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Scientific reports2015; 5; 14106; doi: 10.1038/srep14106

Donkey genome and insight into the imprinting of fast karyotype evolution.

Abstract: The donkey, like the horse, is a promising model for exploring karyotypic instability. We report the de novo whole-genome assemblies of the donkey and the Asiatic wild ass. Our results reflect the distinct characteristics of donkeys, including more effective energy metabolism and better immunity than horses. The donkey shows a steady demographic trajectory. We detected abundant satellite sequences in some inactive centromere regions but not in neocentromere regions, while ribosomal RNAs frequently emerged in neocentromere regions but not in the obsolete centromere regions. Expanded miRNA families and five newly discovered miRNA target genes involved in meiosis may be associated with fast karyotype evolution. APC/C, controlling sister chromatid segregation, cytokinesis, and the establishment of the G1 cell cycle phase were identified by analysis of miRNA targets and rapidly evolving genes.
Publication Date: 2015-09-16 PubMed ID: 26373886PubMed Central: PMC4571621DOI: 10.1038/srep14106Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research explores the genome of the donkey and the Asiatic wild ass to better understand their unique characteristics including their stronger immunity and energy metabolism than horses. In particular, it considers the role of certain genes in rapid karyotype evolution.

Genome Assemblies of Donkey and Asiatic Wild Ass

  • The study centers on the de novo whole-genome assemblies of the donkey and the Asiatic wild ass. These species were selected due to their promising capacity to model karyotypic instability, an important aspect of genomic evolution.
  • The research reflects the distinct characteristics of donkeys, such as better immunity and more effective energy metabolism compared to horses, which also adds to their uniqueness as genomic research subjects.

Distribution of Satellite Sequences and Ribosomal RNAs

  • The researchers found numerous satellite sequences in the inactive centromere regions of the donkey genome but not in the neocentromere regions. Conversely, they detected ribosomal RNAs more frequently in the neocentromere regions and not in the obsolete centromere regions. This distribution helps understand the functional differences between these genomic regions.

Contribution of miRNA Families to Karyotype Evolution

  • The team observed expanded microRNA (miRNA) families and found five new miRNA target genes that seem to be involved in meiosis – a process of cell division that produces reproductive cells.
  • These miRNAs and their targets may be associated with the rapid karyotype evolution observed in these species, contributing to the peculiar characteristics of donkey and Asiatic wild ass genomes.

Identification of the APC/C Complex

  • The anaphase-promoting complex/cyclosome (APC/C), a key regulator of cell division, was identified in the study. APC/C helps control sister chromatid segregation, cytokinesis (the final stage of cell division), and the establishment of the initial phase of the cell cycle, known as the G1 phase.
  • This determination was made through an analysis of miRNA targets and rapidly evolving genes, showcasing the potential of these molecules and processes in understanding, and possibly influencing, karyotypic evolution.

Cite This Article

APA
Huang J, Zhao Y, Bai D, Shiraigol W, Li B, Yang L, Wu J, Bao W, Ren X, Jin B, Zhao Q, Li A, Bao S, Bao W, Xing Z, An A, Gao Y, Wei R, Bao Y, Bao T, Han H, Bai H, Bao Y, Zhang Y, Daidiikhuu D, Zhao W, Liu S, Ding J, Ye W, Ding F, Sun Z, Shi Y, Zhang Y, Meng H, Dugarjaviin M. (2015). Donkey genome and insight into the imprinting of fast karyotype evolution. Sci Rep, 5, 14106. https://doi.org/10.1038/srep14106

Publication

ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English
Volume: 5
Pages: 14106
PII: 14106

Researcher Affiliations

Huang, Jinlong
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Zhao, Yiping
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Bai, Dongyi
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Shiraigol, Wunierfu
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Li, Bei
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Yang, Lihua
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Wu, Jing
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Bao, Wuyundalai
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Ren, Xiujuan
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Jin, Burenqiqige
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Zhao, Qinan
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Li, Anaer
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Bao, Sarula
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Bao, Wuyingga
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Xing, Zhencun
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
An, Aoruga
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Gao, Yahan
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Wei, Ruiyuan
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Bao, Yirugeletu
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Bao, Taoketao
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Han, Haige
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Bai, Haitang
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Bao, Yanqing
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Zhang, Yuhong
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Daidiikhuu, Dorjsuren
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.
Zhao, Wenjing
  • School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China.
Liu, Shuyun
  • School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China.
Ding, Jinmei
  • School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China.
Ye, Weixing
  • Shanghai Personal Biotechnology Limited Company, 218 Yindu Road, Shanghai 200231, P. R. China.
Ding, Fangmei
  • Shanghai Personal Biotechnology Limited Company, 218 Yindu Road, Shanghai 200231, P. R. China.
Sun, Zikui
  • Shanghai Personal Biotechnology Limited Company, 218 Yindu Road, Shanghai 200231, P. R. China.
Shi, Yixiang
  • Shanghai Personal Biotechnology Limited Company, 218 Yindu Road, Shanghai 200231, P. R. China.
Zhang, Yan
  • SRA Inc. 6003 Executive Blvd. Suite 400, Rockville, MD20852, USA.
Meng, He
  • School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China.
Dugarjaviin, Manglai
  • College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, P. R. China.

MeSH Terms

  • Animals
  • Centromere / genetics
  • Computational Biology / methods
  • Equidae / genetics
  • Evolution, Molecular
  • Gene Rearrangement
  • Genome
  • Genomic Imprinting
  • Genomics / methods
  • Karyotype
  • MicroRNAs / genetics
  • Molecular Sequence Annotation
  • RNA Interference
  • RNA, Messenger / genetics
  • Repetitive Sequences, Nucleic Acid

References

This article includes 52 references
  1. Rossel S, Marshall F, Peters J, Pilgram T, Adams MD, O'Connor D. Domestication of the donkey: timing, processes, and indicators.. Proc Natl Acad Sci U S A 2008 Mar 11;105(10):3715-20.
    pmc: PMC2268817pubmed: 18332433doi: 10.1073/pnas.0709692105google scholar: lookup
  2. Beja-Pereira A, England PR, Ferrand N, Jordan S, Bakhiet AO, Abdalla MA, Mashkour M, Jordana J, Taberlet P, Luikart G. African origins of the domestic donkey.. Science 2004 Jun 18;304(5678):1781.
    pubmed: 15205528doi: 10.1126/science.1096008google scholar: lookup
  3. Hintz HF, Cymbaluk NF. Nutrition of the horse.. Annu Rev Nutr 1994;14:243-67.
  4. Izraely H, Choshniak I, Stevens CE, Demment MW, Shkolnik A. Factors determining the digestive efficiency of the domesticated donkey (Equus asinus asinus).. Q J Exp Physiol 1989 Jan;74(1):1-6.
  5. Trifonov VA, Stanyon R, Nesterenko AI, Fu B, Perelman PL, O'Brien PC, Stone G, Rubtsova NV, Houck ML, Robinson TJ, Ferguson-Smith MA, Dobigny G, Graphodatsky AS, Yang F. Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla.. Chromosome Res 2008;16(1):89-107.
    pubmed: 18293107doi: 10.1007/s10577-007-1201-7google scholar: lookup
  6. Bush GL, Case SM, Wilson AC, Patton JL. Rapid speciation and chromosomal evolution in mammals.. Proc Natl Acad Sci U S A 1977 Sep;74(9):3942-6.
    pmc: PMC431793pubmed: 269445doi: 10.1073/pnas.74.9.3942google scholar: lookup
  7. Huang J, Zhao Y, Shiraigol W, Li B, Bai D, Ye W, Daidiikhuu D, Yang L, Jin B, Zhao Q, Gao Y, Wu J, Bao W, Li A, Zhang Y, Han H, Bai H, Bao Y, Zhao L, Zhai Z, Zhao W, Sun Z, Zhang Y, Meng H, Dugarjaviin M. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype.. Sci Rep 2014 May 14;4:4958.
    pmc: PMC4021364pubmed: 24828444doi: 10.1038/srep04958google scholar: lookup
  8. Montefalcone G, Tempesta S, Rocchi M, Archidiacono N. Centromere repositioning.. Genome Res 1999 Dec;9(12):1184-8.
    pmc: PMC311001pubmed: 10613840doi: 10.1101/gr.9.12.1184google scholar: lookup
  9. Carbone L, Nergadze SG, Magnani E, Misceo D, Francesca Cardone M, Roberto R, Bertoni L, Attolini C, Francesca Piras M, de Jong P, Raudsepp T, Chowdhary BP, Guérin G, Archidiacono N, Rocchi M, Giulotto E. Evolutionary movement of centromeres in horse, donkey, and zebra.. Genomics 2006 Jun;87(6):777-82.
    pubmed: 16413164doi: 10.1016/j.ygeno.2005.11.012google scholar: lookup
  10. Cho YS, Hu L, Hou H, Lee H, Xu J, Kwon S, Oh S, Kim HM, Jho S, Kim S, Shin YA, Kim BC, Kim H, Kim CU, Luo SJ, Johnson WE, Koepfli KP, Schmidt-Küntzel A, Turner JA, Marker L, Harper C, Miller SM, Jacobs W, Bertola LD, Kim TH, Lee S, Zhou Q, Jung HJ, Xu X, Gadhvi P, Xu P, Xiong Y, Luo Y, Pan S, Gou C, Chu X, Zhang J, Liu S, He J, Chen Y, Yang L, Yang Y, He J, Liu S, Wang J, Kim CH, Kwak H, Kim JS, Hwang S, Ko J, Kim CB, Kim S, Bayarlkhagva D, Paek WK, Kim SJ, O'Brien SJ, Wang J, Bhak J. The tiger genome and comparative analysis with lion and snow leopard genomes.. Nat Commun 2013;4:2433.
    pmc: PMC3778509pubmed: 24045858doi: 10.1038/ncomms3433google scholar: lookup
  11. Wan QH, Pan SK, Hu L, Zhu Y, Xu PW, Xia JQ, Chen H, He GY, He J, Ni XW, Hou HL, Liao SG, Yang HQ, Chen Y, Gao SK, Ge YF, Cao CC, Li PF, Fang LM, Liao L, Zhang S, Wang MZ, Dong W, Fang SG. Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator.. Cell Res 2013 Sep;23(9):1091-105.
    pmc: PMC3760627pubmed: 23917531doi: 10.1038/cr.2013.104google scholar: lookup
  12. Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, Pignatelli M, Herrero J, Beal K, Nozawa M, Li Q, Wang J, Zhang H, Yu L, Shigenobu S, Wang J, Liu J, Flicek P, Searle S, Wang J, Kuratani S, Yin Y, Aken B, Zhang G, Irie N. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.. Nat Genet 2013 Jun;45(6):701-706.
    pmc: PMC4000948pubmed: 23624526doi: 10.1038/ng.2615google scholar: lookup
  13. Zhou X, Sun F, Xu S, Fan G, Zhu K, Liu X, Chen Y, Shi C, Yang Y, Huang Z, Chen J, Hou H, Guo X, Chen W, Chen Y, Wang X, Lv T, Yang D, Zhou J, Huang B, Wang Z, Zhao W, Tian R, Xiong Z, Xu J, Liang X, Chen B, Liu W, Wang J, Pan S, Fang X, Li M, Wei F, Xu X, Zhou K, Wang J, Yang G. Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations.. Nat Commun 2013;4:2708.
    pmc: PMC3826649pubmed: 24169659doi: 10.1038/ncomms3708google scholar: lookup
  14. Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.. Bioinformatics 2007 May 1;23(9):1061-7.
    pubmed: 17332020doi: 10.1093/bioinformatics/btm071google scholar: lookup
  15. Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel.. Bioinformatics 2003 Oct;19 Suppl 2:ii215-25.
  16. Korf I. Gene finding in novel genomes.. BMC Bioinformatics 2004 May 14;5:59.
    pmc: PMC421630pubmed: 15144565doi: 10.1186/1471-2105-5-59google scholar: lookup
  17. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Lander ES, Lindblad-Toh K. Genome sequence, comparative analysis, and population genetics of the domestic horse.. Science 2009 Nov 6;326(5954):865-7.
    pmc: PMC3785132pubmed: 19892987doi: 10.1126/science.1178158google scholar: lookup
  18. Lorenzen ED, Nogués-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MT, Nielsen R, Ho SY, Goebel T, Graf KE, Byers D, Stenderup JT, Rasmussen M, Campos PF, Leonard JA, Koepfli KP, Froese D, Zazula G, Stafford TW Jr, Aaris-Sørensen K, Batra P, Haywood AM, Singarayer JS, Valdes PJ, Boeskorov G, Burns JA, Davydov SP, Haile J, Jenkins DL, Kosintsev P, Kuznetsova T, Lai X, Martin LD, McDonald HG, Mol D, Meldgaard M, Munch K, Stephan E, Sablin M, Sommer RS, Sipko T, Scott E, Suchard MA, Tikhonov A, Willerslev R, Wayne RK, Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbek C, Willerslev E. Species-specific responses of Late Quaternary megafauna to climate and humans.. Nature 2011 Nov 2;479(7373):359-64.
    pmc: PMC4070744pubmed: 22048313doi: 10.1038/nature10574google scholar: lookup
  19. Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.. Nature 2013 Jul 4;499(7456):74-8.
    pubmed: 23803765doi: 10.1038/nature12323google scholar: lookup
  20. Huelsenbeck JP, Larget B, Swofford D. A compound poisson process for relaxing the molecular clock.. Genetics 2000 Apr;154(4):1879-92.
    pmc: PMC1461022pubmed: 10747076doi: 10.1093/genetics/154.4.1879google scholar: lookup
  21. Nikaido M, Kawai K, Cao Y, Harada M, Tomita S, Okada N, Hasegawa M. Maximum likelihood analysis of the complete mitochondrial genomes of eutherians and a reevaluation of the phylogeny of bats and insectivores.. J Mol Evol 2001 Oct-Nov;53(4-5):508-16.
    pubmed: 11675611doi: 10.1007/s002390010241google scholar: lookup
  22. Waddell PJ, Cao Y, Hasegawa M, Mindell DP. Assessing the Cretaceous superordinal divergence times within birds and placental mammals by using whole mitochondrial protein sequences and an extended statistical framework.. Syst Biol 1999 Mar;48(1):119-37.
    pubmed: 12078636doi: 10.1080/106351599260481google scholar: lookup
  23. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL Jr, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH Jr, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution.. Science 2009 Apr 24;324(5926):522-8.
    pmc: PMC2943200pubmed: 19390049doi: 10.1126/science.1169588google scholar: lookup
  24. Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB. Analyses of pig genomes provide insight into porcine demography and evolution.. Nature 2012 Nov 15;491(7424):393-8.
    pmc: PMC3566564pubmed: 23151582doi: 10.1038/nature11622google scholar: lookup
  25. Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, Rusch DB, Delcher AL, Pop M, Wang W, Fraser CM, Venter JC. The dog genome: survey sequencing and comparative analysis.. Science 2003 Sep 26;301(5641):1898-903.
    pubmed: 14512627doi: 10.1126/science.1086432google scholar: lookup
  26. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome.. Nature 2001 Feb 15;409(6822):860-921.
    pubmed: 11237011doi: 10.1038/35057062google scholar: lookup
  27. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.. Nature 2007 May 10;447(7141):167-77.
    pubmed: 17495919doi: 10.1038/nature05805google scholar: lookup
  28. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. Initial sequencing and comparative analysis of the mouse genome.. Nature 2002 Dec 5;420(6915):520-62.
    pubmed: 12466850doi: 10.1038/nature01262google scholar: lookup
  29. Amor DJ, Bentley K, Ryan J, Perry J, Wong L, Slater H, Choo KH. Human centromere repositioning "in progress".. Proc Natl Acad Sci U S A 2004 Apr 27;101(17):6542-7.
    pmc: PMC404081pubmed: 15084747doi: 10.1073/pnas.0308637101google scholar: lookup
  30. Piras FM, Nergadze SG, Magnani E, Bertoni L, Attolini C, Khoriauli L, Raimondi E, Giulotto E. Uncoupling of satellite DNA and centromeric function in the genus Equus.. PLoS Genet 2010 Feb 12;6(2):e1000845.
  31. Villasante A, Abad JP, Méndez-Lago M. Centromeres were derived from telomeres during the evolution of the eukaryotic chromosome.. Proc Natl Acad Sci U S A 2007 Jun 19;104(25):10542-7.
    pmc: PMC1965549pubmed: 17557836doi: 10.1073/pnas.0703808104google scholar: lookup
  32. Ventura M, Weigl S, Carbone L, Cardone MF, Misceo D, Teti M, D'Addabbo P, Wandall A, Björck E, de Jong PJ, She X, Eichler EE, Archidiacono N, Rocchi M. Recurrent sites for new centromere seeding.. Genome Res 2004 Sep;14(9):1696-703.
    pmc: PMC515314pubmed: 15342555doi: 10.1101/gr.2608804google scholar: lookup
  33. O'Sullivan JM, Pai DA, Cridge AG, Engelke DR, Ganley AR. The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?. Biomol Concepts 2013 Jun;4(3):277-86.
    pmc: PMC5100006pubmed: 25436580doi: 10.1515/bmc-2012-0043google scholar: lookup
  34. Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A. Rfam 11.0: 10 years of RNA families.. Nucleic Acids Res 2013 Jan;41(Database issue):D226-32.
    pmc: PMC3531072pubmed: 23125362doi: 10.1093/nar/gks1005google scholar: lookup
  35. Chang LF, Zhang Z, Yang J, McLaughlin SH, Barford D. Molecular architecture and mechanism of the anaphase-promoting complex.. Nature 2014 Sep 18;513(7518):388-393.
    pmc: PMC4456660pubmed: 25043029doi: 10.1038/nature13543google scholar: lookup
  36. Bharadwaj R, Yu H. The spindle checkpoint, aneuploidy, and cancer.. Oncogene 2004 Mar 15;23(11):2016-27.
    pubmed: 15021889doi: 10.1038/sj.onc.1207374google scholar: lookup
  37. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE.. Bioinformatics 2011 Feb 15;27(4):578-9.
    pubmed: 21149342doi: 10.1093/bioinformatics/btq683google scholar: lookup
  38. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.. Mol Biol Evol 2013 Dec;30(12):2725-9.
    pmc: PMC3840312pubmed: 24132122doi: 10.1093/molbev/mst197google scholar: lookup
  39. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila.. Genome Biol 2003;5(1):R1.
    pmc: PMC395733pubmed: 14709173doi: 10.1186/gb-2003-5-1-r1google scholar: lookup
  40. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.. Genome Res 2008 Jan;18(1):188-96.
    pmc: PMC2134774pubmed: 18025269doi: 10.1101/gr.6743907google scholar: lookup
  41. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.. Genome Res 2010 Sep;20(9):1297-303.
    pmc: PMC2928508pubmed: 20644199doi: 10.1101/gr.107524.110google scholar: lookup
  42. Li H, Durbin R. Inference of human population history from individual whole-genome sequences.. Nature 2011 Jul 13;475(7357):493-6.
    pmc: PMC3154645pubmed: 21753753doi: 10.1038/nature10231google scholar: lookup
  43. Li L, Stoeckert CJ Jr, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes.. Genome Res 2003 Sep;13(9):2178-89.
    pmc: PMC403725pubmed: 12952885doi: 10.1101/gr.1224503google scholar: lookup
  44. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools.. Bioinformatics 2009 Aug 15;25(16):2078-9.
  45. She R, Chu JS, Uyar B, Wang J, Wang K, Chen N. genBlastG: using BLAST searches to build homologous gene models.. Bioinformatics 2011 Aug 1;27(15):2141-3.
    pubmed: 21653517doi: 10.1093/bioinformatics/btr342google scholar: lookup
  46. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput.. Nucleic Acids Res 2004;32(5):1792-7.
    pmc: PMC390337pubmed: 15034147doi: 10.1093/nar/gkh340google scholar: lookup
  47. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.. Mol Biol Evol 2000 Apr;17(4):540-52.
  48. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.. Syst Biol 2010 May;59(3):307-21.
    pubmed: 20525638doi: 10.1093/sysbio/syq010google scholar: lookup
  49. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood.. Mol Biol Evol 2007 Aug;24(8):1586-91.
    pubmed: 17483113doi: 10.1093/molbev/msm088google scholar: lookup
  50. De Bie T, Cristianini N, Demuth JP, Hahn MW. CAFE: a computational tool for the study of gene family evolution.. Bioinformatics 2006 May 15;22(10):1269-71.
    pubmed: 16543274doi: 10.1093/bioinformatics/btl097google scholar: lookup
  51. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.. PLoS One 2010 Jun 25;5(6):e11147.
  52. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. Alignment of whole genomes.. Nucleic Acids Res 1999 Jun 1;27(11):2369-76.
    pmc: PMC148804pubmed: 10325427doi: 10.1093/nar/27.11.2369google scholar: lookup

Citations

This article has been cited 19 times.
  1. Ren X, Liu Y, Zhao Y, Li B, Bai D, Bou G, Zhang X, Du M, Wang X, Bou T, Shen Y, Dugarjaviin M. Analysis of the Whole-Genome Sequences from an Equus Parent-Offspring Trio Provides Insight into the Genomic Incompatibilities in the Hybrid Mule. Genes (Basel) 2022 Nov 23;13(12).
    doi: 10.3390/genes13122188pubmed: 36553455google scholar: lookup
  2. Wang Y, Hua X, Shi X, Wang C. Origin, Evolution, and Research Development of Donkeys. Genes (Basel) 2022 Oct 25;13(11).
    doi: 10.3390/genes13111945pubmed: 36360182google scholar: lookup
  3. Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene. Elife 2022 May 11;11.
    doi: 10.7554/eLife.73346pubmed: 35543411google scholar: lookup
  4. Attia MM, Soliman SM, Salaeh NMK, Salem HM, Alkafafy M, Saad AM, El-Saadony MT, El-Gameel SM. Evaluation of immune responses and oxidative stress in donkeys: Immunological studies provoked by Parascaris equorum infection. Saudi J Biol Sci 2022 Apr;29(4):2173-2179.
    doi: 10.1016/j.sjbs.2021.11.044pubmed: 35531146google scholar: lookup
  5. Bennett EA, Weber J, Bendhafer W, Champlot S, Peters J, Schwartz GM, Grange T, Geigl EM. The genetic identity of the earliest human-made hybrid animals, the kungas of Syro-Mesopotamia. Sci Adv 2022 Jan 14;8(2):eabm0218.
    doi: 10.1126/sciadv.abm0218pubmed: 35030024google scholar: lookup
  6. Li S, Zhao G, Han H, Li Y, Li J, Wang J, Cao G, Li X. Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study. BMC Genomics 2021 Sep 15;22(1):665.
    doi: 10.1186/s12864-021-07984-6pubmed: 34521340google scholar: lookup
  7. Chebii VJ, Mpolya EA, Muchadeyi FC, Domelevo Entfellner JB. Genomics of Adaptations in Ungulates. Animals (Basel) 2021 May 29;11(6).
    doi: 10.3390/ani11061617pubmed: 34072591google scholar: lookup
  8. Zhou Z, Fan Y, Wang G, Lai Z, Gao Y, Wu F, Lei C, Dang R. Detection of Selection Signatures Underlying Production and Adaptive Traits Based on Whole-Genome Sequencing of Six Donkey Populations. Animals (Basel) 2020 Oct 7;10(10).
    doi: 10.3390/ani10101823pubmed: 33036357google scholar: lookup
  9. Klumplerova M, Splichalova P, Oppelt J, Futas J, Kohutova A, Musilova P, Kubickova S, Vodicka R, Orlando L, Horin P. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae. BMC Genomics 2020 Sep 30;21(1):677.
    doi: 10.1186/s12864-020-07089-6pubmed: 32998693google scholar: lookup
  10. Mandáková T, Hloušková P, Koch MA, Lysak MA. Genome Evolution in Arabideae Was Marked by Frequent Centromere Repositioning. Plant Cell 2020 Mar;32(3):650-665.
    doi: 10.1105/tpc.19.00557pubmed: 31919297google scholar: lookup
  11. Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, Paillot R, Bryant N, Vaudin M, Librado P, Orlando L. Improved de novo genomic assembly for the domestic donkey. Sci Adv 2018 Apr;4(4):eaaq0392.
    doi: 10.1126/sciadv.aaq0392pubmed: 29740610google scholar: lookup
  12. Nergadze SG, Piras FM, Gamba R, Corbo M, Cerutti F, McCarter JGW, Cappelletti E, Gozzo F, Harman RM, Antczak DF, Miller D, Scharfe M, Pavesi G, Raimondi E, Sullivan KF, Giulotto E. Birth, evolution, and transmission of satellite-free mammalian centromeric domains. Genome Res 2018 Jun;28(6):789-799.
    doi: 10.1101/gr.231159.117pubmed: 29712753google scholar: lookup
  13. Walter S, Rasche A, Moreira-Soto A, Pfaender S, Bletsa M, Corman VM, Aguilar-Setien A, García-Lacy F, Hans A, Todt D, Schuler G, Shnaiderman-Torban A, Steinman A, Roncoroni C, Veneziano V, Rusenova N, Sandev N, Rusenov A, Zapryanova D, García-Bocanegra I, Jores J, Carluccio A, Veronesi MC, Cavalleri JMV, Drosten C, Lemey P, Steinmann E, Drexler JF. Differential Infection Patterns and Recent Evolutionary Origins of Equine Hepaciviruses in Donkeys. J Virol 2017 Jan 1;91(1).
    doi: 10.1128/JVI.01711-16pubmed: 27795428google scholar: lookup
  14. Burrack LS, Hutton HF, Matter KJ, Clancey SA, Liachko I, Plemmons AE, Saha A, Power EA, Turman B, Thevandavakkam MA, Ay F, Dunham MJ, Berman J. Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome. PLoS Genet 2016 Sep;12(9):e1006317.
    doi: 10.1371/journal.pgen.1006317pubmed: 27662467google scholar: lookup
  15. Zhu Q, Khan MZ, Jing Y, Geng M, Zhang X, Zheng Y, Cao X, Peng Y, Wang C. The Donkey Genome: From Evolutionary Insights to Sustainable Breeding Strategies. Animals (Basel) 2025 Dec 29;16(1).
    doi: 10.3390/ani16010093pubmed: 41514782google scholar: lookup
  16. Parsad R, Bagiyal M, Ahlawat S, Arora R, Gera R, Chhabra P, Sharma U. Unraveling the genetic and physiological potential of donkeys: insights from genomics, proteomics, and metabolomics approaches. Mamm Genome 2025 Mar;36(1):10-24.
    doi: 10.1007/s00335-024-10083-ypubmed: 39510983google scholar: lookup
  17. Rambaldi Migliore N, Bigi D, Milanesi M, Zambonelli P, Negrini R, Morabito S, Verini-Supplizi A, Liotta L, Chegdani F, Agha S, Salim B, Beja-Pereira A, Torroni A, Ajmone-Marsan P, Achilli A, Colli L. Mitochondrial DNA control-region and coding-region data highlight geographically structured diversity and post-domestication population dynamics in worldwide donkeys. PLoS One 2024;19(8):e0307511.
    doi: 10.1371/journal.pone.0307511pubmed: 39197009google scholar: lookup
  18. Brannan EO, Hartley GA, O'Neill RJ. Mechanisms of Rapid Karyotype Evolution in Mammals. Genes (Basel) 2023 Dec 31;15(1).
    doi: 10.3390/genes15010062pubmed: 38254952google scholar: lookup
  19. Santagostino M, Piras FM, Cappelletti E, Del Giudice S, Semino O, Nergadze SG, Giulotto E. Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective. Int J Mol Sci 2020 Apr 18;21(8).
    doi: 10.3390/ijms21082838pubmed: 32325780google scholar: lookup