De novo Assembly and Annotation of the Blood Transcriptome of the Southern Elephant Seal Mirounga leonina from the South Shetland Islands, Antarctica

Kim, Bomi; Ahn, Do-Hwan; Kang, Seunghyun; Jeong, Jihye; Jo, Euna; Kim, Jeong-Hoon; Rhee, Jae-Sung; Park, Hyun

doi:10.1007/s12601-019-0011-0

Cited by 3 publications

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“…The genomic DNA of the southern elephant seal, Mirounga leonina, (Figure 1) was extracted from the blood specimen as described in our previous study [8]; approximately 1 mL of blood sample was collected from a single elephant seal on King George Island, South Shetland Islands, Antarctica. The blood sample (200 µL) was used to obtain high molecular weight gDNA using the QIAGEN MagAttract HMW DNA kit (QIAGEN, Germantown, MD, USA) according to the manufacturer's protocol.…”

Section: Methodsmentioning

confidence: 99%

“…Ab initio gene prediction was performed using SNAP (SNAP, RRID:SCR 002127) [14] and Augustus (Augustus: Gene Prediction, RRID:SCR 008417). MAKER was initially run in est2genome mode, which was based on transcripts for M. leonina generated from the previous results [8]. As further evidence for the annotation, reference proteins from other sequenced mammal species (Arctocephalus gazelle, Leptonychotes weddellii, Odobenus rosmarus, Tursiops truncates, Orcinus orca, Trichechus manatus latirostris, Canis lupus familiaris, Felis catus, Equus caballus, and Homo sapiens) were used in the analysis.…”

Section: Methodsmentioning

confidence: 99%

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

Kim

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Kim

et al. 2020

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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.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%