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For: Low WY, Tearle R, Bickhart DM, Rosen BD, Kingan SB, Swale T, Thibaud-Nissen F, Murphy TD, Young R, Lefevre L, Hume DA, Collins A, Ajmone-Marsan P, Smith TPL, Williams JL. Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nat Commun 2019;10:260. [PMID: 30651564 DOI: 10.1038/s41467-018-08260-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/21/2018] [Indexed: 01/08/2023]  Open
Number Cited by Other Article(s)
51
Li R, Yang P, Dai X, Asadollahpour Nanaei H, Fang W, Yang Z, Cai Y, Zheng Z, Wang X, Jiang Y. A near complete genome for goat genetic and genomic research. Genet Sel Evol 2021;53:74. [PMID: 34507524 PMCID: PMC8434745 DOI: 10.1186/s12711-021-00668-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 09/01/2021] [Indexed: 01/29/2023]  Open
52
Ren Y, MacPhillamy C, To TH, Smith TPL, Williams JL, Low WY. Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes. Genomics 2021;113:3599-3609. [PMID: 34455036 DOI: 10.1016/j.ygeno.2021.08.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 11/27/2022]
53
Jackson EK, Bellott DW, Cho TJ, Skaletsky H, Hughes JF, Pyntikova T, Page DC. Large palindromes on the primate X Chromosome are preserved by natural selection. Genome Res 2021;31:1337-1352. [PMID: 34290043 PMCID: PMC8327919 DOI: 10.1101/gr.275188.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/17/2021] [Indexed: 12/27/2022]
54
Zhang R, Wang J, Xiao Z, Zou C, An Q, Li H, Zhou X, Wu Z, Shi D, Deng Y, Yang S, Wei Y. The Expression Profiles of mRNAs and lncRNAs in Buffalo Muscle Stem Cells Driving Myogenic Differentiation. Front Genet 2021;12:643497. [PMID: 34306003 PMCID: PMC8294193 DOI: 10.3389/fgene.2021.643497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/25/2021] [Indexed: 11/13/2022]  Open
55
Nascimento AV, Romero ARS, Nawaz MY, Cardoso DF, Santos DJA, Gondro C, Tonhati H. An updated Axiom buffalo genotyping array map and mapping of cattle quantitative trait loci to the new water buffalo reference genome assembly. Anim Genet 2021;52:505-508. [PMID: 34106478 DOI: 10.1111/age.13103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 11/30/2022]
56
Li Y, Jin Y, Zhang J, Pan H, Wu L, Liu D, Liu J, Hu J, Shen J. Recovery of human gut microbiota genomes with third-generation sequencing. Cell Death Dis 2021;12:569. [PMID: 34078878 PMCID: PMC8172872 DOI: 10.1038/s41419-021-03829-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022]
57
SNPRBb: economically important trait specific SNP resources of buffalo (Bubalus bubalis). CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01210-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
58
Peng Y, Li H, Liu Z, Zhang C, Li K, Gong Y, Geng L, Su J, Guan X, Liu L, Zhou R, Zhao Z, Guo J, Liang Q, Li X. Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology. Mol Ecol Resour 2021;21:2093-2108. [PMID: 33829635 DOI: 10.1111/1755-0998.13397] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
59
Garg S. Computational methods for chromosome-scale haplotype reconstruction. Genome Biol 2021;22:101. [PMID: 33845884 PMCID: PMC8040228 DOI: 10.1186/s13059-021-02328-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/25/2021] [Indexed: 12/13/2022]  Open
60
KAIRI AMIT, SAHU TANMAYAKUMAR, RAO ATMAKURIRAMAKRISHNA. An information system on genomic elements and predicted protein structures of buffalo (Bubalus bubalis). THE INDIAN JOURNAL OF ANIMAL SCIENCES 2021. [DOI: 10.56093/ijans.v90i11.111494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
61
Curaudeau M, Rozzi R, Hassanin A. The genome of the lowland anoa (Bubalus depressicornis) illuminates the origin of river and swamp buffalo. Mol Phylogenet Evol 2021;161:107170. [PMID: 33798669 DOI: 10.1016/j.ympev.2021.107170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/12/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
62
Shao B, Sun H, Ahmad MJ, Ghanem N, Abdel-Shafy H, Du C, Deng T, Mansoor S, Zhou Y, Yang Y, Zhang S, Yang L, Hua G. Genetic Features of Reproductive Traits in Bovine and Buffalo: Lessons From Bovine to Buffalo. Front Genet 2021;12:617128. [PMID: 33833774 PMCID: PMC8021858 DOI: 10.3389/fgene.2021.617128] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/25/2021] [Indexed: 11/13/2022]  Open
63
Rehman SU, Hassan FU, Luo X, Li Z, Liu Q. Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges. Animals (Basel) 2021;11:904. [PMID: 33809937 PMCID: PMC8004149 DOI: 10.3390/ani11030904] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/17/2022]  Open
64
Pineda PS, Flores EB, Herrera JRV, Low WY. Opportunities and Challenges for Improving the Productivity of Swamp Buffaloes in Southeastern Asia. Front Genet 2021;12:629861. [PMID: 33828581 PMCID: PMC8021093 DOI: 10.3389/fgene.2021.629861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/26/2021] [Indexed: 11/18/2022]  Open
65
Liang D, Zhao P, Si J, Fang L, Pairo-Castineira E, Hu X, Xu Q, Hou Y, Gong Y, Liang Z, Tian B, Mao H, Yindee M, Faruque MO, Kongvongxay S, Khamphoumee S, Liu GE, Wu DD, Barker JSF, Han J, Zhang Y. Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis). Mol Biol Evol 2021;38:1122-1136. [PMID: 33212507 PMCID: PMC7947781 DOI: 10.1093/molbev/msaa279] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
66
Lázaro SF, Tonhati H, Oliveira HR, Silva AA, Nascimento AV, Santos DJA, Stefani G, Brito LF. Genomic studies of milk-related traits in water buffalo (Bubalus bubalis) based on single-step genomic best linear unbiased prediction and random regression models. J Dairy Sci 2021;104:5768-5793. [PMID: 33685677 DOI: 10.3168/jds.2020-19534] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/02/2021] [Indexed: 01/14/2023]
67
Macciotta NPP, Colli L, Cesarani A, Ajmone-Marsan P, Low WY, Tearle R, Williams JL. The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events. Genet Sel Evol 2021;53:20. [PMID: 33639853 PMCID: PMC7912491 DOI: 10.1186/s12711-021-00616-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/17/2021] [Indexed: 01/03/2023]  Open
68
Cosenza G, Gallo D, Auzino B, Gaspa G, Pauciullo A. Complete CSN1S2 Characterization, Novel Allele Identification and Association With Milk Fatty Acid Composition in River Buffalo. Front Genet 2021;11:622494. [PMID: 33613624 PMCID: PMC7890360 DOI: 10.3389/fgene.2020.622494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]  Open
69
Noce A, Qanbari S, González-Prendes R, Brenmoehl J, Luigi-Sierra MG, Theerkorn M, Fiege MA, Pilz H, Bota A, Vidu L, Horwath C, Haraszthy L, Penchev P, Ilieva Y, Peeva T, Lüpcke W, Krawczynski R, Wimmers K, Thiele M, Hoeflich A. Genetic Diversity of Bubalus bubalis in Germany and Global Relations of Its Genetic Background. Front Genet 2021;11:610353. [PMID: 33552127 PMCID: PMC7863760 DOI: 10.3389/fgene.2020.610353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/30/2020] [Indexed: 11/29/2022]  Open
70
Hruska JP, Manthey JD. De novo assembly of a chromosome-scale reference genome for the northern flicker Colaptes auratus. G3 (BETHESDA, MD.) 2021;11:jkaa026. [PMID: 33561233 PMCID: PMC8022726 DOI: 10.1093/g3journal/jkaa026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/12/2020] [Indexed: 11/15/2022]
71
Du H, Diao C, Zhao P, Zhou L, Liu JF. Integrated hybrid de novo assembly technologies to obtain high-quality pig genome using short and long reads. Brief Bioinform 2021;22:6082823. [PMID: 33429431 DOI: 10.1093/bib/bbaa399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/20/2020] [Accepted: 12/08/2020] [Indexed: 11/12/2022]  Open
72
Rafiepour M, Ebrahimie E, Vahidi MF, Salekdeh GH, Niazi A, Dadpasand M, Liang D, Si J, Ding X, Han J, Zhang Y, Qanbari S. Whole-Genome Resequencing Reveals Adaptation Prior to the Divergence of Buffalo Subspecies. Genome Biol Evol 2020;13:5976760. [PMID: 33179728 DOI: 10.1093/gbe/evaa231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 01/30/2023]  Open
73
Doyle SR, Tracey A, Laing R, Holroyd N, Bartley D, Bazant W, Beasley H, Beech R, Britton C, Brooks K, Chaudhry U, Maitland K, Martinelli A, Noonan JD, Paulini M, Quail MA, Redman E, Rodgers FH, Sallé G, Shabbir MZ, Sankaranarayanan G, Wit J, Howe KL, Sargison N, Devaney E, Berriman M, Gilleard JS, Cotton JA. Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm. Commun Biol 2020;3:656. [PMID: 33168940 PMCID: PMC7652881 DOI: 10.1038/s42003-020-01377-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/14/2020] [Indexed: 12/31/2022]  Open
74
Salavati M, Caulton A, Clark R, Gazova I, Smith TPL, Worley KC, Cockett NE, Archibald AL, Clarke SM, Murdoch BM, Clark EL. Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0). Front Genet 2020;11:580580. [PMID: 33193703 PMCID: PMC7645153 DOI: 10.3389/fgene.2020.580580] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/09/2020] [Indexed: 02/04/2023]  Open
75
Buckley RM, Davis BW, Brashear WA, Farias FHG, Kuroki K, Graves T, Hillier LW, Kremitzki M, Li G, Middleton RP, Minx P, Tomlinson C, Lyons LA, Murphy WJ, Warren WC. A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLoS Genet 2020;16:e1008926. [PMID: 33090996 PMCID: PMC7581003 DOI: 10.1371/journal.pgen.1008926] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/10/2020] [Indexed: 12/30/2022]  Open
76
Sun T, Huang GY, Wang ZH, Teng SH, Cao YH, Sun JL, Hanif Q, Chen NB, Lei CZ, Liao YY. Selection signatures of Fuzhong Buffalo based on whole-genome sequences. BMC Genomics 2020;21:674. [PMID: 32993537 PMCID: PMC7526191 DOI: 10.1186/s12864-020-07095-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022]  Open
77
Apolipoprotein A1 and Ceruloplasmin, the key crosstalk players between the liver and adipose tissue during early postpartum of buffaloes: An in-Silico transcriptome based network analysis. Comput Biol Med 2020;126:104024. [PMID: 33059235 DOI: 10.1016/j.compbiomed.2020.104024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/04/2020] [Accepted: 09/26/2020] [Indexed: 11/20/2022]
78
Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication. Nat Commun 2020;11:4739. [PMID: 32958756 PMCID: PMC7505982 DOI: 10.1038/s41467-020-18550-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/26/2020] [Indexed: 12/30/2022]  Open
79
El-Khishin DA, Ageez A, Saad ME, Ibrahim A, Shokrof M, Hassan LR, Abouelhoda MI. Sequencing and assembly of the Egyptian buffalo genome. PLoS One 2020;15:e0237087. [PMID: 32813723 PMCID: PMC7437910 DOI: 10.1371/journal.pone.0237087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/20/2020] [Indexed: 01/09/2023]  Open
80
Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species. G3-GENES GENOMES GENETICS 2020;10:2327-2343. [PMID: 32434754 PMCID: PMC7341147 DOI: 10.1534/g3.120.401090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
81
Hilliard W, MacDonald ML, Lee KH. Chromosome-scale scaffolds for the Chinese hamster reference genome assembly to facilitate the study of the CHO epigenome. Biotechnol Bioeng 2020;117:2331-2339. [PMID: 32410221 DOI: 10.1002/bit.27432] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 04/21/2020] [Accepted: 05/12/2020] [Indexed: 02/03/2023]
82
Genomic Identification, Evolution, and Expression Analysis of Collagen Genes Family in Water Buffalo during Lactation. Genes (Basel) 2020;11:genes11050515. [PMID: 32384775 PMCID: PMC7288458 DOI: 10.3390/genes11050515] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 11/17/2022]  Open
83
Liu Q, Wang X, Xiao Y, Zhao H, Xu S, Wang Y, Wu L, Zhou L, Du T, Lv X, Li J. Sequencing of the black rockfish chromosomal genome provides insight into sperm storage in the female ovary. DNA Res 2020;26:453-464. [PMID: 31711192 PMCID: PMC6993816 DOI: 10.1093/dnares/dsz023] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 11/09/2019] [Indexed: 01/09/2023]  Open
84
Usai G, Mascagni F, Giordani T, Vangelisti A, Bosi E, Zuccolo A, Ceccarelli M, King R, Hassani-Pak K, Zambrano LS, Cavallini A, Natali L. Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020;102:600-614. [PMID: 31808196 DOI: 10.1111/tpj.14635] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 11/13/2019] [Accepted: 11/26/2019] [Indexed: 05/22/2023]
85
Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, Lee J, Pang AWC, Heaton MP, Phillippy AM, Hiendleder S, Smith TPL, Williams JL. Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nat Commun 2020;11:2071. [PMID: 32350247 PMCID: PMC7190621 DOI: 10.1038/s41467-020-15848-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 03/27/2020] [Indexed: 12/30/2022]  Open
86
Mishra DC, Sikka P, Yadav S, Bhati J, Paul SS, Jerome A, Singh I, Nath A, Budhlakoti N, Rao AR, Rai A, Chaturvedi KK. Identification and characterization of trait-specific SNPs using ddRAD sequencing in water buffalo. Genomics 2020;112:3571-3578. [PMID: 32320820 DOI: 10.1016/j.ygeno.2020.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/19/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
87
The long-term restoration of ecosystem complexity. Nat Ecol Evol 2020;4:676-685. [DOI: 10.1038/s41559-020-1154-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 02/19/2020] [Indexed: 12/25/2022]
88
Singh B, Mal G, Kues WA, Yadav PS. The domesticated buffalo - An emerging model for experimental and therapeutic use of extraembryonic tissues. Theriogenology 2020;151:95-102. [PMID: 32320839 DOI: 10.1016/j.theriogenology.2020.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/12/2020] [Accepted: 04/04/2020] [Indexed: 12/16/2022]
89
Jayakumar V, Ishii H, Seki M, Kumita W, Inoue T, Hase S, Sato K, Okano H, Sasaki E, Sakakibara Y. An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data. BMC Genomics 2020;21:243. [PMID: 32241258 PMCID: PMC7114785 DOI: 10.1186/s12864-020-6657-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 12/31/2022]  Open
90
Teterina AA, Willis JH, Phillips PC. Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization. Genetics 2020;214:769-780. [PMID: 32111628 PMCID: PMC7153949 DOI: 10.1534/genetics.119.303018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/24/2020] [Indexed: 12/23/2022]  Open
91
Rice ES, Koren S, Rhie A, Heaton MP, Kalbfleisch TS, Hardy T, Hackett PH, Bickhart DM, Rosen BD, Ley BV, Maurer NW, Green RE, Phillippy AM, Petersen JL, Smith TPL. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. Gigascience 2020;9:giaa029. [PMID: 32242610 PMCID: PMC7118895 DOI: 10.1093/gigascience/giaa029] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/08/2020] [Accepted: 03/10/2020] [Indexed: 12/30/2022]  Open
92
Wang ZL, Zhu YQ, Yan Q, Yan WY, Zheng HJ, Zeng ZJ. A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome. Front Genet 2020;11:279. [PMID: 32292419 PMCID: PMC7119468 DOI: 10.3389/fgene.2020.00279] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/09/2020] [Indexed: 11/13/2022]  Open
93
Verdugo MP, Mullin VE, Scheu A, Mattiangeli V, Daly KG, Maisano Delser P, Hare AJ, Burger J, Collins MJ, Kehati R, Hesse P, Fulton D, Sauer EW, Mohaseb FA, Davoudi H, Khazaeli R, Lhuillier J, Rapin C, Ebrahimi S, Khasanov M, Vahidi SMF, MacHugh DE, Ertuğrul O, Koukouli-Chrysanthaki C, Sampson A, Kazantzis G, Kontopoulos I, Bulatovic J, Stojanović I, Mikdad A, Benecke N, Linstädter J, Sablin M, Bendrey R, Gourichon L, Arbuckle BS, Mashkour M, Orton D, Horwitz LK, Teasdale MD, Bradley DG. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. SCIENCE (NEW YORK, N.Y.) 2020;365:173-176. [PMID: 31296769 DOI: 10.1126/science.aav1002] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 06/14/2019] [Indexed: 11/02/2022]
94
Lu XR, Duan AQ, Li WQ, Abdel-Shafy H, Rushdi HE, Liang SS, Ma XY, Liang XW, Deng TX. Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk production traits in Chinese buffalo breeds. J Dairy Sci 2020;103:4545-4556. [PMID: 32147265 DOI: 10.3168/jds.2019-17364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/13/2020] [Indexed: 11/19/2022]
95
VOLLGER MITCHELLR, LOGSDON GLENNISA, AUDANO PETERA, SULOVARI ARVIS, PORUBSKY DAVID, PELUSO PAUL, WENGER AARONM, CONCEPCION GREGORYT, KRONENBERG ZEVN, MUNSON KATHERINEM, BAKER CARL, SANDERS ASHLEYD, SPIERINGS DIANAC, LANSDORP PETERM, SURTI URVASHI, HUNKAPILLER MICHAELW, EICHLER EVANE. Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads. Ann Hum Genet 2020;84:125-140. [PMID: 31711268 PMCID: PMC7015760 DOI: 10.1111/ahg.12364] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 01/14/2023]
96
Li H, Huang K, Wang P, Feng T, Shi D, Cui K, Luo C, Shafique L, Qian Q, Ruan J, Liu Q. Comparison of Long Non-Coding RNA Expression Profiles of Cattle and Buffalo Differing in Muscle Characteristics. Front Genet 2020;11:98. [PMID: 32174968 PMCID: PMC7054449 DOI: 10.3389/fgene.2020.00098] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 01/29/2020] [Indexed: 02/02/2023]  Open
97
Luo X, Zhou Y, Zhang B, Zhang Y, Wang X, Feng T, Li Z, Cui K, Wang Z, Luo C, Li H, Deng Y, Lu F, Han J, Miao Y, Mao H, Yi X, Ai C, Wu S, Li A, Wu Z, Zhuo Z, Da Giang D, Mitra B, Vahidi MF, Mansoor S, Al-Bayatti SA, Sari EM, Gorkhali NA, Prastowo S, Shafique L, Ye G, Qian Q, Chen B, Shi D, Ruan J, Liu Q. Understanding divergent domestication traits from the whole-genome sequencing of swamp- and river-buffalo populations. Natl Sci Rev 2020;7:686-701. [PMID: 34692087 PMCID: PMC8289072 DOI: 10.1093/nsr/nwaa024] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/27/2019] [Accepted: 02/12/2020] [Indexed: 01/01/2023]  Open
98
Ghoreishifar SM, Moradi-Shahrbabak H, Fallahi MH, Jalil Sarghale A, Moradi-Shahrbabak M, Abdollahi-Arpanahi R, Khansefid M. Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis. BMC Genet 2020;21:16. [PMID: 32041535 PMCID: PMC7011551 DOI: 10.1186/s12863-020-0824-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 02/04/2020] [Indexed: 01/06/2023]  Open
99
Zhang Y, Colli L, Barker JSF. Asian water buffalo: domestication, history and genetics. Anim Genet 2020;51:177-191. [PMID: 31967365 DOI: 10.1111/age.12911] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2019] [Indexed: 12/15/2022]
100
Liu R, Low WY, Tearle R, Koren S, Ghurye J, Rhie A, Phillippy AM, Rosen BD, Bickhart DM, Smith TPL, Hiendleder S, Williams JL. New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes. BMC Genomics 2019;20:1000. [PMID: 31856728 PMCID: PMC6923926 DOI: 10.1186/s12864-019-6364-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/02/2019] [Indexed: 12/27/2022]  Open
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