Supplementary Methods Synteny blocks identification




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SUPPLEMENTARY INFORMATION

Supplementary Methods

Synteny blocks identification


Pairwise orthologous relations between each pair of species was built based on OrthoDB7 and independently at each of the hierarchical level of interest: vertebrate, amniote, eutheria, boereoeutheria, euarchontoglires. Along the length of the human genome, pairwise relations are grouped into collinear blocks, when more than 2 proteins were next to each other, allowing for 1 intervening non-similar orthologous gene inside the collinear block. For each position on the human genome, 5 pairwise blocks are combined, the combinations have to include human and a species at the root of the investigated phylogeny. The combinations of blocks are scored according to the total phylogenetic distance between all pairs of species, the total number of orthologous marker in the block (relaying the length of the block) and the assembly quality (N content) of the species in the block. The block with the higher score is chosen for each position along the human genome. This is again computed independently for each clade. Each block is in the end extended by 15kb, corresponding to the average distance between two genes on human chromosome 1.


Conservation computation, phastCons parameters


PhastCons with the –most-conserved options was run on all merged alignments. The phastCons parameters used were: target-coverage: 0.3, expected-length: 50. The phylogenetic tree model used was from UCSC browser:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP100way/hg19.100way.phyloP100way.mod
CEGA content in all species

Synteny blocks







Vertebrata

Amniota

Eutheria

Boreoeutheria

Euarchontoglires

Ailuropoda Melanoleuca

1155246

53114411

126303475

120757569

-

Anolis Carolinensis

112986896

302696418

-

-

-

Bos Taurus

4013760

156827377

443972394

639219448

-

Callithrix Jacchus

-

3359826

81416882

133715194

460800835

Canis Familiaris

23444030

282499808

449877823

559969029

-

Cavia Porcellus

65099005

465937715

692211137

620953495

828165983

Choloepus Hoffmanni

-

-

255145

-

-

Danio Rerio

97171916

-

-

-

-

Dasypus Novemcinctus

-

-

4273182

-

-

Dipodomys Ordii

-

147603

472749

790606

3842806

Echinops Telfairi

-

-

4265898

-

-

Equus Caballus

3853398

105252292

210301749

437711014

-

Erinaceus Europaeus

-

59243

277124

151712

-

Felis Catus

445931

71884727

163559693

385818355

-

Gadus Morhua

3204642

-

-

-

-

Gallus Gallus

167813251

356293304

-

-

-

Gasterosteus Aculeatus

3252149

-

-

-

-

Gorilla Gorilla

7003233

21599327

25287843

69004371

271865036

Homo Sapiens

607036651

1479626156

1677125891

1763045997

1830671980

Ictidomys Tridecemlineatus

-

33050042

103518902

180495074

505974412

Loxodonta Africana

13069520

359123915

1773255718

-

-

Macaca Mulatta

-

1687860

3049898

29899925

151202820

Meleagris Gallopavo

2118094

60162115

-

-

-

Microcebus Murinus

-

-

1807531

1195742

3106986

Monodelphis Domestica

41666921

392679725

-

-

-

Mus Musculus

241899376

698406769

757622306

763382251

966756420

Mustela Putorius Furo

3307197

40777923

82037033

188729423

-

Myotis Lucifugus

8168695

114244083

222855390

227935633

-

Nomascus Leucogenys

5607403

59541808

143610661

234653989

713343177

Ochotona Princeps

-

128857

4680550

4305830

13047782

Oreochromis Niloticus

31141743

-

-

-

-

Ornithorhynchus Anatinus

18172975

76014469

-

-

-

Oryctolagus Cuniculus

6521512

149439524

362467391

493948392

747905113

Oryzias Latipes

12271397

-

-

-

-

Otolemur Garnettii

2743603

81322260

219480319

475365845

742555639

Pan Troglodytes

711460

70182255

84984417

255356517

638386577

Pelodiscus Sinensis

186974532

358609317

-

-

-

Pongo Abelii

-

39539382

88531778

201036946

438991636

Procavia Capensis

-

-

4975328

-

-

Pteropus Vampyrus

225953

648429

2682011

8220669

-

Rattus Norvegicus

192857

23778249

53607022

102155194

269069754

Sarcophilus Harrisii

9798787

89465626

-

-

-

Sorex Araneus

-

-

2443062

2681335

-

Sus Scrofa

656337

18028954

29536549

46764715

-

Taeniopygia Guttata

13754186

82103511

-

-

-

Takifugu Rubripes

25512681

-

-

-

-

Tarsius Syrichta

-

-

25325

114374

466568

Tetraodon Nigroviridis

4072567

-

-

-

-

Tupaia Belangeri

-

-

505786

1338627

5394532

Tursiops Truncatus

1259225

1017899

1107209

6308760

-

Vicugna Pacos

483288

979811

2998671

7602028

-

Xenopus Tropicalis

116833949

-

-

-

-

Xiphophorus Maculatus

6081571

-

-

-

-

Conserved elements






Vertebrata

Amniota

Eutheria

Boreoeutheria

Euarchontoglires

AiluropodaMelanoleuca

1155246

126303475

53114411

120757569

-

AnolisCarolinensis

112986896

-

302696418

-

-

BosTaurus

4013760

443972394

156827377

639219448

-

CallithrixJacchus

-

81416882

3359826

133715194

460800835

CanisFamiliaris

23444030

449877823

282499808

559969029

-

CaviaPorcellus

65099005

692211137

465937715

620953495

828165983

CholoepusHoffmanni

-

255145

-

-

-

DanioRerio

97171916

-

-

-

-

DasypusNovemcinctus

-

4273182

-

-

-

DipodomysOrdii

-

472749

147603

790606

3842806

EchinopsTelfairi

-

4265898

-

-

-

EquusCaballus

3853398

210301749

105252292

437711014

-

ErinaceusEuropaeus

-

277124

59243

151712

-

FelisCatus

445931

163559693

71884727

385818355

-

GadusMorhua

3204642

-

-

-

-

GallusGallus

167813251

-

356293304

-

-

GasterosteusAculeatus

3252149

-

-

-

-

GorillaGorilla

7003233

25287843

21599327

69004371

271865036

HomoSapiens

607036651

1677125891

1479626156

1763045997

1830671980

IctidomysTridecemlineatus

-

103518902

33050042

180495074

505974412

LoxodontaAfricana

13069520

1773255718

359123915

-

-

MacacaMulatta

-

3049898

1687860

29899925

151202820

MeleagrisGallopavo

2118094

-

60162115

-

-

MicrocebusMurinus

-

1807531

-

1195742

3106986

MonodelphisDomestica

41666921

-

392679725

-

-

MusMusculus

241899376

757622306

698406769

763382251

966756420

MustelaPutoriusFuro

3307197

82037033

40777923

188729423

-

MyotisLucifugus

8168695

222855390

114244083

227935633

-

NomascusLeucogenys

5607403

143610661

59541808

234653989

713343177

OchotonaPrinceps

-

4680550

128857

4305830

13047782

OreochromisNiloticus

31141743

-

-

-

-

OrnithorhynchusAnatinus

18172975

-

76014469

-

-

OryctolagusCuniculus

6521512

362467391

149439524

493948392

747905113

OryziasLatipes

12271397

-

-

-

-

OtolemurGarnettii

2743603

219480319

81322260

475365845

742555639

PanTroglodytes

711460

84984417

70182255

255356517

638386577

PelodiscusSinensis

186974532

-

358609317

-

-

PongoAbelii

-

88531778

39539382

201036946

438991636

ProcaviaCapensis

-

4975328

-

-

-

PteropusVampyrus

225953

2682011

648429

8220669

-

RattusNorvegicus

192857

53607022

23778249

102155194

269069754

SarcophilusHarrisii

9798787

-

89465626

-

-

SorexAraneus

-

2443062

-

2681335

-

SusScrofa

656337

29536549

18028954

46764715

-

TaeniopygiaGuttata

13754186

-

82103511

-

-

TakifuguRubripes

25512681

-

-

-

-

TarsiusSyrichta

-

25325

-

114374

466568

TetraodonNigroviridis

4072567

-

-

-

-

TupaiaBelangeri

-

505786

-

1338627

5394532

TursiopsTruncatus

1259225

1107209

1017899

6308760

-

VicugnaPacos

483288

2998671

979811

7602028

-

XenopusTropicalis

116833949

-

-

-

-

Xiphophorus_Maculatus

622549

-

-

-

-

CNCs





Vertebrata

Eutheria

Amniota

Boreoeutheria

Euarchontoglires

Ailuropoda_Melanoleuca

36062

10656857

2767877

9532512

-

Anolis_Carolinensis

1439840

-

12109255

-

-

Bos_Taurus

76884

37732031

9274010

48795880

-

Callithrix_Jacchus

-

5564971

119388

9624554

30490715

Canis_Familiaris

781005

42266166

15530278

45852165

-

Cavia_Porcellus

1667472

59071428

22053818

47877761

62818463

Choloepus_Hoffmanni

-

18503

-

-

-

Danio_Rerio

2220350

-

-

-

-

Dasypus_Novemcinctus

-

196989

-

-

-

Dipodomys_Ordii

-

41949

7603

84368

330018

Echinops_Telfairi

-

151385

-

-

-

Equus_Caballus

126398

19785823

5766978

36553265

-

Erinaceus_Europaeus

-

5909

542

4660

-

Felis_Catus

22426

15207880

3663800

30121772

-

Gadus_Morhua

115732

-

-

-

-

Gallus_Gallus

3564822

-

22951507

-

-

Gasterosteus_Aculeatus

295956

-

-

-

-

Gorilla_Gorilla

27632

1900534

998491

4387323

16151441

Homo_Sapiens

6203030

122349353

52502674

116262245

119334783

Ictidomys_Tridecemlineatus

-

8964776

1484747

16736982

42034118

Loxodonta_Africana

248270

128981182

17476917

-

-

Macaca_Mulatta

-

268156

46482

2309083

10525438

Macropus_Eugenii

-

-

0

-

-

Meleagris_Gallopavo

46499

-

3908432

-

-

Microcebus_Murinus

-

147299

0

77821

249508

Monodelphis_Domestica

672877

-

10027103

-

-

Mus_Musculus

3677304

57428591

25361806

52336586

67732334

Mustela_Putorius_Furo

83911

7763061

2095836

15456877

-

Myotis_Lucifugus

284842

22740918

6791271

22179420

-

Nomascus_Leucogenys

53328

9999123

2957758

15125796

49786118

Ochotona_Princeps

-

285854

13074

262076

866024

Oreochromis_Niloticus

1005318

-

-

-

-

Ornithorhynchus_Anatinus

477507

-

3064271

-

-

Oryctolagus_Cuniculus

207480

32705964

7909912

37573803

56325800

Oryzias_Latipes

586618

-

-

-

-

Otolemur_Garnettii

139056

21613462

5057438

37834492

56117484

Pan_Troglodytes

9241

5004572

3282966

17523483

40972449

Pelodiscus_Sinensis

2402430

-

12222809

-

-

Pongo_Abelii

-

6457231

1718718

11390994

28265171

Procavia_Capensis

-

316305

0

-

-

Pteropus_Vampyrus

13474

236633

31577

746752

-

Rattus_Norvegicus

2573

4132746

1113895

7187567

19460530

Sarcophilus_Harrisii

203626

-

2902770

-

-

Sorex_Araneus

-

132701

0

98086

-

Sus_Scrofa

14521

3086677

1350588

4228892

-

Taeniopygia_Guttata

347020

-

4806755

-

-

Takifugu_Rubripes

1036255

-

-

-

-

Tarsius_Syrichta

-

2609

0

13903

34622

Tetraodon_Nigroviridis

277161

-

-

-

-

Tupaia_Belangeri

-

32308

0

93245

265901

Tursiops_Truncatus

38011

101227

49935

532687

-

Vicugna_Pacos

13316

287607

30452

634972

-

Xenopus_Tropicalis

2059476

-

-

-

-

Xiphophorus_Maculatus

242375

-

-

-

-


CEGA data and assemblies used

CEGA was based on OrthoDB7.



List of species in CEGA and the corresponding assembly used:



Species Name

Common Name

Assembly

Homo Sapiens

Human

GRCh37

Pan Troglodytes

Chimp

CHIMP2.1.4

Gorilla Gorilla

Gorilla

gorGor3.1

Pongo Abelii

Orangutan

PPYG2

Nomascus Leucogenys

Gibbon

Nleu1.0

Macaca Mulatta

Rhesus Macaque

MMUL_1

Callithrix Jacchus

Marmoset

C_jacchus3.2.1

Tarsius Syrichta

Tarsier

tarSyr1

Microcebus Murinus

Mouse lemur

micMur1

Otolemur Garnettii

Bushbaby

OtoGar3

Tupaia Belangeri

Tree shrew

TREESHREW

Mus Musculus

Mouse

GRCm38

Rattus Norvegicus

Rat

Rnor_5.0

Dipodomys Ordii

Kangaroo rat

dipOrd1

Cavia Porcellus

Guinea pig

cavPor3

Ictidomys Tridecemlineatus

Squirrel

spetri2

Oryctolagus Cuniculus

Rabbit

oryCun2

Ochotona Princeps

Pika

pika

Mustela Putorius Furo

Ferret

MusPutFur1.0

Ailuropoda Melanoleuca

Panda

ailMel1

Canis Familiaris

Dog

CanFam3.1

Equus Caballus

Horse

EquCab2

Myotis Lucifugus

Microbat

Myoluc2.0

Pteropus Vampyrus

Megabat

pteVam1

Bos Taurus

Cow

UMD3.1

Tursiops Truncatus

Dolphin

turTru1

Sus Scrofa

Pig

Sscrofa10.2

Vicugna Pacos

Alpaca

vicPac1

Erinaceus Europaeus

Hedgehog

HEDGEHOG

Sorex Araneus

Shrew

COMMON_SHREW1

Loxodonta Africana

Elephant

loxAfr3

Procavia Capensis

Rock hyrax

proCap1

Echinops Telfairi

Tenrec

TENREC

Choloepus Hoffmanni

Sloth

choHof1

Dasypus Novemcinctus

Armadillo

dasNov2

Sarcophilus Harrisii

Tasmanian devil

DEVIL7.0

Macropus Eugenii

Wallaby

Meug_1.0

Monodelphis Domestica

Opossum

BROADO5

Ornithorhynchus Anatinus

Platypus

OANA5

Gallus Gallus

Chicken

Galgal4

Meleagris Gallopavo

Turkey

UMD2

Taeniopygia Guttata

Zebra finch

taeGut3.2.4

Anolis Carolinensis

Lizard

AnoCar2.0

Pelodiscus Sinensis

Chinese turtle

PelSin_1.0

Xenopus Tropicalis

X.tropicalis

JGI_4.2

Latimeria Chalumnae

Coelacanth

LatCha1

Xiphophorus Maculatus

Platyfish

Xipmac4.4.2

Oryzias Latipes

Medaka

MEDAKA1

Oreochromis Niloticus

Nile tilapia

Orenil1.1

Takifugu Rubripes

Fugu

FUGU4

Tetraodon Nigroviridis

Tetraodon

TETRAODON8

Gasterosteus Aculeatus

Stickleback

BROADS1

Gadus Morhua

Atlantic cod

gadMor1

Danio Rerio

Zebrafish

Zv9

Callorhinchus Milii

Elephant shark

calMil1

Petromyzon Marinus

Lamprey

Pmarinus_7.0





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