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For: Wang B, Ekblom R, Bunikis I, Siitari H, Höglund J. Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution. BMC Genomics 2014;15:180. [PMID: 24602261 PMCID: PMC4022176 DOI: 10.1186/1471-2164-15-180] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 02/26/2014] [Indexed: 01/19/2023]  Open
Number Cited by Other Article(s)
1
Ottenburghs J. Avian introgression patterns are consistent with Haldane's Rule. J Hered 2022;113:363-370. [PMID: 35134952 PMCID: PMC9308041 DOI: 10.1093/jhered/esac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022]  Open
2
Charlesworth D, Graham C, Trivedi U, Gardner J, Bergero R. PromethION sequencing and assembly of the genome of Micropoecilia picta, a fish with a highly Degenerated Y chromosome. Genome Biol Evol 2021;13:6326803. [PMID: 34297069 PMCID: PMC8449826 DOI: 10.1093/gbe/evab171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2021] [Indexed: 11/13/2022]  Open
3
Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists. Sci Rep 2020;10:18236. [PMID: 33106560 PMCID: PMC7588437 DOI: 10.1038/s41598-020-75270-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 09/21/2020] [Indexed: 02/07/2023]  Open
4
Minias P, Dunn PO, Whittingham LA, Johnson JA, Oyler-McCance SJ. Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse. Sci Rep 2019;9:6407. [PMID: 31015535 PMCID: PMC6478925 DOI: 10.1038/s41598-019-42885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/11/2019] [Indexed: 12/30/2022]  Open
5
Marcionetti A, Rossier V, Roux N, Salis P, Laudet V, Salamin N. Insights into the Genomics of Clownfish Adaptive Radiation: Genetic Basis of the Mutualism with Sea Anemones. Genome Biol Evol 2019;11:869-882. [PMID: 30830203 PMCID: PMC6430985 DOI: 10.1093/gbe/evz042] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2019] [Indexed: 02/06/2023]  Open
6
Kozma R, Rödin-Mörch P, Höglund J. Genomic regions of speciation and adaptation among three species of grouse. Sci Rep 2019;9:812. [PMID: 30692562 PMCID: PMC6349846 DOI: 10.1038/s41598-018-36880-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 11/27/2018] [Indexed: 12/30/2022]  Open
7
Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S. Chromosome assembly of large and complex genomes using multiple references. Genome Res 2018;28:1720-1732. [PMID: 30341161 PMCID: PMC6211643 DOI: 10.1101/gr.236273.118] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 09/24/2018] [Indexed: 11/25/2022]
8
Tiley GP, Kimball RT, Braun EL, Burleigh JG. Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution. BMC Genomics 2018;19:336. [PMID: 29739321 PMCID: PMC5941490 DOI: 10.1186/s12864-018-4711-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 04/23/2018] [Indexed: 12/31/2022]  Open
9
Gayk ZG, Le Duc D, Horn J, Lindsay AR. Genomic insights into natural selection in the common loon (Gavia immer): evidence for aquatic adaptation. BMC Evol Biol 2018;18:64. [PMID: 29703132 PMCID: PMC5921391 DOI: 10.1186/s12862-018-1181-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/16/2018] [Indexed: 11/12/2022]  Open
10
Lischer HEL, Shimizu KK. Reference-guided de novo assembly approach improves genome reconstruction for related species. BMC Bioinformatics 2017;18:474. [PMID: 29126390 PMCID: PMC5681816 DOI: 10.1186/s12859-017-1911-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 11/01/2017] [Indexed: 12/31/2022]  Open
11
Kang L, George P, Price DK, Sharakhov I, Michalak P. Mapping Genomic Scaffolds to Chromosomes Using Laser Capture Microdissection in Application to Hawaiian Picture-Winged Drosophila. Cytogenet Genome Res 2017;152:204-212. [PMID: 29130948 DOI: 10.1159/000481790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2017] [Indexed: 11/19/2022]  Open
12
Pardal S, Drews A, Alves JA, Ramos JA, Westerdahl H. Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit. Immunogenetics 2017;69:463-478. [PMID: 28534224 PMCID: PMC5486808 DOI: 10.1007/s00251-017-0993-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/22/2017] [Indexed: 11/29/2022]
13
Willoughby JR, Ivy JA, Lacy RC, Doyle JM, DeWoody JA. Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species. PLoS One 2017;12:e0175996. [PMID: 28423000 PMCID: PMC5396937 DOI: 10.1371/journal.pone.0175996] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/04/2017] [Indexed: 12/01/2022]  Open
14
Rousselle M, Faivre N, Ballenghien M, Galtier N, Nabholz B. Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies. Genome Biol Evol 2016;8:3108-3119. [PMID: 27590089 PMCID: PMC5174731 DOI: 10.1093/gbe/evw214] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
15
Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016;25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
16
Delph LF, Demuth JP. Haldane’s Rule: Genetic Bases and Their Empirical Support. J Hered 2016;107:383-91. [DOI: 10.1093/jhered/esw026] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/27/2016] [Indexed: 11/14/2022]  Open
17
Wright AE, Harrison PW, Zimmer F, Montgomery SH, Pointer MA, Mank JE. Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution. Mol Ecol 2016;24:1218-35. [PMID: 25689782 PMCID: PMC4737241 DOI: 10.1111/mec.13113] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 02/02/2023]
18
Kozma R, Melsted P, Magnússon KP, Höglund J. Looking into the past - the reaction of three grouse species to climate change over the last million years using whole genome sequences. Mol Ecol 2016;25:570-80. [PMID: 26607571 DOI: 10.1111/mec.13496] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 01/08/2023]
19
Heidaritabar M, Calus MPL, Megens HJ, Vereijken A, Groenen MAM, Bastiaansen JWM. Accuracy of genomic prediction using imputed whole-genome sequence data in white layers. J Anim Breed Genet 2016;133:167-79. [PMID: 26776363 DOI: 10.1111/jbg.12199] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/26/2015] [Indexed: 01/17/2023]
20
Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLoS One 2015;10:e0143929. [PMID: 26716693 PMCID: PMC4696846 DOI: 10.1371/journal.pone.0143929] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/12/2015] [Indexed: 01/30/2023]  Open
21
Oyler-McCance SJ, Cornman RS, Jones KL, Fike JA. Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds. Heredity (Edinb) 2015;115:452-9. [PMID: 26014526 PMCID: PMC4611240 DOI: 10.1038/hdy.2015.46] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 03/13/2015] [Accepted: 04/07/2015] [Indexed: 01/29/2023]  Open
22
Dunn CW, Ryan JF. The evolution of animal genomes. Curr Opin Genet Dev 2015;35:25-32. [PMID: 26363125 DOI: 10.1016/j.gde.2015.08.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/18/2015] [Accepted: 08/20/2015] [Indexed: 11/18/2022]
23
Hoen DR, Hickey G, Bourque G, Casacuberta J, Cordaux R, Feschotte C, Fiston-Lavier AS, Hua-Van A, Hubley R, Kapusta A, Lerat E, Maumus F, Pollock DD, Quesneville H, Smit A, Wheeler TJ, Bureau TE, Blanchette M. A call for benchmarking transposable element annotation methods. Mob DNA 2015;6:13. [PMID: 26244060 PMCID: PMC4524446 DOI: 10.1186/s13100-015-0044-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/22/2015] [Indexed: 12/31/2022]  Open
24
Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015;145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
25
Miller JM, Moore SS, Stothard P, Liao X, Coltman DW. Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics 2015;16:397. [PMID: 25990117 PMCID: PMC4438629 DOI: 10.1186/s12864-015-1618-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/05/2015] [Indexed: 02/08/2023]  Open
26
Hormozdiari F, Eskin E. Memory efficient assembly of human genome. J Bioinform Comput Biol 2015;13:1550008. [PMID: 25603998 DOI: 10.1142/s0219720015500080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
27
Koepfli KP, Paten B, O'Brien SJ. The Genome 10K Project: a way forward. Annu Rev Anim Biosci 2015;3:57-111. [PMID: 25689317 PMCID: PMC5837290 DOI: 10.1146/annurev-animal-090414-014900] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
28
Differential introgression and effective size of marker type influence phylogenetic inference of a recently divergent avian group (Phasianidae: Tympanuchus). Mol Phylogenet Evol 2014;84:1-13. [PMID: 25554526 DOI: 10.1016/j.ympev.2014.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 11/20/2022]
29
McMahon BJ, Teeling EC, Höglund J. How and why should we implement genomics into conservation? Evol Appl 2014;7:999-1007. [PMID: 25553063 PMCID: PMC4231591 DOI: 10.1111/eva.12193] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 06/19/2014] [Indexed: 12/14/2022]  Open
30
Ekblom R, Wolf JBW. A field guide to whole-genome sequencing, assembly and annotation. Evol Appl 2014;7:1026-42. [PMID: 25553065 PMCID: PMC4231593 DOI: 10.1111/eva.12178] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/20/2014] [Indexed: 12/12/2022]  Open
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