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A Research Strategy to Examine the Taxonomy of the Red Wolf (2020)

Chapter: Appendix E: Whole-Genome Resources

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Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
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Appendix E

Whole-Genome Resources

Whole-genome resources available for download and analysis (number of genomes in parentheses) from the GenBank public database (National Center for Biotechnology Information or NCBI).1 Genomes are listed by species, subspecies, or breed (for domestic dog), and the unique accession number is given for each relevant genome. Genomes are also listed by relevant geographic regions.-

___________________

1 See https://www.ncbi.nlm.nih.gov/.

Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
×
Species/Subspecies/Breed Group/Citation Accession Numbers^
Red Wolf (Canis rufus) – captive population
United States – 3 total
Captive breeding program 1, RKW SRR7976417
Captive breeding program 1, RKW SRR7976418
Captive breeding program 1, RKW SRR7976419
Red Wolf (Canis rufus)
Southern United States – 1 total
Texas/Louisiana UC SRR8066613
Gray Wolf (Canis lupus)
United States – 15 total
Alaska (9 genomes, 4 locations): GCA_902723875.1
GCA_902724055.1
Anaktuvuk Pass GCA_902724085.1
Cape Espenberg GCA_902724725.1
Nunalleq GCA_902725025.1
Onion Portage GCA_902725065.1
GCA_902725125.1
GCA_902725135.1
GCA_902725145.1
Yellowstone x 3 samples 1, RKW *
Wisconsin, Great Lakes 1, RKW *
Minnesota, Great Lakes 1, RKW *
Isle Royale NP, Great Lakes 1, RKW *
Canada – 7 total
Northwest Territories GCA 902724515.1
Labrador GCA 902724285.1
Quebec 1, RKW SRR4191781
Canada – 7 total
Quebec NHGRI SRR7107954
Algonquin (Eastern wolf) 1, RKW SSR7976407
Algonquin (Eastern wolf) 1, RKW SSR7976409
Algonquin (Eastern Timber wolf) UC SRR8066610
Mexican Gray Wolf (Canis lupus baileyi)
United States – 1 total
New Mexico 1, RKW SRR7976431
Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
×
Species/Subspecies/Breed Group/Citation Accession Numbers^
Chinese Gray Wolf (Canis lupus orientalis) outgroup
San Diego Zoo GCA_007922845.1
Coyote (Canis latrans)
Western United States – 10 total
California IBE SRR1518485
California IBE SRR1518486
California IBE SRR1518487
California NHGRI SRR7107770
California 1, RKW SRR7976411
California UM SRR3574870
Alaska UC SRR8049186
Missouri UC SRR8049188
Midwest IBE SRR1518489
Midwest NHGRI SRR7107772
Northeastern United States/Canada – 4 total
Ohio 1, RKW SRR4381545
Ohio 1, RKW SRR7976430
Quebec 1, RKW SRR7976434
Illinois 1, RKW SRR7976416
Southeastern United States/Mexico – 7 total
Florida 1, RKW SRR3960583
Florida 1, RKW SRR4029416
Florida 1, RKW SRR7976412
Alabama 1, RKW SRR7976409
Alabama IBE SRR1518488
Alabama NHGRI SRR7107771
Mexico UC SRR8049187
Domestic Dog (Canis lupus familiaris)
Historical samples
Greenland - historical GCA_902724955.1
Russia - historical GCA_902724965.1
Modern samples
boxer (released in 2020) dog10k GCF_000002285.3
basenji (released in 2020) dog10k GCA_013276365.1
German Shepherd (released in 2020) dog10k GCA_008641055.3
German Shepherd (released in 2020) dog10k GCA_011100685.1
Labrador Retriever (released in 2019) dog10k GCA_014441545.1
Great Dane (released in 2019) dog10k CGA_005444595.1
Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
×
Species/Subspecies/Breed Group/Citation Accession Numbers^
United States – 7 total
Alaska: GCA_902724585.1
Deering GCA_902724695.1
GCA_902724735.1
GCA_902724845.1
GCA_902724935.1
GCA_902725015.1
GCA_902725165.1
Canada – 8 total
Fort Churchill GCA_902724315.1
Kuuk GCA_902724255.1
Qilalukan GCA_902724295.1
GCA_902724785.1
GCA_902724795.1
GCA_902724815.1
GCA_902724885.1
GCA_902724905.1
Greenland – 30 total
Obersten GCA_902724145.1
Thule GCA 902724165.1
Nuuk GCA_902724215.1
Hekla Havn GCA_902724235.1
Scorsbysund GCA_902724245.1
Siorapaluk GCA_902724305.1
Saunders Island GCA 902724575.1
Uummannaq GCA_902724595.1
Tasiilaq GCA_902724605.1
GCA_902724615.1
GCA 902724625.1
GCA_902724645.1
GCA_902724675.1
GCA_902724745.1
GCA_902724755.1
GCA_902724765.1
GCA_902724775.1
GCA_902724805.1
GCA_902724825.1
GCA 902724855.1
GCA 902724865.1
GCA 902724875.1
GCA 902724895.1
GCA 902724915.1
GCA 902724925.1
GCA_902725005.1
GCA_902725035.1
GCA_902725045.1
GCA_902725055.1
GCA 902725075.1
Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
×
Species/Subspecies/Breed Group/Citation Accession Numbers^
Russia – 3 total
Nenets GCA_902724945.1
Kamchatka GCA_902724975.1
Chuchki GCA 902725115.1

^ If accession numbers (beginning with GCA) are not available then raw data numbers (beginning with SRR) are provided along with a citation or submitting institution/source for the sequences, or both, to contact to obtain the compiled genome sequence/contigs.

* SRR number is not available but raw sequences and/or genomic sequences/contigs can be obtained by directly contacting Robert Wayne at UCLA.

1 = vonHoldt BM, Cahill JA, Fan Z, Gronau I, Robinson J, Pollinger JP, Shapiro B, Wall J, Wayne RK. 2016. Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. Science Advances, 2(7):e1501714. doi:10.1126/sciadv.

RKW = Robert K. Wayne at UCLA

UM = University of Michigan

UC = University of Copenhagen

IBE = IBE CSIS-Universitat Pompeau Fabra

NHGRI = National Human Genome Research Institute, NIH

Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
×

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Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
×
Page 113
Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
×
Page 114
Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
×
Page 115
Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
×
Page 116
Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
×
Page 117
Suggested Citation:"Appendix E: Whole-Genome Resources." National Academies of Sciences, Engineering, and Medicine. 2020. A Research Strategy to Examine the Taxonomy of the Red Wolf. Washington, DC: The National Academies Press. doi: 10.17226/25891.
×
Page 118
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A Research Strategy to Examine the Taxonomy of the Red Wolf provides independent guidance about taxonomic research on the red wolf, Canis rufus. Building from the 2019 report Evaluating the Taxonomic Status of the Mexican Gray Wolf and the Red Wolf, this report reviews and ranks research applications to determine the taxonomy of wild canid populations in southern Louisiana and other relevant locations. The report then develops a research strategy to examine the evolutionary relationships between ancient red wolves, the extant managed red wolf populations, and the unidentified canid populations.

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