Genome 10K: a proposition to Obtain Whole Genome Sequence For 10,000 Vertebrate Species




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Methods:


Branch length estimates:

Appendix 1: Policy issues


  • The Genome 10K consortium members recognize this endeavor to be a noncommercial research program without “reach-through” IP agreements.

  • All individual(s)/institute(s) contributing biomaterials for sequencing thus comply with the above mentioned noncommercial policy and acknowledge that contributed samples have been collected and distributed in accordance with applicable national and international laws and regulations.

  • The reference materials used for genome sequencing should be clearly identified, accessible and where possible, adhere to best practices for biodiversity repositories (particularly concerning taxonomic identification of voucher specimens/tissues and genome size estimation [38]). Reference documentation should include digital images/CT scans of the morphological voucher specimens, geospatial coordinates of the specimen collection site [39] and other emerging metadata standards proposed for genome sequences [40].

  • Deposition and publication will follow the Ft Lauderdale agreement in accord with prior best practices in genomic research, including release of primary sequence data to the international databases within 24 hours and release of the full genome assemblies as soon as quality assurance is complete.



Appendix 2: Detailed table of classes, orders, families, genera and species


Group

Orders

Families

Genera

Species

Mammals

Afrosoricida

2/2 - 100%

7/19 - 36%

7/51 - 13%

Mammals

Artiodactyla

10/10 - 100%

81/89 - 91%

156/240 - 65%

Mammals

Carnivora

15/15 - 100%

82/126 - 65%

131/287 - 45%

Mammals

Cetacea

11/11 - 100%

38/40 - 95%

80/84 - 95%

Mammals

Chiroptera

13/18 - 72%

74/203 - 36%

162/1116 - 14%

Mammals

Cingulata

1/1 - 100%

3/9 - 33%

4/21 - 19%

Mammals

Dasyuromorphia

2/3 - 66%

3/23 - 13%

3/71 - 4%

Mammals

Dermoptera

1/1 - 100%

1/2 - 50%

1/2 - 50%

Mammals

Didelphimorphia

1/1 - 100%

6/17 - 35%

8/87 - 9%

Mammals

Diprotodontia

11/11 - 100%

19/39 - 48%

27/143 - 18%

Mammals

Erinaceomorpha

1/1 - 100%

4/10 - 40%

6/24 - 25%

Mammals

Hyracoidea

1/1 - 100%

3/3 - 100%

4/4 - 100%

Mammals

Lagomorpha

2/3 - 66%

7/13 - 53%

16/92 - 17%

Mammals

Macroscelidea

1/1 - 100%

3/4 - 75%

3/15 - 20%

Mammals

Microbiotheria

1/1 - 100%

1/1 - 100%

1/1 - 100%

Mammals

Monotremata

2/2 - 100%

2/3 - 66%

2/5 - 40%

Mammals

Notoryctemorphia

1/1 - 100%

1/1 - 100%

1/2 - 50%

Mammals

Paucituberculata

1/1 - 100%

3/3 - 100%

3/6 - 50%

Mammals

Peramelemorphia

2/3 - 66%

3/8 - 37%

3/21 - 14%

Mammals

Perissodactyla

3/3 - 100%

6/6 - 100%

16/17 - 94%

Mammals

Pholidota

1/1 - 100%

1/1 - 100%

6/8 - 75%

Mammals

Pilosa

4/4 - 100%

5/5 - 100%

7/10 - 70%

Mammals

Primates

14/15 - 93%

54/69 - 78%

145/376 - 38%

Mammals

Proboscidea

1/1 - 100%

2/2 - 100%

3/3 - 100%

Mammals

Rodentia

29/33 - 87%

118/481 - 24%

274/2277 - 12%

Mammals

Scandentia

2/2 - 100%

3/5 - 60%

9/20 - 45%

Mammals

Sirenia

2/2 - 100%

2/3 - 66%

2/5 - 40%

Mammals

Soricomorpha

3/4 - 75%

19/45 - 42%

26/428 - 6%

Mammals

Tubulidentata

1/1 - 100%

1/1 - 100%

1/1 - 100%

Birds

Anseriformes

3/3 - 100%

41/52 - 78%

129/162 - 79%

Birds

Apodiformes

2/3 - 66%

97/125 - 77%

238/429 - 55%

Birds

Caprimulgiformes

5/5 - 100%

17/22 - 77%

47/118 - 39%

Birds

Charadriiformes

14/18 - 77%

66/90 - 73%

208/383 - 54%

Birds

Ciconiiformes

3/3 - 100%

32/39 - 82%

69/116 - 59%

Birds

Coliiformes

1/1 - 100%

2/2 - 100%

5/6 - 83%

Birds

Columbiformes

1/2 - 50%

31/44 - 70%

129/311 - 41%

Birds

Coraciiformes

9/11 - 81%

34/51 - 66%

96/209 - 45%

Birds

Cuculiformes

1/1 - 100%

22/36 - 61%

53/138 - 38%

Birds

Falconiformes

3/3 - 100%

60/83 - 72%

145/304 - 47%

Birds

Galliformes

5/5 - 100%

56/80 - 70%

131/290 - 45%

Birds

Gaviiformes

1/1 - 100%

1/1 - 100%

3/5 - 60%

Birds

Gruiformes

9/10 - 90%

32/59 - 54%

73/196 - 37%

Birds

Musophagiformes

1/1 - 100%

5/6 - 83%

16/23 - 69%

Birds

Opisthicomiformes

1/1 - 100%

1/1 - 100%

1/1 - 100%

Birds

Passeriformes

90/107 - 84%

838/1226 - 68%

2796/5756 - 48%

Birds

Pelecaniformes

7/7 - 100%

8/9 - 88%

30/62 - 48%

Birds

Phaethontiformes

1/1 - 100%

1/1 - 100%

3/3 - 100%

Birds

Phoenicopteriformes

1/1 - 100%

3/3 - 100%

4/5 - 80%

Birds

Piciformes

5/5 - 100%

53/68 - 77%

255/398 - 64%

Birds

Podicipediformes

1/1 - 100%

5/6 - 83%

11/22 - 50%

Birds

Procellariiformes

4/4 - 100%

19/27 - 70%

52/112 - 46%

Birds

Psittaciformes

1/1 - 100%

67/85 - 78%

186/364 - 51%

Birds

Sphenisciformes

1/1 - 100%

6/6 - 100%

13/17 - 76%

Birds

Strigiformes

2/2 - 100%

21/29 - 72%

64/195 - 32%

Birds

Struthioniformes

6/6 - 100%

14/15 - 93%

37/59 - 62%

Birds

Trogoniformes

1/1 - 100%

5/6 - 83%

25/39 - 64%

Amphibians

Anura

32/48 - 66%

107/411 - 26%

302/5532 - 5%

Amphibians

Caudata

10/10 - 100%

32/66 - 48%

86/552 - 15%

Amphibians

Gymnophiona

3/3 - 100%

5/33 - 15%

6/176 - 3%

Reptiles

Testudines

10/14 - 71%

43/98 - 43%

60/295 20%

Reptiles

Sphenodontia

0/1 - 0%

0/1 - 0%

0/1 0%

Reptiles

Squamata

35/41 - 85%

309/758 - 40%

735/3996 18%

Reptiles




1/1 - 100%

8/9 - 89%

21/25 - 84%

Fishes

Petromyzontiformes

1/1 - 100%

2/10 - 20%

2/38 - 5%

Fishes

Myxiniformes

1/1 - 100%

2/6 - 33%

3/24 - 12%

Fishes

Rajiformes

1/1 - 100%

8/16 - 50%

25/107 - 23%

Fishes

Torpediniformes

2/4 - 50%

2/5 - 40%

5/15 - 33%

Fishes

Heterodontiformes

1/1 - 100%

1/1 - 100%

3/5 - 60%

Fishes

Squaliformes

1/1 - 100%

2/2 - 100%

14/19 - 73%

Fishes

Orectolobiformes

5/5 - 100%

7/8 - 87%

13/17 - 76%

Fishes

Carcharhiniformes

6/8 - 75%

27/37 - 72%

70/140 - 50%

Fishes

Echinorhiniformes

1/1 - 100%

1/1 - 100%

1/1 - 100%

Fishes

Lamniformes

5/5 - 100%

8/10 - 80%

11/14 - 78%

Fishes

Hexanchiformes

3/3 - 100%

4/4 - 100%

5/6 - 83%

Fishes

Chimaeriformes

3/3 - 100%

4/4 - 100%

9/18 - 50%

Fishes

Lepidosireniformes

2/2 - 100%

2/2 - 100%

2/8 - 25%

Fishes

Ceratodontiformes

0/1 - 0%

0/1 - 0%

0/1 - 0%

Fishes

Coelacanthiformes

1/1 - 100%

1/1 - 100%

1/2 - 50%

Fishes

Acipenseriformes

2/2 - 100%

3/7 - 42%

5/38 - 13%

Fishes

Semionotiformes

1/1 - 100%

2/2 - 100%

4/7 - 57%

Fishes

Amiiformes

1/1 - 100%

1/1 - 100%

1/1 - 100%

Fishes

Elopiformes

2/2 - 100%

2/2 - 100%

5/7 - 71%

Fishes

Anguilliformes

14/15 - 93%

27/70 - 38%

52/159 - 32%

Fishes

Clupeiformes

4/6 - 66%

20/53 - 37%

38/142 - 26%

Fishes

Cypriniformes

4/5 - 80%

43/327 - 13%

92/1588 - 5%

Fishes

Characiformes

10/13 - 76%

44/104 - 42%

78/325 - 24%

Fishes

Siluriformes

14/37 - 37%

45/282 - 15%

71/929 - 7%

Fishes

Gymnotiformes

4/7 - 57%

5/21 - 23%

5/45 - 11%

Fishes

Esociformes

2/2 - 100%

4/4 - 100%

7/11 - 63%

Fishes

Salmoniformes

4/4 - 100%

17/36 - 47%

27/188 - 14%

Fishes

Gadiformes

9/11 - 81%

31/52 - 59%

54/132 - 40%

Fishes

Batrachoidiformes

1/1 - 100%

4/9 - 44%

7/16 - 43%

Fishes

Lophiiformes

10/12 - 83%

16/24 - 66%

21/45 - 46%

Fishes

Cyprinodontiformes

8/9 - 88%

29/109 - 26%

87/626 - 13%

Fishes

Beloniformes

5/5 - 100%

17/31 - 54%

36/97 - 37%

Fishes

Scorpaeniformes

20/32 - 62%

63/130 - 48%

149/465 - 32%

Fishes

Perciformes

114/151 - 75%

492/1108 - 44%

1213/4698 - 25%

Fishes

Pleuronectiformes

11/11 - 100%

64/95 - 67%

91/213 - 42%

Fishes

Osteoglossiformes

6/6 - 100%

9/28 - 32%

10/142 - 7%

Fishes

Polypteriformes

0/1 - 0%

0/2 - 0%

0/9 - 0%

Fishes

Gonorynchiformes

2/4 - 50%

2/7 - 28%

2/10 - 20%

Fishes

Mugiliformes

1/1 - 100%

5/8 - 62%

6/26 - 23%

Fishes

Tetraodontiformes

10/10 - 100%

51/69 - 73%

92/181 - 50%

Fishes

Myliobatiformes

6/7 - 85%

18/22 - 81%

57/112 - 50%

Fishes

Atheriniformes

6/8 - 75%

13/33 - 39%

19/174 - 10%

Fishes

Synbranchiformes

2/2 - 100%

5/6 - 83%

6/19 - 31%

Fishes

Beryciformes

7/7 - 100%

12/18 - 66%

30/49 - 61%

Fishes

Stomiiformes

6/7 - 85%

18/21 - 85%

30/52 - 57%

Fishes

Albuliformes

1/1 - 100%

1/2 - 50%

2/14 - 14%

Fishes

Pristiformes

1/1 - 100%

2/2 - 100%

4/5 - 80%

Fishes

Zeiformes

4/5 - 80%

8/11 - 72%

12/17 - 70%

Fishes

Gasterosteiformes

7/10 - 70%

21/37 - 56%

31/98 - 31%

Fishes

Myctophiformes

2/2 - 100%

18/32 - 56%

28/90 - 31%

Fishes

Aulopiformes

12/14 - 85%

24/32 - 75%

36/68 - 52%

Fishes

Lampridiformes

6/6 - 100%

8/9 - 88%

10/15 - 66%

Fishes

Percopsiformes

2/3 - 66%

2/3 - 66%

2/4 - 50%

Fishes

Polymixiiformes

1/1 - 100%

1/1 - 100%

3/4 - 75%

Fishes

Stephanoberyciformes

5/7 - 71%

9/17 - 52%

10/49 - 20%

Fishes

Dactylopteriformes

1/1 - 100%

2/2 - 100%

3/4 - 75%

Fishes

Ophidiiformes

3/3 - 100%

12/18 - 66%

14/24 - 58%

Fishes

Argentiniformes

4/6 - 66%

8/21 - 38%

13/32 - 40%

Fishes

Ateleopodiformes

1/1 - 100%

1/2 - 50%

1/3 - 33%

Fishes

Notacanthiformes

2/2 - 100%

4/4 - 100%

6/7 - 85%

Fishes

Rhiniformes

1/1 - 100%

1/1 - 100%

1/1 - 100%

Fishes




9/10 - 90%

15/24 - 62%

32/74 - 43%


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