Literature DB >> 28736437

Dissecting evolution and disease using comparative vertebrate genomics.

Jennifer R S Meadows1, Kerstin Lindblad-Toh1,2.   

Abstract

With the generation of more than 100 sequenced vertebrate genomes in less than 25 years, the key question arises of how these resources can be used to inform new or ongoing projects. In the past, this diverse collection of sequences from human as well as model and non-model organisms has been used to annotate the human genome and to increase the understanding of human disease. In the future, comparative vertebrate genomics in conjunction with additional genomic resources will yield insights into the processes of genome function, evolution, speciation, selection and adaptation, as well as the quantification of species diversity. In this Review, we discuss how the genomics of non-human organisms can provide insights into vertebrate biology and how this can contribute to the understanding of human physiology and health.

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Year:  2017        PMID: 28736437     DOI: 10.1038/nrg.2017.51

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  88 in total

1.  Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.

Authors:  Derek M Bickhart; Benjamin D Rosen; Sergey Koren; Brian L Sayre; Alex R Hastie; Saki Chan; Joyce Lee; Ernest T Lam; Ivan Liachko; Shawn T Sullivan; Joshua N Burton; Heather J Huson; John C Nystrom; Christy M Kelley; Jana L Hutchison; Yang Zhou; Jiajie Sun; Alessandra Crisà; F Abel Ponce de León; John C Schwartz; John A Hammond; Geoffrey C Waldbieser; Steven G Schroeder; George E Liu; Maitreya J Dunham; Jay Shendure; Tad S Sonstegard; Adam M Phillippy; Curtis P Van Tassell; Timothy P L Smith
Journal:  Nat Genet       Date:  2017-03-06       Impact factor: 38.330

2.  Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Authors:  F Tajima
Journal:  Genetics       Date:  1989-11       Impact factor: 4.562

3.  Worldwide frequency distribution of the 'Gait keeper' mutation in the DMRT3 gene.

Authors:  M Promerová; L S Andersson; R Juras; M C T Penedo; M Reissmann; T Tozaki; R Bellone; S Dunner; P Hořín; F Imsland; P Imsland; S Mikko; D Modrý; K H Roed; D Schwochow; J L Vega-Pla; H Mehrabani-Yeganeh; N Yousefi-Mashouf; E G Cothran; G Lindgren; L Andersson
Journal:  Anim Genet       Date:  2014-01-21       Impact factor: 3.169

4.  Complex population structure in African village dogs and its implications for inferring dog domestication history.

Authors:  Adam R Boyko; Ryan H Boyko; Corin M Boyko; Heidi G Parker; Marta Castelhano; Liz Corey; Jeremiah D Degenhardt; Adam Auton; Marius Hedimbi; Robert Kityo; Elaine A Ostrander; Jeffrey Schoenebeck; Rory J Todhunter; Paul Jones; Carlos D Bustamante
Journal:  Proc Natl Acad Sci U S A       Date:  2009-08-03       Impact factor: 11.205

5.  Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.

Authors:  Miguel Carneiro; Carl-Johan Rubin; Federica Di Palma; Nuno Ferrand; Kerstin Lindblad-Toh; Leif Andersson; Frank W Albert; Jessica Alföldi; Alvaro Martinez Barrio; Gerli Pielberg; Nima Rafati; Shumaila Sayyab; Jason Turner-Maier; Shady Younis; Sandra Afonso; Bronwen Aken; Joel M Alves; Daniel Barrell; Gerard Bolet; Samuel Boucher; Hernán A Burbano; Rita Campos; Jean L Chang; Veronique Duranthon; Luca Fontanesi; Hervé Garreau; David Heiman; Jeremy Johnson; Rose G Mage; Ze Peng; Guillaume Queney; Claire Rogel-Gaillard; Magali Ruffier; Steve Searle; Rafael Villafuerte; Anqi Xiong; Sarah Young; Karin Forsberg-Nilsson; Jeffrey M Good; Eric S Lander
Journal:  Science       Date:  2014-08-29       Impact factor: 47.728

6.  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

7.  A high-resolution map of human evolutionary constraint using 29 mammals.

Authors:  Kerstin Lindblad-Toh; Manuel Garber; Or Zuk; Michael F Lin; Brian J Parker; Stefan Washietl; Pouya Kheradpour; Jason Ernst; Gregory Jordan; Evan Mauceli; Lucas D Ward; Craig B Lowe; Alisha K Holloway; Michele Clamp; Sante Gnerre; Jessica Alföldi; Kathryn Beal; Jean Chang; Hiram Clawson; James Cuff; Federica Di Palma; Stephen Fitzgerald; Paul Flicek; Mitchell Guttman; Melissa J Hubisz; David B Jaffe; Irwin Jungreis; W James Kent; Dennis Kostka; Marcia Lara; Andre L Martins; Tim Massingham; Ida Moltke; Brian J Raney; Matthew D Rasmussen; Jim Robinson; Alexander Stark; Albert J Vilella; Jiayu Wen; Xiaohui Xie; Michael C Zody; Jen Baldwin; Toby Bloom; Chee Whye Chin; Dave Heiman; Robert Nicol; Chad Nusbaum; Sarah Young; Jane Wilkinson; Kim C Worley; Christie L Kovar; Donna M Muzny; Richard A Gibbs; Andrew Cree; Huyen H Dihn; Gerald Fowler; Shalili Jhangiani; Vandita Joshi; Sandra Lee; Lora R Lewis; Lynne V Nazareth; Geoffrey Okwuonu; Jireh Santibanez; Wesley C Warren; Elaine R Mardis; George M Weinstock; Richard K Wilson; Kim Delehaunty; David Dooling; Catrina Fronik; Lucinda Fulton; Bob Fulton; Tina Graves; Patrick Minx; Erica Sodergren; Ewan Birney; Elliott H Margulies; Javier Herrero; Eric D Green; David Haussler; Adam Siepel; Nick Goldman; Katherine S Pollard; Jakob S Pedersen; Eric S Lander; Manolis Kellis
Journal:  Nature       Date:  2011-10-12       Impact factor: 49.962

8.  High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research.

Authors:  Kathrin Reichwald; Chris Lauber; Indrajit Nanda; Jeanette Kirschner; Nils Hartmann; Susanne Schories; Ulrike Gausmann; Stefan Taudien; Markus B Schilhabel; Karol Szafranski; Gernot Glöckner; Michael Schmid; Alessandro Cellerino; Manfred Schartl; Christoph Englert; Matthias Platzer
Journal:  Genome Biol       Date:  2009-02-11       Impact factor: 13.583

9.  Comparative genomic data of the Avian Phylogenomics Project.

Authors:  Guojie Zhang; Bo Li; Cai Li; M Thomas P Gilbert; Erich D Jarvis; Jun Wang
Journal:  Gigascience       Date:  2014-12-11       Impact factor: 6.524

10.  Genome-wide analysis reveals selection for important traits in domestic horse breeds.

Authors:  Jessica L Petersen; James R Mickelson; Aaron K Rendahl; Stephanie J Valberg; Lisa S Andersson; Jeanette Axelsson; Ernie Bailey; Danika Bannasch; Matthew M Binns; Alexandre S Borges; Pieter Brama; Artur da Câmara Machado; Stefano Capomaccio; Katia Cappelli; E Gus Cothran; Ottmar Distl; Laura Fox-Clipsham; Kathryn T Graves; Gérard Guérin; Bianca Haase; Telhisa Hasegawa; Karin Hemmann; Emmeline W Hill; Tosso Leeb; Gabriella Lindgren; Hannes Lohi; Maria Susana Lopes; Beatrice A McGivney; Sofia Mikko; Nicholas Orr; M Cecilia T Penedo; Richard J Piercy; Marja Raekallio; Stefan Rieder; Knut H Røed; June Swinburne; Teruaki Tozaki; Mark Vaudin; Claire M Wade; Molly E McCue
Journal:  PLoS Genet       Date:  2013-01-17       Impact factor: 5.917

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  14 in total

1.  Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model.

Authors:  Brandon D Velie; Mette Lillie; Kim Jäderkvist Fegraeus; Maria K Rosengren; Marina Solé; Maja Wiklund; Carl-Fredrik Ihler; Eric Strand; Gabriella Lindgren
Journal:  BMC Genomics       Date:  2019-02-04       Impact factor: 3.969

Review 2.  What animals can teach us about evolution, the human genome, and human disease.

Authors:  Kerstin Lindblad-Toh
Journal:  Ups J Med Sci       Date:  2020-02-14       Impact factor: 2.384

3.  Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations.

Authors:  Pamela Wiener; Christelle Robert; Abulgasim Ahbara; Mazdak Salavati; Ayele Abebe; Adebabay Kebede; David Wragg; Juliane Friedrich; Deepali Vasoya; David A Hume; Appolinaire Djikeng; Mick Watson; James G D Prendergast; Olivier Hanotte; Joram M Mwacharo; Emily L Clark
Journal:  Genome Biol Evol       Date:  2021-03-01       Impact factor: 3.416

4.  Building the vertebrate codex using the gene breaking protein trap library.

Authors:  Noriko Ichino; MaKayla R Serres; Rhianna M Urban; Mark D Urban; Anthony J Treichel; Kyle J Schaefbauer; Lauren E Tallant; Gaurav K Varshney; Kimberly J Skuster; Melissa S McNulty; Camden L Daby; Ying Wang; Hsin-Kai Liao; Suzan El-Rass; Yonghe Ding; Weibin Liu; Jennifer L Anderson; Mark D Wishman; Ankit Sabharwal; Lisa A Schimmenti; Sridhar Sivasubbu; Darius Balciunas; Matthias Hammerschmidt; Steven Arthur Farber; Xiao-Yan Wen; Xiaolei Xu; Maura McGrail; Jeffrey J Essner; Shawn M Burgess; Karl J Clark; Stephen C Ekker
Journal:  Elife       Date:  2020-08-11       Impact factor: 8.713

5.  Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research.

Authors:  Zhijin Liu; Xinxin Tan; Pablo Orozco-terWengel; Xuming Zhou; Liye Zhang; Shilin Tian; Zhongze Yan; Huailiang Xu; Baoping Ren; Peng Zhang; Zuofu Xiang; Binghua Sun; Christian Roos; Michael W Bruford; Ming Li
Journal:  Gigascience       Date:  2018-09-01       Impact factor: 6.524

6.  Adding resolution and dimensionality to comparative genomics: moving from reference genomes to clade genomics.

Authors:  Jeffrey Rogers
Journal:  Genome Biol       Date:  2018-08-14       Impact factor: 13.583

7.  Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations.

Authors:  Salvador Daniel Rivas-Carrillo; Mats E Pettersson; Carl-Johan Rubin; Patric Jern
Journal:  Proc Natl Acad Sci U S A       Date:  2018-10-08       Impact factor: 11.205

8.  Contrasting Patterns of Rapid Molecular Evolution within the p53 Network across Mammal and Sauropsid Lineages.

Authors:  Courtney N Passow; Anne M Bronikowski; Heath Blackmon; Shikha Parsai; Tonia S Schwartz; Suzanne E McGaugh
Journal:  Genome Biol Evol       Date:  2019-03-01       Impact factor: 3.416

9.  The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene.

Authors:  Pernille Nilsson; Monica H Solbakken; Boris V Schmid; Russell J S Orr; Ruichen Lv; Yujun Cui; Yajun Song; Yujiang Zhang; Helle T Baalsrud; Ole K Tørresen; Nils Chr Stenseth; Ruifu Yang; Kjetill S Jakobsen; William Ryan Easterday; Sissel Jentoft
Journal:  Genome Biol Evol       Date:  2020-02-01       Impact factor: 3.416

10.  Chick fetal organ spheroids as a model to study development and disease.

Authors:  Soran Dakhel; Wayne I L Davies; Justin V Joseph; Tushar Tomar; Silvia Remeseiro; Lena Gunhaga
Journal:  BMC Mol Cell Biol       Date:  2021-07-05
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