Literature DB >> 19892987

Genome sequence, comparative analysis, and population genetics of the domestic horse.

C M Wade1, E Giulotto, S Sigurdsson, M Zoli, S Gnerre, F Imsland, T L Lear, D L Adelson, E Bailey, R R Bellone, H Blöcker, O Distl, R C Edgar, M Garber, T Leeb, E Mauceli, J N MacLeod, M C T Penedo, J M Raison, T Sharpe, J Vogel, L Andersson, D F Antczak, T Biagi, M M Binns, B P Chowdhary, S J Coleman, G Della Valle, S Fryc, G Guérin, T Hasegawa, E W Hill, J Jurka, A Kiialainen, G Lindgren, J Liu, E Magnani, J R Mickelson, J Murray, S G Nergadze, R Onofrio, S Pedroni, M F Piras, T Raudsepp, M Rocchi, K H Røed, O A Ryder, S Searle, L Skow, J E Swinburne, A C Syvänen, T Tozaki, S J Valberg, M Vaudin, J R White, M C Zody, E S Lander, K Lindblad-Toh.   

Abstract

We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.

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Year:  2009        PMID: 19892987      PMCID: PMC3785132          DOI: 10.1126/science.1178158

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  17 in total

1.  Evolutionary formation of new centromeres in macaque.

Authors:  Mario Ventura; Francesca Antonacci; Maria Francesca Cardone; Roscoe Stanyon; Pietro D'Addabbo; Angelo Cellamare; L James Sprague; Evan E Eichler; Nicoletta Archidiacono; Mariano Rocchi
Journal:  Science       Date:  2007-04-13       Impact factor: 47.728

2.  Evolutionary movement of centromeres in horse, donkey, and zebra.

Authors:  Lucia Carbone; Solomon G Nergadze; Elisa Magnani; Doriana Misceo; Maria Francesca Cardone; Roberta Roberto; Livia Bertoni; Carmen Attolini; Maria Francesca Piras; Pieter de Jong; Terje Raudsepp; Bhanu P Chowdhary; Gérard Guérin; Nicoletta Archidiacono; Mariano Rocchi; Elena Giulotto
Journal:  Genomics       Date:  2006-01-18       Impact factor: 5.736

3.  Genome sequence, comparative analysis and haplotype structure of the domestic dog.

Authors:  Kerstin Lindblad-Toh; Claire M Wade; Tarjei S Mikkelsen; Elinor K Karlsson; David B Jaffe; Michael Kamal; Michele Clamp; Jean L Chang; Edward J Kulbokas; Michael C Zody; Evan Mauceli; Xiaohui Xie; Matthew Breen; Robert K Wayne; Elaine A Ostrander; Chris P Ponting; Francis Galibert; Douglas R Smith; Pieter J DeJong; Ewen Kirkness; Pablo Alvarez; Tara Biagi; William Brockman; Jonathan Butler; Chee-Wye Chin; April Cook; James Cuff; Mark J Daly; David DeCaprio; Sante Gnerre; Manfred Grabherr; Manolis Kellis; Michael Kleber; Carolyne Bardeleben; Leo Goodstadt; Andreas Heger; Christophe Hitte; Lisa Kim; Klaus-Peter Koepfli; Heidi G Parker; John P Pollinger; Stephen M J Searle; Nathan B Sutter; Rachael Thomas; Caleb Webber; Jennifer Baldwin; Adal Abebe; Amr Abouelleil; Lynne Aftuck; Mostafa Ait-Zahra; Tyler Aldredge; Nicole Allen; Peter An; Scott Anderson; Claudel Antoine; Harindra Arachchi; Ali Aslam; Laura Ayotte; Pasang Bachantsang; Andrew Barry; Tashi Bayul; Mostafa Benamara; Aaron Berlin; Daniel Bessette; Berta Blitshteyn; Toby Bloom; Jason Blye; Leonid Boguslavskiy; Claude Bonnet; Boris Boukhgalter; Adam Brown; Patrick Cahill; Nadia Calixte; Jody Camarata; Yama Cheshatsang; Jeffrey Chu; Mieke Citroen; Alville Collymore; Patrick Cooke; Tenzin Dawoe; Riza Daza; Karin Decktor; Stuart DeGray; Norbu Dhargay; Kimberly Dooley; Kathleen Dooley; Passang Dorje; Kunsang Dorjee; Lester Dorris; Noah Duffey; Alan Dupes; Osebhajajeme Egbiremolen; Richard Elong; Jill Falk; Abderrahim Farina; Susan Faro; Diallo Ferguson; Patricia Ferreira; Sheila Fisher; Mike FitzGerald; Karen Foley; Chelsea Foley; Alicia Franke; Dennis Friedrich; Diane Gage; Manuel Garber; Gary Gearin; Georgia Giannoukos; Tina Goode; Audra Goyette; Joseph Graham; Edward Grandbois; Kunsang Gyaltsen; Nabil Hafez; Daniel Hagopian; Birhane Hagos; Jennifer Hall; Claire Healy; Ryan Hegarty; Tracey Honan; Andrea Horn; Nathan Houde; Leanne Hughes; Leigh Hunnicutt; M Husby; Benjamin Jester; Charlien Jones; Asha Kamat; Ben Kanga; Cristyn Kells; Dmitry Khazanovich; Alix Chinh Kieu; Peter Kisner; Mayank Kumar; Krista Lance; Thomas Landers; Marcia Lara; William Lee; Jean-Pierre Leger; Niall Lennon; Lisa Leuper; Sarah LeVine; Jinlei Liu; Xiaohong Liu; Yeshi Lokyitsang; Tashi Lokyitsang; Annie Lui; Jan Macdonald; John Major; Richard Marabella; Kebede Maru; Charles Matthews; Susan McDonough; Teena Mehta; James Meldrim; Alexandre Melnikov; Louis Meneus; Atanas Mihalev; Tanya Mihova; Karen Miller; Rachel Mittelman; Valentine Mlenga; Leonidas Mulrain; Glen Munson; Adam Navidi; Jerome Naylor; Tuyen Nguyen; Nga Nguyen; Cindy Nguyen; Thu Nguyen; Robert Nicol; Nyima Norbu; Choe Norbu; Nathaniel Novod; Tenchoe Nyima; Peter Olandt; Barry O'Neill; Keith O'Neill; Sahal Osman; Lucien Oyono; Christopher Patti; Danielle Perrin; Pema Phunkhang; Fritz Pierre; Margaret Priest; Anthony Rachupka; Sujaa Raghuraman; Rayale Rameau; Verneda Ray; Christina Raymond; Filip Rege; Cecil Rise; Julie Rogers; Peter Rogov; Julie Sahalie; Sampath Settipalli; Theodore Sharpe; Terrance Shea; Mechele Sheehan; Ngawang Sherpa; Jianying Shi; Diana Shih; Jessie Sloan; Cherylyn Smith; Todd Sparrow; John Stalker; Nicole Stange-Thomann; Sharon Stavropoulos; Catherine Stone; Sabrina Stone; Sean Sykes; Pierre Tchuinga; Pema Tenzing; Senait Tesfaye; Dawa Thoulutsang; Yama Thoulutsang; Kerri Topham; Ira Topping; Tsamla Tsamla; Helen Vassiliev; Vijay Venkataraman; Andy Vo; Tsering Wangchuk; Tsering Wangdi; Michael Weiand; Jane Wilkinson; Adam Wilson; Shailendra Yadav; Shuli Yang; Xiaoping Yang; Geneva Young; Qing Yu; Joanne Zainoun; Lisa Zembek; Andrew Zimmer; Eric S Lander
Journal:  Nature       Date:  2005-12-08       Impact factor: 49.962

4.  Widespread origins of domestic horse lineages.

Authors:  C Vilà; J A Leonard; A Gotherstrom; S Marklund; K Sandberg; K Liden; R K Wayne; H Ellegren
Journal:  Science       Date:  2001-01-19       Impact factor: 47.728

5.  Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla.

Authors:  Vladimir A Trifonov; Roscoe Stanyon; Anastasia I Nesterenko; Beiyuan Fu; Polina L Perelman; Patricia C M O'Brien; Gary Stone; Nadezhda V Rubtsova; Marlys L Houck; Terence J Robinson; Malcolm A Ferguson-Smith; Gauthier Dobigny; Alexander S Graphodatsky; Fengtang Yang
Journal:  Chromosome Res       Date:  2008       Impact factor: 5.239

6.  Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.

Authors:  Richard A Gibbs; Jeremy F Taylor; Curtis P Van Tassell; William Barendse; Kellye A Eversole; Clare A Gill; Ronnie D Green; Debora L Hamernik; Steven M Kappes; Sigbjørn Lien; Lakshmi K Matukumalli; John C McEwan; Lynne V Nazareth; Robert D Schnabel; George M Weinstock; David A Wheeler; Paolo Ajmone-Marsan; Paul J Boettcher; Alexandre R Caetano; Jose Fernando Garcia; Olivier Hanotte; Paola Mariani; Loren C Skow; Tad S Sonstegard; John L Williams; Boubacar Diallo; Lemecha Hailemariam; Mario L Martinez; Chris A Morris; Luiz O C Silva; Richard J Spelman; Woudyalew Mulatu; Keyan Zhao; Colette A Abbey; Morris Agaba; Flábio R Araujo; Rowan J Bunch; James Burton; Chiara Gorni; Hanotte Olivier; Blair E Harrison; Bill Luff; Marco A Machado; Joel Mwakaya; Graham Plastow; Warren Sim; Timothy Smith; Merle B Thomas; Alessio Valentini; Paul Williams; James Womack; John A Woolliams; Yue Liu; Xiang Qin; Kim C Worley; Chuan Gao; Huaiyang Jiang; Stephen S Moore; Yanru Ren; Xing-Zhi Song; Carlos D Bustamante; Ryan D Hernandez; Donna M Muzny; Shobha Patil; Anthony San Lucas; Qing Fu; Matthew P Kent; Richard Vega; Aruna Matukumalli; Sean McWilliam; Gert Sclep; Katarzyna Bryc; Jungwoo Choi; Hong Gao; John J Grefenstette; Brenda Murdoch; Alessandra Stella; Rafael Villa-Angulo; Mark Wright; Jan Aerts; Oliver Jann; Riccardo Negrini; Mike E Goddard; Ben J Hayes; Daniel G Bradley; Marcos Barbosa da Silva; Lilian P L Lau; George E Liu; David J Lynn; Francesca Panzitta; Ken G Dodds
Journal:  Science       Date:  2009-04-24       Impact factor: 47.728

Review 7.  Potential applications of equine genomics in dissecting diseases and fertility.

Authors:  Bhanu P Chowdhary; Nandina Paria; Terje Raudsepp
Journal:  Anim Reprod Sci       Date:  2008-04-29       Impact factor: 2.145

8.  Clinical and electroretinographic characteristics of congenital stationary night blindness in the Appaloosa and the association with the leopard complex.

Authors:  Lynne S Sandmeyer; Carrie B Breaux; Sheila Archer; Bruce H Grahn
Journal:  Vet Ophthalmol       Date:  2007 Nov-Dec       Impact factor: 1.644

9.  Limited number of patrilines in horse domestication.

Authors:  Gabriella Lindgren; Niclas Backström; June Swinburne; Linda Hellborg; Annika Einarsson; Kaj Sandberg; Gus Cothran; Carles Vilà; Matthew Binns; Hans Ellegren
Journal:  Nat Genet       Date:  2004-03-14       Impact factor: 38.330

10.  Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

Authors:  Tarjei S Mikkelsen; Matthew J Wakefield; Bronwen Aken; Chris T Amemiya; Jean L Chang; Shannon Duke; Manuel Garber; Andrew J Gentles; Leo Goodstadt; Andreas Heger; Jerzy Jurka; Michael Kamal; Evan Mauceli; Stephen M J Searle; Ted Sharpe; Michelle L Baker; Mark A Batzer; Panayiotis V Benos; Katherine Belov; Michele Clamp; April Cook; James Cuff; Radhika Das; Lance Davidow; Janine E Deakin; Melissa J Fazzari; Jacob L Glass; Manfred Grabherr; John M Greally; Wanjun Gu; Timothy A Hore; Gavin A Huttley; Michael Kleber; Randy L Jirtle; Edda Koina; Jeannie T Lee; Shaun Mahony; Marco A Marra; Robert D Miller; Robert D Nicholls; Mayumi Oda; Anthony T Papenfuss; Zuly E Parra; David D Pollock; David A Ray; Jacqueline E Schein; Terence P Speed; Katherine Thompson; John L VandeBerg; Claire M Wade; Jerilyn A Walker; Paul D Waters; Caleb Webber; Jennifer R Weidman; Xiaohui Xie; Michael C Zody; Jennifer A Marshall Graves; Chris P Ponting; Matthew Breen; Paul B Samollow; Eric S Lander; Kerstin Lindblad-Toh
Journal:  Nature       Date:  2007-05-10       Impact factor: 49.962

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  294 in total

1.  Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences.

Authors:  Wei-Hao Shang; Tetsuya Hori; Atsushi Toyoda; Jun Kato; Kris Popendorf; Yasubumi Sakakibara; Asao Fujiyama; Tatsuo Fukagawa
Journal:  Genome Res       Date:  2010-06-09       Impact factor: 9.043

2.  Chromatin configuration and epigenetic landscape at the sex chromosome bivalent during equine spermatogenesis.

Authors:  Claudia Baumann; Christopher M Daly; Sue M McDonnell; Maria M Viveiros; Rabindranath De La Fuente
Journal:  Chromosoma       Date:  2011-01-28       Impact factor: 4.316

3.  The transposable element profile of the anolis genome: How a lizard can provide insights into the evolution of vertebrate genome size and structure.

Authors:  Marc Tollis; Stéphane Boissinot
Journal:  Mob Genet Elements       Date:  2011-07-01

4.  Retrofitting the genome: L1 extinction follows endogenous retroviral expansion in a group of muroid rodents.

Authors:  Issac K Erickson; Michael A Cantrell; LuAnn Scott; Holly A Wichman
Journal:  J Virol       Date:  2011-09-28       Impact factor: 5.103

Review 5.  Establishment of the vertebrate kinetochores.

Authors:  Tetsuya Hori; Tatsuo Fukagawa
Journal:  Chromosome Res       Date:  2012-07       Impact factor: 5.239

6.  Identification of equine major histocompatibility complex haplotypes using polymorphic microsatellites.

Authors:  C T Tseng; D Miller; J Cassano; E Bailey; D F Antczak
Journal:  Anim Genet       Date:  2010-12       Impact factor: 3.169

7.  Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication.

Authors:  Alessandro Achilli; Anna Olivieri; Pedro Soares; Hovirag Lancioni; Baharak Hooshiar Kashani; Ugo A Perego; Solomon G Nergadze; Valeria Carossa; Marco Santagostino; Stefano Capomaccio; Michela Felicetti; Walid Al-Achkar; M Cecilia T Penedo; Andrea Verini-Supplizi; Massoud Houshmand; Scott R Woodward; Ornella Semino; Maurizio Silvestrelli; Elena Giulotto; Luísa Pereira; Hans-Jürgen Bandelt; Antonio Torroni
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-30       Impact factor: 11.205

Review 8.  Understanding eukaryotic chromosome segregation from a comparative biology perspective.

Authors:  Snezhana Oliferenko
Journal:  J Cell Sci       Date:  2018-07-20       Impact factor: 5.285

9.  Realistic artificial DNA sequences as negative controls for computational genomics.

Authors:  Juan Caballero; Arian F A Smit; Leroy Hood; Gustavo Glusman
Journal:  Nucleic Acids Res       Date:  2014-05-06       Impact factor: 16.971

10.  Evidence of positive selection for a glycogen synthase (GYS1) mutation in domestic horse populations.

Authors:  Annette M McCoy; Robert Schaefer; Jessica L Petersen; Peter L Morrell; Megan A Slamka; James R Mickelson; Stephanie J Valberg; Molly E McCue
Journal:  J Hered       Date:  2013-11-08       Impact factor: 2.645

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