De novo Assembly and Annotation of the Blood Transcriptome of the Southern Elephant Seal Mirounga leonina from the South Shetland Islands, Antarctica
The southern elephant seal Mirounga leonina is the largest member of the phocid seals and is a highly sexually dimorphic predator at circumpolar regions. In this study, we generated the first high-quality de novo assembly of the blood transcriptome of M . leonina using the Illumina MiSeq platform. A...
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| Published in | Ocean science journal Vol. 54; no. 2; pp. 307 - 315 |
|---|---|
| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Seoul
Korea Institute of Ocean Science & Technology and The Korean Society of Oceanography
01.06.2019
Springer Nature B.V 한국해양과학기술원 |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1738-5261 2005-7172 |
| DOI | 10.1007/s12601-019-0011-0 |
Cover
| Abstract | The southern elephant seal
Mirounga leonina
is the largest member of the phocid seals and is a highly sexually dimorphic predator at circumpolar regions. In this study, we generated the first high-quality
de novo
assembly of the blood transcriptome of
M
.
leonina
using the Illumina MiSeq platform. A total of 40.5 million raw reads were obtained and assembled using the Oases assembly platform, resulting in 46,445 contigs with an N50 value of 634 bp. We performed functional gene annotations through pathway analyses of the Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Ortholog comparison revealed that a high proportion of the
M
.
leonina
blood transcriptome had significant sequence homology within pinnipeds.
M. leonine
, a deep and long-diving seal, is routinely exposed to progressive hypoxia during dives. KEGG analyses detected an intact hypoxia-inducible factor-1 (HIF-1) signaling pathway, which is a key metabolism pathway in the adaptive homeostatic responses to hypoxia. In the blood transcriptome, many essential genes involved in innate immunity were detected, which suggests that the blood serves as a host defense modulator against exogenous infections in
M. leonina
. This genomic resource will be useful for understanding adaptive metabolism upon repeated breath-hold dives and determining the health status of southern elephant seals without the need to sacrifice them in experiments. |
|---|---|
| AbstractList | The southern elephant seal Mirounga leonina is the largest member of the phocid seals and is a highly sexually dimorphic predator at circumpolar regions. In this study, we generated the first high-quality de novo assembly of the blood transcriptome of M. leonina using the Illumina MiSeq platform. A total of 40.5 million raw reads were obtained and assembled using the Oases assembly platform, resulting in 46,445 contigs with an N50 value of 634 bp. We performed functional gene annotations through pathway analyses of the Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Ortholog comparison revealed that a high proportion of the M. leonina blood transcriptome had significant sequence homology within pinnipeds. M. leonine, a deep and long-diving seal, is routinely exposed to progressive hypoxia during dives. KEGG analyses detected an intact hypoxia-inducible factor-1 (HIF-1) signaling pathway, which is a key metabolism pathway in the adaptive homeostatic responses to hypoxia. In the blood transcriptome, many essential genes involved in innate immunity were detected, which suggests that the blood serves as a host defense modulator against exogenous infections in M. leonina. This genomic resource will be useful for understanding adaptive metabolism upon repeated breath-hold dives and determining the health status of southern elephant seals without the need to sacrifice them in experiments. KCI Citation Count: 0 The southern elephant seal Mirounga leonina is the largest member of the phocid seals and is a highly sexually dimorphic predator at circumpolar regions. In this study, we generated the first high-quality de novo assembly of the blood transcriptome of M . leonina using the Illumina MiSeq platform. A total of 40.5 million raw reads were obtained and assembled using the Oases assembly platform, resulting in 46,445 contigs with an N50 value of 634 bp. We performed functional gene annotations through pathway analyses of the Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Ortholog comparison revealed that a high proportion of the M . leonina blood transcriptome had significant sequence homology within pinnipeds. M. leonine , a deep and long-diving seal, is routinely exposed to progressive hypoxia during dives. KEGG analyses detected an intact hypoxia-inducible factor-1 (HIF-1) signaling pathway, which is a key metabolism pathway in the adaptive homeostatic responses to hypoxia. In the blood transcriptome, many essential genes involved in innate immunity were detected, which suggests that the blood serves as a host defense modulator against exogenous infections in M. leonina . This genomic resource will be useful for understanding adaptive metabolism upon repeated breath-hold dives and determining the health status of southern elephant seals without the need to sacrifice them in experiments. The southern elephant seal Mirounga leonina is the largest member of the phocid seals and is a highly sexually dimorphic predator at circumpolar regions. In this study, we generated the first high-quality de novo assembly of the blood transcriptome of M. leonina using the Illumina MiSeq platform. A total of 40.5 million raw reads were obtained and assembled using the Oases assembly platform, resulting in 46,445 contigs with an N50 value of 634 bp. We performed functional gene annotations through pathway analyses of the Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Ortholog comparison revealed that a high proportion of the M. leonina blood transcriptome had significant sequence homology within pinnipeds. M. leonine, a deep and long-diving seal, is routinely exposed to progressive hypoxia during dives. KEGG analyses detected an intact hypoxia-inducible factor-1 (HIF-1) signaling pathway, which is a key metabolism pathway in the adaptive homeostatic responses to hypoxia. In the blood transcriptome, many essential genes involved in innate immunity were detected, which suggests that the blood serves as a host defense modulator against exogenous infections in M. leonina. This genomic resource will be useful for understanding adaptive metabolism upon repeated breath-hold dives and determining the health status of southern elephant seals without the need to sacrifice them in experiments. |
| Author | Kim, Bo-Mi Park, Hyun Kang, Seunghyun Rhee, Jae-Sung Ahn, Do-Hwan Jeong, Jihye Kim, Jeong-Hoon Jo, Euna |
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| Copyright | Korea Institute of Ocean Science & Technology (KIOST) and the Korean Society of Oceanography (KSO) and Springer Science+Business Media B.V. 2019 Copyright Springer Nature B.V. 2019 |
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PLoS One 12:e0169366 AkiraSUematsuSTakeuchiOPathogen recognition and innate immunity2006124783801 KimB-MAhnD-HKimJ-HJungJ-WRheeJ-SParkHDe novo assembly and annotation of the blood transcriptome of the southern giant petrel Macronectes giganteus from the South Shetland Islands, AntarcticaMar Genomics201842636610.1016/j.margen.2018.05.003 MoreyJSBurek HuntingtonKACampbellMClaussTMGoertzCEHobbsRCLunardiDMoorsAJNeelyMGSchwackeLHVan DolahFMDe novo transcriptome assembly and RNA-Seq expression analysis in blood from beluga whales of Bristol Bay, AKMar Genomics201735779210.1016/j.margen.2017.08.001 Zenteno-SavínTVazquez-MedinaJPCantu-MedellinNPonganisPJElsnerRAbeleDVazquez-MedinaJPZenteno-SavinTIschemia/reperfusion in diving birds and mammals: how they avoid oxidative damageOxidative stress aquatic ecosystems2012OxfordWiley-Blackwell178190 ChaussabelDAssessment of immune status using blood transcriptomics and potential implications for global healthSemin Immunol201527586610.1016/j.smim.2015.03.002 CrockerDEKhudyakovJIChampagneCDOxidative stress in northern elephant seals: integration of omics approaches with ecological and experimental studiesComp Biochem Phys A20162009410310.1016/j.cbpa.2016.02.011 ConesaAGötzSGarcía-GómezJMTerolJTalónMRoblesMBlast2GO: a universal tool for annotation, visualization and analysis in functional genomics researchBioinformatics2005213674367610.1093/bioinformatics/bti610 11_CR12 A Mortazavi (11_CR23) 2008; 5 M Biuw (11_CR2) 2007; 104 S Mohr (11_CR20) 2007; 13 JS Morey (11_CR22) 2017; 35 AM Bolger (11_CR3) 2014; 30 JP Vázquez-Medina (11_CR26) 2011; 214 DE Crocker (11_CR6) 2016; 200 D Chaussabel (11_CR4) 2015; 27 GJG Hofmeyr (11_CR13) 2015 J Spitz (11_CR25) 2015; 187 A Gordon (11_CR11) 2010 A Conesa (11_CR5) 2005; 21 E Humble (11_CR14) 2016; 16 S Akira (11_CR1) 2006; 124 R Elsner (11_CR8) 1999 CR McMahon (11_CR19) 2005; 35 MH Schulz (11_CR24) 2012; 28 T Zenteno-Savín (11_CR27) 2012 R Elsner (11_CR7) 1983 RM Laws (11_CR18) 1994 AD Foote (11_CR10) 2015; 47 A Fabrizius (11_CR9) 2016; 17 JI Khudyakov (11_CR16) 2015; 16 P Johnson (11_CR15) 2005; 39 JS Morey (11_CR21) 2016; 17 B-M Kim (11_CR17) 2018; 42 |
| References_xml | – reference: JohnsonPElsnerRZenteno-SavínTHypoxia inducible factor proteomics and diving adaptations in ringed sealFree Radical Bio Me20053920521210.1016/j.freeradbiomed.2005.03.008 – reference: KhudyakovJIPreeyanonLChampagneCDOrtizRMCrockerDETranscriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insightsBMC Genomics2015166410.1186/s12864-015-1253-6 – reference: MohrSLiewCCThe peripheral-blood transcriptome: new insights into disease and risk assessmentTrends Mol Med20071342243210.1016/j.molmed.2007.08.003 – reference: HofmeyrGJGMirounga leoninaThe IUCN Red List of Threatened Species 20152015 – reference: Hoff ML, Fabrizius A, Czech-Damal NU, Folkow LP, Burmester T (2017) Transcriptome analysis identifies key metabolic changes in the hooded seal (Cystophora cristata) brain in response to hypoxia and reoxygenation. PLoS One 12:e0169366 – reference: Zenteno-SavínTVazquez-MedinaJPCantu-MedellinNPonganisPJElsnerRAbeleDVazquez-MedinaJPZenteno-SavinTIschemia/reperfusion in diving birds and mammals: how they avoid oxidative damageOxidative stress aquatic ecosystems2012OxfordWiley-Blackwell178190 – reference: ChaussabelDAssessment of immune status using blood transcriptomics and potential implications for global healthSemin Immunol201527586610.1016/j.smim.2015.03.002 – reference: GordonAHannonGFastx-toolkitFASTQ/A short-reads pre-processing tools2010 – reference: CrockerDEKhudyakovJIChampagneCDOxidative stress in northern elephant seals: integration of omics approaches with ecological and experimental studiesComp Biochem Phys A20162009410310.1016/j.cbpa.2016.02.011 – reference: FabriziusAHoffMLEnglerGFolkowLPBurmesterTWhen the brain goes diving: transcriptome analysis reveals a reduced aerobic energy metabolism and increased stress proteins in the seal brainBMC Genomics20161758310.1186/s12864-016-2892-y – reference: MortazaviAWilliamsBAMcCueKSchaefferLWoldBMapping and quantifying mammalian transcriptomes by RNAseqNat Methods2008562162810.1038/nmeth.1226 – reference: Vázquez-MedinaJPZenteno-SavínTTiftMSFormanHJCrockerDEOrtizRMApnea stimulates the adaptive response to oxidative stress in elephant seal pupsJ Exp Biol20112144193420010.1242/jeb.063644 – reference: SpitzJBecquetVRosenDATritesAWA nutrigenomic approach to detect nutritional stress from gene expression in blood samples drawn from Steller sea lionsComp Biochem Phys A201518721422310.1016/j.cbpa.2015.02.006 – reference: ElsnerRLiving in water: solutions to physiological problemsReynolds III JE, Rommel SA (eds) Biology of marine mammals1999Washington DCSmithsonian Institution Press73116 – reference: KimB-MAhnD-HKimJ-HJungJ-WRheeJ-SParkHDe novo assembly and annotation of the blood transcriptome of the southern giant petrel Macronectes giganteus from the South Shetland Islands, AntarcticaMar 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| Snippet | The southern elephant seal
Mirounga leonina
is the largest member of the phocid seals and is a highly sexually dimorphic predator at circumpolar regions. In... The southern elephant seal Mirounga leonina is the largest member of the phocid seals and is a highly sexually dimorphic predator at circumpolar regions. In... |
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| SubjectTerms | Aquatic mammals Aquatic Pollution Blood Earth and Environmental Science Earth Sciences Encyclopaedias Genes Genomes Hypoxia Immunity Marine & Freshwater Sciences Marine mammals Metabolism Mirounga leonina Oases Oceanography Predators Seals Waste Water Technology Water Management Water Pollution Control 해양학 |
| Title | De novo Assembly and Annotation of the Blood Transcriptome of the Southern Elephant Seal Mirounga leonina from the South Shetland Islands, Antarctica |
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