leonina was 2.42 Gb long, with a contig N50 length of 54 Mb and a maximum length of 111.6 Mb. The M. leonina genome contained 20,457 predicted protein-coding genes and possessed 41.51% repeated sequences. The completeness of the M. leonina genome was evaluated using benchmarking universal single-copy orthologous genes (BUSCOs): the assembly was highly complete, containing 95.6% of the core set of mammalian genes. The high-quality genomic information on M. leonina will be essential for further understanding of adaptive metabolism upon repeated breath-hold dives and the exploration of molecular mechanisms contributing to its unique biochemical and physiological characteristics. The southern elephant seal genome project was deposited at NCBI (National Center for Biotechnology Information) under BioProject number PRJNA587380.

Highlights

Elephant seals have been highlighted as a crucial animal model for studying their unique behavior, physiology, population dynamics, and geographical distribution
Seals undergo a long fasting period, and the energy generated from the blubber-fat allows them stay on land for over a month without food and water
The number of scaffolds in the southern elephant seal genome assembly was 1.115, and 54 scaffolds were over 10 Mb long and occupied 90.6% of our assembly (Supplementary Table S1.)

Summary

Introduction

Elephant seals have been highlighted as a crucial animal model for studying their unique behavior, physiology, population dynamics, and geographical distribution. Genome information of M. leonina could help to understand the unique physiological and metabolic adaptations, such as the ability to spend large amounts of time in the sea as a mammal, survive in a frigid environment, perform repeated breath-hold dives, engage in deep-diving and long-ranging predation, tolerate routine hypoxia, and fast during the nursing period. The de novo genome assembly was performed using the paired-end sequence reads from the partitioned library as input for the Supernova assembler (RRID:SCR 016756) v2.1.1 (10× Genomics, San Francisco, CA, USA) [9] with default parameters.

Results

Conclusion