Sex chromosome evolution

Jan 8, 2018

Several lines of our recent research have had mammalian sex chromosome evolution as a common theme. We have been studying the genomic determinants of X chromosome inactivation (XCI; Carrel et al. 2006). By contrasting the evolution of genes on sex chromosomes in eutherians with that of their autosomal homologs in marsupials and monotremes, we were able to shed light on the earliest stages of eutherian sex chromosome evolution (Wilson and Makova 2009). We also recently generated a comprehensive list of pseudogenes on the human Y and studied what determines whether a gene will survive or die on this chromosome (Wilson Sayres and Makova 2013). To test whether selection or drift leads to loss of genes on chromosome Y, we sequenced and analyzed all X-degenerate Y chromosome genes in gorilla (Goto et al. 2009) and are currently characterizing such genes in other primates. (Figure : Wilson Sayres & Makova 2013). Collaborators: Laura Carrel, Paul Medvedev.

Members

Robert Harris

Research Assistant Professor

Marta Tomaszkiewicz

Research Assistant Professor

Publications

M Cechova, R Vegesna, M Tomaszkiewicz, RS Harris, D Chen, S Rangavittal, P Medvedev, KD Makova. Dynamic evolution of great ape Y chromosomes. IN PRESS P NATL ACAD SCI USA, 2020.

Preprint Sex chromosome DOI

R Vegesna, M Tomaszkiewicz, OA Ryder, R Campos-Sánchez, P Medvedev, M DeGiorgio, KD Makova. Ampliconic genes on the great ape Y chromosomes: Rapid evolution of copy number but conservation of expression levels. GENOME BIOL EVOL, 2020.

PDF Sex chromosome DOI

R Vegesna, M Tomaszkiewicz, P Medvedev, KD Makova. Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes. PLOS GENET, 2019.

Sex chromosome DOI

S Rangavittal, N Stopa, M Tomaszkiewicz, K Sahlin, KD Makova, P Medvedev. DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies. BMC GENOMICS, 2019.

Sex chromosome DOI

RS Harris, M Cechova, KD Makova. Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data. BIOINFORMATICS, 2019.

Code Sex chromosome DOI

M Cechova, RS Harris, M Tomaszkiewicz, B Arbeithuber, F Chiaromonte, KD Makova. High Satellite Repeat Turnover in Great Apes Studied with Short- and Long-read Technologies. MOL BIOL EVOL, 2019.

Sex chromosome DOI

K Sahlin, M Tomaszkiewicz, KD Makova, P Medvedev. Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon. NAT COMMUN, 2018.

Sex chromosome DOI

S Warris, E Schijlen, H van de Geest, R Vegesna, T Hesselink, B te Lintel Hekkert, G Sanchez Perez, P Medvedev, KD Makova, D de Ridder. Correcting palindromes in long reads after whole-genome amplification. BMC GENOMICS, 2018.

Sex chromosome DOI

D Ye, AA Zaidi, M Tomaszkiewicz, K Anthony, C Liebowitz, M DeGiorgio, MD Shriver, KD Makova. High Levels of Copy Number Variation of Ampliconic Genes across Major Human Y Haplogroups. GENOME BIOL EVOL, 2018.

Sex chromosome DOI

S Rangavittal, RS Harris, M Cechova, M Tomaszkiewicz, R Chikhi, KD Makova, P Medvedev. RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly. BIOINFORMATICS, 2018.

Sex chromosome DOI

M Tomaszkiewicz, P Medvedev, KD Makova. Y and W Chromosome Assemblies: Approaches and Discoveries. TRENDS GENET, 2017.

Sex chromosome DOI

M Tomaszkiewicz, S Rangavittal, M Cechova, R Campos-Sánchez, HW Fescemyer, RS Harris, D Ye, PCM O’Brien, R Chikhi, OA Ryder, MA Ferguson-Smith, P Medvedev, KD Makova. A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. GENOME RES, 2016.

Sex chromosome DOI

EM Kvikstad, KD Makova. Rapid Evolution of Genes on the Human X Chromosome. eLS, 2013.

Sex chromosome DOI

MA Wilson Sayres, KD Makova. Gene Survival and Death on the Human Y Chromosome. MOL BIOL EVOL, 2013.

Sex chromosome DOI

MA Wilson Sayres, KD Makova. Genome analyses substantiate male mutation bias in many species. BIOESSAYS, 2011.

Sex chromosome DOI

MA Wilson Sayres, C Venditti, M Pagel, KD Makova. DO VARIATIONS IN SUBSTITUTION RATES AND MALE MUTATION BIAS CORRELATE WITH LIFE-HISTORY TRAITS? A STUDY OF 32 MAMMALIAN GENOMES. EVOLUTION, 2011.

Regional variation Sex chromosome DOI

Z Lombard, C Park, KD Makova, M Ramsay. A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis. BIOL DIRECT, 2011.

Sex chromosome DOI

C Park, L Carrel, KD Makova. Strong Purifying Selection at Genes Escaping X Chromosome Inactivation. MOL BIOL EVOL, 2010.

Sex chromosome DOI

MA Wilson, KD Makova. Genomic Analyses of Sex Chromosome Evolution. ANNU REV GENOM HUM G, 2009.

Sex chromosome DOI

MA Wilson, KD Makova. Evolution and Survival on Eutherian Sex Chromosomes. PLOS GENET, 2009.

Sex chromosome DOI

H Goto, L Peng, KD Makova. Evolution of X-Degenerate Y Chromosome Genes in Greater Apes: Conservation of Gene Content in Human and Gorilla, But Not Chimpanzee. J MOL EVOL, 2009.

Sex chromosome DOI

AN Lau, L Peng, H Goto, L Chemnick, OA Ryder, KD Makova. Horse Domestication and Conservation Genetics of Przewalski's Horse Inferred from Sex Chromosomal and Autosomal Sequences. MOL BIOL EVOL, 2009.

Sex chromosome DOI

RA Gibbs, J Rogers, MG Katze, R Bumgarner, GM Weinstock, ER Mardis, KA Remington, RL Strausberg, JC Venter, RK Wilson, MA Batzer, CD Bustamante, EE Eichler, MW Hahn, RC Hardison, KD Makova, W Miller, A Milosavljevic, RE Palermo, A Siepel, JM Sikela, T Attaway, S Bell, KE Bernard, CJ Buhay, MN Chandrabose, M Dao, C Davis, KD Delehaunty, Y Ding, HH Dinh, S Dugan-Rocha, LA Fulton, RA Gabisi, TT Garner, J Godfrey, AC Hawes, J Hernandez, S Hines, M Holder, J Hume, SN Jhangiani, V Joshi, ZM Khan, EF Kirkness, A Cree, RG Fowler, S Lee, LR Lewis, Z Li, Y-S Liu, SM Moore, DM Muzny, LV Nazareth, DN Ngo, GO Okwuonu, G Pai, D Parker, HA Paul, CM Pfannkoch, CS Pohl, Y-H Rogers, SJ Ruiz, A Sabo, J Santibanez, BW Schneider, SM Smith, EJ Sodergren, AF Svatek, TR Utterback, S Vattathil, W Warren, CS White, AT Chinwalla, Y Feng, AL Halpern, LW Hillier, X Huang, P Minx, JO Nelson, KH Pepin, X Qin, GG Sutton, E Venter, BP Walenz, JW Wallis, KC Worley, S-P Yang, SM Jones, MA Marra, M Rocchi, JE Schein, R Baertsch, L Clarke, M Csürös, J Glasscock, RA Harris, PH Havlak, AR Jackson, H Jiang, Y Liu, DN Messina, Y Shen, HX-Z Song, T Wylie, L Zhang, E Birney, K Han, MK Konkel, J Lee, AFA Smit, B Ullmer, H Wang, J Xing, RC Burhans, Z Cheng, JE Karro, J Ma, B Raney, X She, MJ Cox, JP Demuth, LJ Dumas, S-G Han, J Hopkins, A Karimpour-Fard, YH Kim, JR Pollack, T Vinar, C Addo-Quaye, J Degenhardt, A Denby, MJ Hubisz, A Indap, C Kosiol, BT Lahn, HA Lawson, A Marklein, R Nielsen, EJ Vallender, AG Clark, B Ferguson, RD Hernandez, K Hirani, H Kehrer-Sawatzki, J Kolb, S Patil, L-L Pu, Y Ren, DG Smith, DA Wheeler, I Schenck, EV Ball, R Chen, DN Cooper, B Giardine, F Hsu, WJ Kent, A Lesk, DL Nelson, WE O’Brien, K Prüfer, PD Stenson, JC Wallace, H Ke, X-M Liu, P Wang, AP Xiang, F Yang, GP Barber, D Haussler, D Karolchik, AD Kern, RM Kuhn, KE Smith, AS Zwieg. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome. SCIENCE, 2007.

Sex chromosome DOI

MP Goetting-Minesky, KD Makova. Mammalian Male Mutation Bias: Impacts of Generation Time and Regional Variation in Substitution Rates. J MOL EVOL, 2006.

Regional variation Sex chromosome DOI

L Carrel, C Park, S Tyekucheva, J Dunn, F Chiaromonte, KD Makova. Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome. PLOS GENET, 2006.

Sex chromosome DOI

J Taylor, S Tyekucheva, M Zody, F Chiaromonte, KD Makova. Strong and Weak Male Mutation Bias at Different Sites in the Primate Genomes: Insights from the Human-Chimpanzee Comparison. MOL BIOL EVOL, 2006.

Regional variation Sex chromosome DOI

International Chicken Genome Sequencing Consortium, LW Hillier, W Miller, E Birney, W Warren, RC Hardison, CP Ponting, P Bork, DW Burt, MAM Groenen, ME Delany, JB Dodgson, AT Chinwalla, PF Cliften, SW Clifton, KD Delehaunty, C Fronick, RS Fulton, TA Graves, C Kremitzki, D Layman, V Magrini, JD McPherson, TL Miner, P Minx, WE Nash, MN Nhan, JO Nelson, LG Oddy, CS Pohl, J Randall-Maher, SM Smith, JW Wallis, S-P Yang, MN Romanov, CM Rondelli, B Paton, J Smith, D Morrice, L Daniels, HG Tempest, L Robertson, JS Masabanda, DK Griffin, A Vignal, V Fillon, L Jacobbson, S Kerje, L Andersson, RPM Crooijmans, J Aerts, JJ van der Poel, H Ellegren, RB Caldwell, SJ Hubbard, DV Grafham, AM Kierzek, SR McLaren, IM Overton, H Arakawa, KJ Beattie, Y Bezzubov, PE Boardman, JK Bonfield, MDR Croning, RM Davies, MD Francis, SJ Humphray, CE Scott, RG Taylor, C Tickle, WRA Brown, J Rogers, J-M Buerstedde, SA Wilson, L Stubbs, I Ovcharenko, L Gordon, S Lucas, MM Miller, H Inoko, T Shiina, J Kaufman, J Salomonsen, K Skjoedt, GK-S Wong, J Wang, B Liu, J Wang, J Yu, H Yang, M Nefedov, M Koriabine, PJ deJong, L Goodstadt, C Webber, NJ Dickens, I Letunic, M Suyama, D Torrents, C von Mering, EM Zdobnov, KD Makova, A Nekrutenko, L Elnitski, P Eswara, DC King, S Yang, S Tyekucheva, A Radakrishnan, RS Harris, F Chiaromonte, J Taylor, J He, M Rijnkels, S Griffiths-Jones, A Ureta-Vidal, MM Hoffman, J Severin, SMJ Searle, AS Law, D Speed, D Waddington, Z Cheng, E Tuzun, EE Eichler, Z Bao, P Flicek, DD Shteynberg, MR Brent, JM Bye, EJ Huckle, S Chatterji, C Dewey, L Pachter, A Kouranov, Z Mourelatos, AG Hatzigeorgiou, AH Paterson, R Ivarie, M Brandstrom, E Axelsson, N Backstrom, S Berlin, MT Webster, O Pourquie, A Reymond, C Ucla, SE Antonarakis, M Long, JJ Emerson, E Betrán, I Dupanloup, H Kaessmann, AS Hinrichs, G Bejerano, TS Furey, RA Harte, B Raney, A Siepel, WJ Kent, D Haussler, E Eyras, R Castelo, JF Abril, S Castellano, F Camara, G Parra, R Guigo, G Bourque, G Tesler, PA Pevzner, AFA Smit, LA Fulton, ER Mardis, RK Wilson. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. NATURE, 2004.

Regional variation Sex chromosome DOI

Rat Genome Sequencing Project Consortium, RA Gibbs, GM Weinstock, ML Metzker, DM Muzny, EJ Sodergren, S Scherer, G Scott, D Steffen, KC Worley, PE Burch, GO Okwuonu, S Hines, LR Lewis, C DeRamo, O Delgado, S Dugan-Rocha, G Miner, M Morgan, AC Hawes, R Gill, CRA Holt, MD Adams, PG Amanatides, H Baden-Tillson, M Barnstead, S Chin, CA Evans, S Ferriera, C Fosler, A Glodek, Z Gu, D Jennings, CL Kraft, T Nguyen, CM Pfannkoch, C Sitter, GG Sutton, JC Venter, T Woodage, D Smith, H-M Lee, E Gustafson, P Cahill, A Kana, L Doucette-Stamm, K Weinstock, K Fechtel, RB Weiss, DM Dunn, ED Green, RW Blakesley, GG Bouffard, PJ de Jong, K Osoegawa, B Zhu, MA Marra, JE Schein, I Bosdet, C Fjell, SM Jones, M Krzywinski, C Mathewson, A Siddiqui, N Wye, JD McPherson, S Zhao, CM Fraser, J Shetty, S Shatsman, K Geer, Y Chen, S Abramzon, WC Nierman, RA Gibbs, GM Weinstock, PH Havlak, R Chen, K James Durbin, A Egan, Y Ren, HX-Z Song, B Li, Y Liu, X Qin, S Cawley, GM Weinstock, KC Worley, AJ Cooney, RA Gibbs, LM D’Souza, K Martin, J Qian Wu, ML Gonzalez-Garay, AR Jackson, KJ Kalafus, MP McLeod, A Milosavljevic, D Virk, A Volkov, DA Wheeler, Z Zhang, JA Bailey, EE Eichler, E Tuzun, E Birney, E Mongin, A Ureta-Vidal, C Woodwark, EM Zdobnov, P Bork, M Suyama, D Torrents, M Alexandersson, BJ Trask, JM Young, D Smith, H Huang, K Fechtel, H Wang, H Xing, K Weinstock, S Daniels, D Gietzen, J Schmidt, K Stevens, U Vitt, J Wingrove, F Camara, M Mar Albà, JF Abril, R Guigo, AFA Smit, I Dubchak, EM Rubin, O Couronne, A Poliakov, N Hübner, D Ganten, C Goesele, O Hummel, T Kreitler, Y-A Lee, J Monti, H Schulz, H Zimdahl, H Himmelbauer, H Lehrach, HJ Jacob, S Bromberg, J Gullings-Handley, MI Jensen-Seaman, AE Kwitek, J Lazar, D Pasko, PJ Tonellato, S Twigger, CP Ponting, JM Duarte, S Rice, L Goodstadt, SA Beatson, RD Emes, EE Winter, C Webber, P Brandt, G Nyakatura, M Adetobi, F Chiaromonte, L Elnitski, P Eswara, RC Hardison, M Hou, D Kolbe, KD Makova, W Miller, A Nekrutenko, C Riemer, S Schwartz, J Taylor, S Yang, Y Zhang, K Lindpaintner, TD Andrews, M Caccamo, M Clamp, L Clarke, V Curwen, R Durbin, E Eyras, SMJ Searle, GM Cooper, S Batzoglou, M Brudno, A Sidow, EA Stone, J Craig Venter, BA Payseur, G Bourque, C López-Otín, XS Puente, K Chakrabarti, S Chatterji, C Dewey, L Pachter, N Bray, VB Yap, A Caspi, G Tesler, PA Pevzner, D Haussler, KM Roskin, R Baertsch, H Clawson, TS Furey, AS Hinrichs, D Karolchik, WJ Kent, KR Rosenbloom, H Trumbower, M Weirauch, DN Cooper, PD Stenson, B Ma, MR Brent, M Arumugam, DD Shteynberg, RR Copley, MS Taylor, H Riethman, U Mudunuri, J Peterson, M Guyer, A Felsenfeld, S Old, S Mockrin, F Collins. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. NATURE, 2004.

Regional variation Sex chromosome DOI

KD Makova, W-H Li. Strong male-driven evolution of DNA sequences in humans and apes. NATURE, 2002.

Regional variation Sex chromosome DOI

W-H Li, S Yi, KD Makova. Male-driven evolution. CURR OPIN GENET DEV, 2002.

Regional variation Sex chromosome DOI

Sex chromosome evolution

Credit: Audrey Guiblet

Members

Robert Harris

Research Assistant Professor

Marta Tomaszkiewicz

Research Assistant Professor

Publications