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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...the sensitivity and specificity of SV detection.Population analyses based on genomic SNP, indel, and microsatellite markers suggest that cattle can be divided into three major genetic groups (MacHugh et al. 1997; Bolormaa et al. 2013; Pérez O'Brien et al. 2014), including Asian indicine, Eurasian taurine...
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Research: The house fly Y Chromosome is young and minimally differentiated from its ancient X Chromosome partner
- Richard P. Meisel,
- Christopher A. Gonzales,
- and Hoang Luu
Genome Res. August 2017 27: 1417-1426; Published in Advance June 15, 2017, doi:10.1101/gr.215509.116
...). The house fly karyotype resembles that of the ancestral brachyceran, with five large euchromatic elements and a heterochromatic sex chromosome pair (Boyes et al. 1964). As in other species with that ancestral karyotype, the house fly X and Y Chromosomes can be distinguished based on their length...
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Research: Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal
- Pille Hallast,
- Pierpaolo Maisano Delser,
- Chiara Batini,
- Daniel Zadik,
- Mariano Rocchi,
- Werner Schempp,
- Chris Tyler-Smith,
- and Mark A. Jobling
Genome Res. April 2016 26: 427-439; Published in Advance February 16, 2016, doi:10.1101/gr.198754.115
...Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal Pille Hallast 1 , 2 , Pierpaolo Maisano Delser 1 , 6 , Chiara Batini 1 , Daniel Zadik 1 , Mariano Rocchi 3...
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Letter: Global distribution of genomic diversity underscores rich complex history of continental human populations
- Adam Auton,
- Katarzyna Bryc,
- Adam R. Boyko,
- Kirk E. Lohmueller,
- John Novembre,
- Andy Reynolds,
- Amit Indap,
- Mark H. Wright,
- Jeremiah D. Degenhardt,
- Ryan N. Gutenkunst,
- Karen S. King,
- Matthew R. Nelson,
- and Carlos D. Bustamante
Genome Res. May 2009 19: 795-803; Published in Advance February 13, 2009, doi:10.1101/gr.088898.108
...and East Asian populations. Using structure with K = 3 we estimated an average of 32.5% European ancestry in Mexican individuals (95% 6 3.3% confidence interval [C.I.]; see Fig. 1B), which is lower than some previous estimates based on microsatellite or ‘‘ancestry informative’’ markers (Salari et al. 2005...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...recombination map for a rhesus macaque pedigree using crossovers among 241 microsatellite loci (Rogers et al. 2006) also suggested reduced recombination per megabase in rhesus relative to human. Demographic analysis of two rhesus macaque populations The estimated effective population sizes, based on the number...
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LETTER: Complex SNP-Based Haplotypes in Three Human Helicases: Implications for Cancer Association Studies
- Dimitra Trikka,
- Zhe Fang,
- Alex Renwick,
- Sally H. Jones,
- Ranajit Chakraborty,
- Marek Kimmel,
- and David L. Nelson
Genome Res. April 1, 2002 12: 627-639; doi:10.1101/gr.176702
...the variation observed in the helicases in the four ethnic groups. Creation of complex haplotypes based on multiple markers can strengthen the power of association studies, and such data will be further useful in comparisons of haplotype frequencies and distributions across the human and the human population...
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LETTER: Genetic Evidence on the Origins of Indian Caste Populations
- Michael Bamshad,
- Toomas Kivisild,
- W. Scott Watkins,
- Mary E. Dixon,
- Chris E. Ricker,
- Baskara B. Rao,
- J. Mastan Naidu,
- B.V. Ravi Prasad,
- P. Govinda Reddy,
- Arani Rasanayagam,
- Surinder S. Papiha,
- Richard Villems,
- Alan J. Redd,
- Michael F. Hammer,
- Son V. Nguyen,
- Marion L. Carroll,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. June 1, 2001 11: 994-1004; Published in Advance May 8, 2001, doi:10.1101/gr.173301
...in the upper castes. Importantly, five different types of data (mtDNA HVR1 sequence, mtDNA RSPs, Y-chromosome STRs, Y-chromosome biallelic polymorphisms, and autosomal Alu polymorphisms) support the same general pattern: relatively smaller genetic distances from European populations as one moves from lower...
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LETTER: Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms
- W. Scott Watkins,
- Alan R. Rogers,
- Christopher T. Ostler,
- Steve Wooding,
- Michael J. Bamshad,
- Anna-Marie E. Brassington,
- Marion L. Carroll,
- Son V. Nguyen,
- Jerilyn A. Walker,
- B.V. Ravi Prasad,
- P. Govinda Reddy,
- Pradipta K. Das,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. July 2003 13: 1607-1618; Published in Advance June 12, 2003, doi:10.1101/gr.894603
...progressed to include studies of mtDNA ( Cann et al. 1987 ; Vigilant et al. 1991 ; Stoneking and Soodyall 1996 ; Ingman et al. 2000 ; Bamshad et al. 2001 ), Y-chromosome variation ( Hammer et al. 1998 ; Seielstad et al. 1999 ; Forster et al. 2000 ), -wide polymorphic autosomal microsatellite variation...
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LETTER: CeRep25B Forms Chromosome-Specific Minisatellite Arrays in Caenorhabditis elegans
- Dave Pilgrim
Genome Res. November 1, 1998 8: 1192-1201; doi:10.1101/gr.8.11.1192
...occurrences of the repeat. Sequences in which fewer than 22/24 bases matched the consensus were ignored. No match outside C. elegans was found. Apart from a single copy of CeRep25B on cosmid C07E3 (two mismatches to 24-bp consensus) on Chromosome II, 13 different C. elegans cosmids in two large clusters...
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LETTER: Detection of Numerous Y Chromosome Biallelic Polymorphisms by Denaturing High-Performance Liquid Chromatography
- Peter A. Underhill,
- Li Jin,
- Alice A. Lin,
- S. Qasim Mehdi,
- Trefor Jenkins,
- Douglas Vollrath,
- Ronald W. Davis,
- L. Luca Cavalli-Sforza,
- and Peter J. Oefner
Genome Res. October 1, 1997 7: 996-1005; doi:10.1101/gr.7.10.996
...et al. 1991 ). Although allowing the analysis of human history based on populations rather than the history of individual genes ( Goldstein et al. 1995 ; Jorde et al. 1995 ), autosomal polymorphic tandem repeat motifs, such as microsatellites, are also subject to recombination processes, high...

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