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Cetacean Genomes Project Samples

May 14, 2020

Here you can find information on what species and types of samples are needed, and how to preserve samples for genomic sequencing and annotation.

The major requirement for long-read sequencing and scaffolding is availability of fresh tissues that yield relatively large amounts of ultra-high quality (UHQ) DNA and intact chromatin, which preserves the 3D structure in the nuclei for Hi-C. These technologies currently require fresh blood, muscle or organ tissue, or cultured cells that are preserved to maintain megabase-length DNA and RNA. Preservation of genetic material  typically involves rapid freezing and storage at less than or equal to –80°C, or culture of live cells, both of which have limited feasibility for protected species (due to sampling methods) and in many field conditions. Short-term preservation in 90-percent ethanol can also be effective, at least for DNA preservation (see "Sample Collection and Shipping" link in the box to the right). 

The data table below lists samples that we have identified as likely to meet the UHQ specifications needed for PacBio long-read sequencing, BioNano optical mapping, and Hi-C chromatin-linked sequencing. 

We are seeking samples for the remaining cetacean species. If you know of appropriately preserved samples, please let us know! If you are sampling cetaceans as part of your research or a stranding network, please use the collection and storage methods described below to collect appropriate samples. Although it is not certain that resources will be available for sequencing all species, obtaining appropriate samples is the first and most critical step. Even if you plan to complete genome sequencing of the samples, please let us know so we can avoid duplication of effort.

 

Full table view: Open Dataset In New Window

Cetacean Genomes Samples

IDCommon_English_nameGenusSpeciesSubspeciesLocalityTissue_typeSexStorageComments
6Bowhead WhaleBalaenamysticetuskidneyFLiquid_N2samples provided to DNAzoo, 2019
4Bryde's WhaleBalaenopteraedenikidneyFLiquid_N2samples provided to DNAzoo, 2019
97Fin WhaleBalaenopteraphysalusUNKNOWNunkFLiquid_N2cultured fibroblasts
98Commerson's DolphinCephalorhynchuscommersoniiSEA WORLD, ORLANDOEYEMLiquid_N2cultured fibroblasts
132Long-Beaked Common DolphinDelphinuscapensisFluke wedge (photographed), dorsal flank wedge biopsyMLiquid_N2cultured fibroblasts
99Long-Beaked Common DolphinDelphinuscapensisUNKNOWNunkMLiquid_N2cultured fibroblasts
100Long-Beaked Common DolphinDelphinuscapensisUSASKINMLiquid_N2cultured fibroblasts
101Long-Beaked Common DolphinDelphinuscapensisUSASKINMLiquid_N2cultured fibroblasts
102Long-Beaked Common DolphinDelphinuscapensisUSASKINFLiquid_N2cultured fibroblasts
103Short-Beaked Common DolphinDelphinusdelphisBLACK'S BEACHBACK NEAR DORSAL FINMLiquid_N2cultured fibroblasts
104Short-Beaked Common DolphinDelphinusdelphisUNKNOWNunkFLiquid_N2cultured fibroblasts
105Short-Beaked Common DolphinDelphinusdelphisSEA WORLDCORNEAMLiquid_N2cultured fibroblasts
106Short-Beaked Common DolphinDelphinusdelphisCALIFORNIASKINFLiquid_N2cultured fibroblasts
20Gray WhaleEschrichtiusrobustuskidneyFLiquid_N2samples provided to DNAzoo, 2019
107Gray WhaleEschrichtiusrobustusSANTA BARBARACORNEAMLiquid_N2cultured fibroblasts
22North Atlantic Right WhaleEubalaenaglacialiskidneyMLiquid_N2samples provided to DNAzoo, 2019
108Pygmy Killer WhaleFeresaattenuataMEXICOFLANKMLiquid_N2cultured fibroblasts
141Short-Finned Pilot WhaleGlobicephalamacrorhynchusBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
142Short-Finned Pilot WhaleGlobicephalamacrorhynchusBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
143Short-Finned Pilot WhaleGlobicephalamacrorhynchusBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
144Short-Finned Pilot WhaleGlobicephalamacrorhynchusBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
145Short-Finned Pilot WhaleGlobicephalamacrorhynchusBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
146Short-Finned Pilot WhaleGlobicephalamacrorhynchusBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
133Short-Finned Pilot WhaleGlobicephalamacrorhynchusBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
134Short-Finned Pilot WhaleGlobicephalamacrorhynchusBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
26Long-Finned Pilot WhaleGlobicephalamelaskidneyMLiquid_N2samples provided to DNAzoo, 2019
109Pygmy Sperm WhaleKogiabrevicepsSEA WORLD - SWC170246TRACHEAFLiquid_N2cultured fibroblasts
35Dwarf Sperm WhaleKogiasimakidneyMLiquid_N2samples provided to DNAzoo, 2019
36Atlantic White-Sided DolphinLagenorhynchusacutuskidneyFLiquid_N2samples provided to DNAzoo, 2019
110Northern Right Whale DolphinLissodelphisborealisSEA WORLDTRACHEAFLiquid_N2cultured fibroblasts
111Northern Right Whale DolphinLissodelphisborealisSEA WORLDTRACHEAFLiquid_N2cultured fibroblasts
112Humpback WhaleMegapteranovaeangliaeUSASKINMLiquid_N2cultured fibroblasts
148Blainville's Beaked WhaleMesoplodondensirostrisBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
149Blainville's Beaked WhaleMesoplodondensirostrisBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
150Blainville's Beaked WhaleMesoplodondensirostrisBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
50Blainville's Beaked WhaleMesoplodondensirostriskidneyFLiquid_N2samples provided to DNAzoo, 2019
113Blainville's Beaked WhaleMesoplodondensirostrisORLANDO FLTRACHEAMLiquid_N2cultured fibroblasts
51Gervais' Beaked WhaleMesoplodoneuropaeuskidneyFLiquid_N2samples provided to DNAzoo, 2019
59Stejneger's Beaked WhaleMesoplodonstejnegerikidneyFLiquid_N2samples provided to DNAzoo, 2019
114Killer WhaleOrcinusorcaSEA WORLDPLACENTAMLiquid_N2cultured fibroblasts
115Killer WhaleOrcinusorcaSEA WORLDCORDFLiquid_N2cultured fibroblasts
116Killer WhaleOrcinusorcaSEA WORLD - SWC170242BLOOD VESSELFLiquid_N2cultured fibroblasts
147Melon-Headed WhalePeponocephalaelectraBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
67Melon-Headed WhalePeponocephalaelectrakidneyMLiquid_N2samples provided to DNAzoo, 2019
131Harbour PorpoisePhocoenaphocoenaGuadalupe-Nipomo Dunes (North), Oceano, San Luis ObispoAorta, peduncle skin, tail flukeMLiquid_N2cultured fibroblasts
70Harbour PorpoisePhocoenaphocoenakidneyFLiquid_N2samples provided to DNAzoo, 2019
117VaquitaPhocoenasinusSAN FELIPE, MEXICO; NOAAR SIDE BEHIND DORSAL FINFLiquid_N2cultured fibroblasts
118VaquitaPhocoenasinusSAN FELIPE, MEXICO; NOAARIGHT MESOVARIUMFLiquid_N2cultured fibroblasts
119Sperm WhalePhysetermacrocephalusUNKNOWNFLANKMLiquid_N2cultured fibroblasts
120Sperm WhalePhysetermacrocephalusUNKNOWNunkMLiquid_N2cultured fibroblasts
73Sperm WhalePhysetermacrocephaluskidneyFLiquid_N2samples provided to DNAzoo, 2019
138False Killer WhalePseudorcacrassidensBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
139False Killer WhalePseudorcacrassidensBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
140False Killer WhalePseudorcacrassidensBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
151False Killer WhalePseudorcacrassidensBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
152False Killer WhalePseudorcacrassidensBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
153False Killer WhalePseudorcacrassidensBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
154False Killer WhalePseudorcacrassidensBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
137False Killer WhalePseudorcacrassidensBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
121Pantropical Spotted DolphinStenellaattenuataIFSFLANKFLiquid_N2cultured fibroblasts
135Pantropical Spotted DolphinStenellaattenuataBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
136Pantropical Spotted DolphinStenellaattenuataBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
84Pantropical Spotted DolphinStenellaattenuatakidneyMLiquid_N2samples provided to DNAzoo, 2019
86Clymene DolphinStenellaclymenekidneyMLiquid_N2samples provided to DNAzoo, 2019
157Striped DolphinStenellacoeruleoalbafibroblastsMLiquid_N2cultured fibroblasts
88Atlantic Spotted DolphinStenellafrontaliskidneyMLiquid_N2samples provided to DNAzoo, 2019
123Spinner DolphinStenellalongirostrisMEXICOFLANKFLiquid_N2cultured fibroblasts
89Spinner DolphinStenellalongirostrisorientaliseastern PacifickidneyFLiquid_N2samples provided to DNAzoo, 2019
122Rough-Toothed DolphinStenobredanensisMEXICOFLANKMLiquid_N2cultured fibroblasts
155Common Bottlenose DolphinTursiopstruncatusBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
156Common Bottlenose DolphinTursiopstruncatusBig Island, Hawaiiskin biopsyULiquid_N2cultured fibroblasts
124Common Bottlenose DolphinTursiopstruncatusSEA WORLDCORDMLiquid_N2cultured fibroblasts
125Common Bottlenose DolphinTursiopstruncatusSEA WORLDSKINMLiquid_N2cultured fibroblasts
126Common Bottlenose DolphinTursiopstruncatusNOSCCORNEA?FLiquid_N2cultured fibroblasts
127Common Bottlenose DolphinTursiopstruncatusSEA WORLDOVARYFLiquid_N2cultured fibroblasts
128Common Bottlenose DolphinTursiopstruncatusSEA WORLDOVARYFLiquid_N2cultured fibroblasts
129Common Bottlenose DolphinTursiopstruncatusUNKNOWNunkMLiquid_N2cultured fibroblasts
95Cuvier's Beaked WhaleZiphiuscavirostriskidneyMLiquid_N2samples provided to DNAzoo, 2019

 

Last updated by Southwest Fisheries Science Center on 08/19/2022