Novel Megaptera novaeangliae (Humpback whale) haplotype chromosome-level reference genome.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
10 Oct 2024
10 Oct 2024
Historique:
received:
21
05
2024
accepted:
23
09
2024
medline:
11
10
2024
pubmed:
11
10
2024
entrez:
10
10
2024
Statut:
epublish
Résumé
The sequencing of a kidney sample (KW2013002) from a stranded Megaptera novaeangliae (Humpback whale) calf is the first chromosome-level reference genome for this species
Identifiants
pubmed: 39389970
doi: 10.1038/s41597-024-03922-9
pii: 10.1038/s41597-024-03922-9
doi:
Types de publication
Journal Article
Dataset
Langues
eng
Sous-ensembles de citation
IM
Pagination
1113Informations de copyright
© 2024. The Author(s).
Références
Carminati, M.-V. G. et al. Megaptera novaeangliae isolate KW2013002, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBGMDX010000001.1 (2024).
Jackson, J. A. et al. Global diversity and oceanic divergence of humpback whales (Megaptera novaeangliae). Proc. R. Soc. B 281, 1786, https://doi.org/10.1098/rspb.2013.3222 (2014).
doi: 10.1098/rspb.2013.3222
Roman, J. & McCarthy, J. J. The whale pump: marine mammals enhance primary productivity in a coastal basin. PLoS One 5, 10, https://doi.org/10.1371/journal.pone.0013255 (2010).
doi: 10.1371/journal.pone.0013255
McGowen, M. R. et al. Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture. Syst. Biol. 69, 479–501, https://doi.org/10.1093/sysbio/syz068 (2020).
doi: 10.1093/sysbio/syz068
Morin, P. A. et al. Building genomic infrastructure: Sequencing platinum‐standard reference‐quality genomes of all cetacean species. Marine Mammal Science 36(4), 1356–1366, https://doi.org/10.1111/mms.12721 (2020).
doi: 10.1111/mms.12721
GenBank. Megaptera novaeangliae (humpback whale) genome assembly, megNov1, GCA_004329385.1. National Center for Biotechnology Information (NCBI). Available from: https://www.ncbi.nlm.nih.gov/assembly/GCA_004329385.1 (2019).
Tollis, M. et al. Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae). Molecular Biology and Evolution 36(8), 1746–1763, https://doi.org/10.1093/molbev/msz099 (2019).
doi: 10.1093/molbev/msz099
Carminati, M.-V. G. et al. Novel Megaptera novaeangliae (Humpback whale) haplotype reference genome [Dataset]. Dryad https://doi.org/10.5061/dryad.dv41ns271 (2024).
NCBI Sequence Read Archive https://www.ncbi.nlm.nih.gov/sra/SRP506011 (2024).
GenBank. Balaenoptera musculus (blue whale) genome assembly, mBalMus1.pri.v3, GCA_009873245.3. National Center for Biotechnology Information (NCBI). Available from: https://www.ncbi.nlm.nih.gov/assembly/GCA_009873245.3 (2020).
Katoh, K., Rozewicki, J. & Yamada, K. D. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20(4), 1160–1166, https://doi.org/10.1093/bib/bbx108 (2019).
doi: 10.1093/bib/bbx108
Allio, R., Donegà, S., Galtier, N. & Nabholz, B. Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker. Molecular Biology and Evolution 34(11), 2762–2772, https://doi.org/10.1093/molbev/msx197 (2017).
doi: 10.1093/molbev/msx197
Cummins, J. Mitochondrial DNA in mammalian reproduction. Reviews of reproduction 3(3), 172–182, https://doi.org/10.1530/ror.0.0030172 (1998).
doi: 10.1530/ror.0.0030172
Carminati, M.-V. G. et al. Megaptera novaeangliae voucher NIST KW2013002 mitochondrion, complete genome. https://identifiers.org/ncbi/nucleotide:PP475430.1 (2024).
Genome Assembly mEubGla1.1hap2.+XY (Eubalena glacialis), https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_028564815.1/ (2023).
Genome Assembly mBalAcu1.1 (Balaenoptera acutorostrata), https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_949987535.1/ (2023).
Genome Assembly mBalRic1.hap2 (Balaenoptera ricei) https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_028023285.1/ (2023).
Genome Assembly mTurTru1.mat.Y (Tursiops truncatus) https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_011762595.1/ (2020).
Genome Assembly mOrcOrc1.1 (Orcinus orca) https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_937001465.1/ (2022).
Genome Assembly mKogBre1haplotype1 (Kogia breviceps) https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_026419965.1/ (2022).
Genome Assembly ASM283717v5 (Physeter catodon), https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002837175.3/ (2023).
Genome Assembly Loxafr3.0 (Loxodonta africana, https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001905.1/ (2009).
Genome Assembly mHipAmp2.hap2 (Hippopotamus amphibius kiboko) https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_030028045.1/ (2023).
Eschrichtius robustus Genome sequencing and assembly https://www.ncbi.nlm.nih.gov/bioproject/PRJNA707533/ (2023).
Genome Assembly Oros_1.0 (Odobenus rosmarus divergens), https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000321225.1/ (2013).
Genome Assembly TriManLat1.0 (Trichechus manatus latirostris), https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000243295.1/ (2012).
Genome assembly Neophocaena_asiaeorientalis_V1.1 (Neophocaena asiaeorientalis asiaeorientalis), https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_003031525.2/ (2018).
Genome Assembly mGloMel1.1 (Globicephala melas), https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_963455315.1/ (2023).
Genome assembly mMesDen1 primary haplotype (Mesoplodon densirostris), https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_025265405.1/ (2022).
Justin Chu. JupiterPlot. GitHub repository. https://github.com/JustinChu/JupiterPlot (2018).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30, 772–780, https://doi.org/10.1093/molbev/mst010 (2013).
doi: 10.1093/molbev/mst010
Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274, https://doi.org/10.1093/molbev/msu300 (2015).
doi: 10.1093/molbev/msu300
Smith, S. A. LSD2: Least-Squares Dating for Estimating Species Divergence Times. Bioinformatics 35(21), 4429–4431 (2019).
Kuznetsov, D. et al. OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic Acids Res 51, D445–D451, https://doi.org/10.1093/nar/gkac998 (2023).
doi: 10.1093/nar/gkac998