The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Prado Martinez, Javier ^a   Hernando Herraez, Irene ^a   Lorente Galdos, Belen ^a   Dabad, Marc ^a   Ramirez, Oscar ^a   Baeza Delgado, Carlos ^b   Morcillo Suarez, Carlos ^a,c   Alkan, Can ^d,e   Hormozdiari, Fereydoun ^d   Raineri, Emanuele ^f   Estellé, Jordi ^f,g   Fernandez Callejo, Marcos ^a   Valles, Mònica ^a   Ritscher, Lars ^h   Schöneberg, Torsten ^h   de la Calle Mustienes, Elisa ⁱ   Casillas, Sònia ^j   Rubio Acero, Raquel ^j   Melé, Marta ^a,k   Engelken, Johannes ^a,l   Caceres, Mario ^j,m   Gomez Skarmeta, Jose Luis ⁱ   Gut, Marta ^f   Bertranpetit, Jaume ^a   Gut, Ivo G ^f   Abello, Teresa ⁿ   Eichler, Evan E ^d,o   Mingarro, Ismael ^b   Lalueza Fox, Carles ^a   Navarro, Arcadi ^a,c,k,m   Marques Bonet, Tomas ^a,m   more..

^a CSIC   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

^c UNIVERSITAT POMPEU FABRA   (Spain)

^d UNIVERSITY OF WASHINGTON   (United States)

^e BILKENT UNIVERSITY   (Turkey)

^f PNT PCB   (Spain)

^g UMR1313 GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE   (France)

^h UNIVERSITY OF LEIPZIG   (Germany)

ⁱ UNIVERSIDAD PABLO DE OLAVIDE   (Spain)

^j UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^k CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^l MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^m INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

ⁿ Parc Zoològic de Barcelona   (Spain)

^o Howard Hugues Medical Institute   (United States)

more..

Author keywords

Albinism; Conservation; Genome; Gorilla; Inbreeding

Indexed keywords

ARGININE; GLYCINE;

AMINO ACID SUBSTITUTION; ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; GENE; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; GORILLA; HETEROZYGOSITY; INBREEDING; MALE; NONHUMAN; OCULOCUTANEOUS ALBINISM; SINGLE NUCLEOTIDE POLYMORPHISM; SLC45A2 GENE; ZYGOSITY;

AMINO ACID SEQUENCE; ANIMALS; FEMALE; GENOMICS; GORILLA GORILLA; HETEROZYGOTE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INBREEDING; MALE; MEMBRANE TRANSPORT PROTEINS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; MUTATION; SEQUENCE ANALYSIS, DNA;

GORILLA GORILLA GORILLA;

EID: 84878356117     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-363     Document Type: Article

References (35)

1. Sabater Pi J. An albino lowland gorilla from rio Muni, West Africa, and notes on its adaptation to captivity. Folia Primatol 1967, 7:155-160. 10.1159/000155115, 6055275.
2. Márquez M, Serafin A, Fernández-Bellon H, Serrat S, Ferrer-Admetlla A, Bertranpetit J, Ferrer I, Pumarola M. Neuropathologic findings in an aged albino gorilla. Vet Pathol 2008, 45:531-537. 10.1354/vp.45-4-531, 18587101.
3. Grønskov K, Ek J, Brondum-Nielsen K. Oculocutaneous albinism. Orphanet J Rare Dis 2007, 2:43. 10.1186/1750-1172-2-43, 2211462, 17980020.
4. Martínez-Arias R, Comas D, Andrés A, Abelló MT, Domingo-Roura X, Bertranpetit J. The tyrosinase gene in gorillas and the albinism of " Snowflake" Pigment Cell Res 2000, 13:467-470. 10.1034/j.1600-0749.2000.130609.x, 11153699.
5. Robbins MM, Bermejo M, Cipolletta C, Magliocca F, Parnell RJ, Stokes E. Social structure and life-history patterns in western gorillas (Gorilla gorilla gorilla). Am J Primatol 2004, 64:145-159. 10.1002/ajp.20069, 15470749.
6. Harcourt AH, Stewart KJS. Gorilla Society: conflict, compromise and cooperation between sexes 2007, Chicago: The University of Chicago Press.
7. Vigilant L, Bradley BJ. Genetic variation in gorillas. Am J Primatol 2004, 64:161-172. 10.1002/ajp.20070, 15470746.
8. Thalmann O, Fischer A, Lankester F, Paabo S, Vigilant L, Thalmann O, Fischer A, Lankester F, Paabo S, Vigilant L. The complex evolutionary history of gorillas: insights from genomic data. Mol Biol Evol 2007, 24:146-158. 10.1093/molbev/msl160, 17065595.
9. Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-bonet T, Mccarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A. Insights into hominid evolution from the gorilla genome sequence. Nature 2012, 483:169-175. 10.1038/nature10842, 3303130, 22398555.
10. Ventura M, Catacchio CR, Alkan C, Marques-Bonet T, Sajjadian S, Graves TA, Hormozdiari F, Navarro A, Malig M, Baker C, Lee C, Turner EH, Chen L, Kidd JM, Archidiacono N, Shendure J, Wilson RK, Eichler EE. Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. Genome Res 2011, 21:1640-1649. 10.1101/gr.124461.111, 3202281, 21685127.
11. Nsubuga AM, Holzman J, Chemnick LG, Ryder OA. The cryptic genetic structure of the North American captive gorilla population. Conserv Gen 2009, 11:161-172.
12. Marco-Sola S, Sammeth M, Guigó R, Ribeca P. The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods 2012,
13. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
14. Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 2003, 31:3812-3814. 10.1093/nar/gkg509, 168916, 12824425.
15. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods 2010, 7:248-249. 10.1038/nmeth0410-248, 2855889, 20354512.
16. Newton JM, Cohen-Barak O, Hagiwara N, Gardner JM, Davisson MT, King RA, Brilliant MH. Mutations in the human orthologue of the mouse underwhite gene (uw) underlie a new form of oculocutaneous albinism, OCA4. Am J Hum Genet 2001, 69:981-988. 10.1086/324340, 1274374, 11574907.
17. Fukamachi S, Shimada A, Shima A. Mutations in the gene encoding B, a novel transporter protein, reduce melanin content in medaka. Nat Genet 2001, 28:381-385. 10.1038/ng584, 11479596.
18. Mariat D, Taourit S, Guérin G. A mutation in the MATP gene causes the cream coat colour in the horse. Genet Sel Evol 2003, 35:119-133. 10.1186/1297-9686-35-1-119, 2732686, 12605854.
19. Gunnarsson U, Hellström AR, Tixier-Boichard M, Minvielle F, Bed'hom B, Ito S, Jensen P, Rattink A, Vereijken A, Andersson L. Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail. Genetics 2007, 175:867-877. 10.1534/genetics.106.063107, 1800597, 17151254.
20. Inagaki K, Suzuki T, Ito S, Suzuki N, Adachi K, Okuyama T, Nakata Y, Shimizu H, Matsuura H, Oono T, Iwamatsu H, Kono M, Tomita Y. Oculocutaneous albinism type 4: six novel mutations in the membrane-associated transporter protein gene and their phenotypes. Pigment Cell Res 2006, 19:451-453. 10.1111/j.1600-0749.2006.00332.x, 16965274.
21. Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH, Von Heijne G. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 2005, 433:377-381. 10.1038/nature03216, 15674282.
22. Martínez-Gil L, Saurí A, Vilar M, Pallás V, Mingarro I. Membrane insertion and topology of the p7B movement protein of Melon Necrotic Spot Virus (MNSV). Virology 2007, 367:348-357. 10.1016/j.virol.2007.06.006, 17610929.
23. Martínez-Gil L, Pérez-Gil J, Mingarro I, Martinez-Gil L, Perez-Gil J. The surfactant peptide KL 4 sequence is inserted with a transmembrane orientation into the endoplasmic reticulum membrane. Biophys J 2008, 95:36-38.
24. Charlesworth D, Willis JH. The genetics of inbreeding depression. Nat Rev Genet 2009, 10:783-796. 10.1038/nrg2664, 19834483.
25. Charpentier MJE, Widdig A, Alberts SC. Inbreeding depression in non-human primates: a historical review of methods used and empirical data. Am J Primatol 2007, 69:1370-1386. 10.1002/ajp.20445, 17486606.
26. Pemberton TJ, Absher D, Feldman MW, Myers RM, Rosenberg NA, Li JZ. Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet 2012, 91:275-292. 10.1016/j.ajhg.2012.06.014, 3415543, 22883143.
27. Chowdhury R, Bois PRJ, Feingold E, Sherman SL, Vivian G. Genetic analysis of variation in human meiotic recombination. PLoS Genet 2009, 5.
28. Harcourt AH, Stewart KS, Fossey D. Male emigration and female transfer in wild mountain gorilla. Nature 1976, 263:226-227.
29. Douadi MI, Gatti S, Levrero F, Duhamel G, Bermejo M, Vallet D, Menard N, Petit EJ. Sex-biased dispersal in western lowland gorillas (Gorilla gorilla gorilla). Mol Ecol 2007, 16:2247-2259. 10.1111/j.1365-294X.2007.03286.x, 17561888.
30. Bradley BJ, Doran-Sheehy DM, Lukas D, Boesch C, Vigilant L. Dispersed male networks in western gorillas. Curr Biol 2004, 14:510-513. 10.1016/j.cub.2004.02.062, 15043817.
31. Stokes EJ, Parnell RJ, Olejniczak C. Female dispersal and reproductive success in wild western lowland gorillas (Gorilla gorilla gorilla). Behav Ecol Sociobiol 2003, 54:329-339.
32. Bergl RA, Vigilant L. Genetic analysis reveals population structure and recent migration within the highly fragmented range of the Cross River gorilla (Gorilla gorilla diehli). Mol Ecol 2007, 16:501-516. 10.1111/j.1365-294X.2006.03159.x, 17257109.
33. Adey A, Morrison HG, Asan, Xun X, Kitzman JO, Turner EH, Stackhouse B, MacKenzie AP, Caruccio NC, Zhang X, Shendure J. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol 2010, 11:R119. 10.1186/gb-2010-11-12-r119, 3046479, 21143862.
34. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie WR, Hicks J, Wigler M. Tumour evolution inferred by single-cell sequencing. Nature 2011, 472:90-94. 10.1038/nature09807, 21399628.
35. Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Zaranek AW, Lee J-H, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 2012, 487:190-195. 10.1038/nature11236, 3397394, 22785314.