A Research Strategy to Examine the Taxonomy of the Red Wolf (2020)
Chapter: Appendix E: Whole-Genome Resources
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Appendix E
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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.
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.-
___________________
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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