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New high copy tandem repeat in the content of the chicken W chromosome

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Abstract

The content of repetitive DNA in avian genomes is considerably less than in other investigated vertebrates. The first descriptions of tandem repeats were based on the results of routine biochemical and molecular biological experiments. Both satellite DNA and interspersed repetitive elements were annotated using library-based approach and de novo repeat identification in assembled genome. The development of deep-sequencing methods provides datasets of high quality without preassembly allowing one to annotate repetitive elements from unassembled part of genomes. In this work, we search the chicken assembly and annotate high copy number tandem repeats from unassembled short raw reads. Tandem repeat (GGAAA)n has been identified and found to be the second after telomeric repeat (TTAGGG)n most abundant in the chicken genome. Furthermore, (GGAAA)n repeat forms expanded arrays on the both arms of the chicken W chromosome. Our results highlight the complexity of repetitive sequences and update data about organization of sex W chromosome in chicken.

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Abbreviations

CIOMS:

Council for International Organizations of Medical Sciences

CR1:

Chicken repeat 1

DAPI:

4′,6-diamidino-2-phenylindole

Galgal4:

Gallus_gallus-4.0 assembly of the chicken genome (GCA_000002315.2)

Galgal5:

Gallus_gallus-5.0 assembly of the chicken genome (GCA_000002315.3)

Gb:

Billions of base pairs

ICGSC:

International Chicken Genome Sequencing Consortium

LINE:

Long interspersed element

LTR:

Long terminal repeat

Mb:

Millions of base pairs

NOR:

Nucleolus organizer region

SINE:

Short interspersed element

SSC:

Sodium salt citrate

TRF:

Tandem repeat finder

References

  • Abrusán G, Krambeck HJ, Junier T, Giordano J, Warburton PE (2008) Biased distributions and decay of long interspersed nuclear elements in the chicken genome. Genetics 178(1):573–581. https://doi.org/10.1534/genetics.106.061861

    Article  PubMed  PubMed Central  Google Scholar 

  • Arthur RR, Straus NA (1978) DNA-sequence organization in the genome of the domestic chicken (Gallus domesticus). Can J Biochem 56:257–263

    Article  CAS  Google Scholar 

  • Bellott DW, Skaletsky H, Cho TJ, Brown L, Locke D, Chen N, Galkina S, Pyntikova T, Koutseva N, Graves T, Kremitzki C, Warren WC, Clark AG, Gaginskaya E, Wilson RK, Page DC (2017) Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. Nat Genet 49(3):387–394

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bellott DW, Skaletsky H, Pyntikova T, Mardis ER, Graves T, Kremitzki C, Brown LG, Rozen S, Warren WC, Wilson RK, Page DC (2010) Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature 466:612–613

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Belotserkovskii BP, Veselkov AG, Filippov SA, Dobrynin VN, Mirkin SM, Frank-Kamenetskii MD (1990) Formation of intramolecular triplex in homopurine-homopyrimidine mirror repeats with point substitutions. Nucleic Acids Res 18:6621–6624

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27(2):573–580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beridze T (1986) Satellite DNA. In: Beridze (ed). Published by Springer-Verlag, 1986. Hardcover. Berlin, Heidelberg, New York, London: Springer Verlag

  • Berlin S, Ellegren H (2004) Chicken W: a genetically uniform chromosome in a highly variable genome. Proc Natl Acad Sci U S A 101(45):15967–15969

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Biltueva LS, Prokopov DY, Makunin AI, Komissarov AS, Kudryavtseva AV, Lemskaya NA, Vorobieva NV, Serdyukova NA, Romanenko SA, Gladkikh OL, Graphodatsky AS (2017) Genomic organization and physical mapping of Tandemly arranged repetitive DNAs in Sterlet (Acipenser Ruthenus). Cytogenet Genome Res. https://doi.org/10.1159/000479472

  • Biscotti MA, Olmo E, Heslop-Harrison JS (2015) Repetitive DNA in eukaryotic genomes. Chromosom Res 23(3):415–420. https://doi.org/10.1007/s10577-015-9499-z

    Article  CAS  Google Scholar 

  • Burt DW (2002) Origin and evolution of avian microchromosomes. Cytogenet Genome Res 96:97–112

    Article  CAS  PubMed  Google Scholar 

  • Burt DW (2005) Chicken genome: current status and future opportunities. Genome Res 15:1692–1698

    Article  CAS  PubMed  Google Scholar 

  • Callan HG (1986) Lampbrush chromosomes. Mol Biol Biochem Biophys 36:1–252

    Article  CAS  PubMed  Google Scholar 

  • Chen N, Bellott DW, Page DC, Clark AG (2012) Identification of avian W-linked contigs by short-read sequencing. BMC Genomics 13:183. https://doi.org/10.1186/1471-2164-13-183

    Article  PubMed  PubMed Central  Google Scholar 

  • Cheng YK, Pettitt BM (1992) Stabilities of double- and triple-strand helical nucleic acids. Prog Biophys Mol Biol 58(3):225–257

    Article  CAS  PubMed  Google Scholar 

  • Cortez D, Marin R, Toledo-Flores D, Froidevaux L, Liechti A, Waters PD, Grützner F, Kaessmann H (2014) Origins and functional evolution of Y chromosomes across mammals. Nature 508:488–493

    Article  CAS  PubMed  Google Scholar 

  • Cui J, Zhao W, Huang Z, Jarvis ED, Gilbert MTP, Walker PJ, Holmes EC, Zhang G (2014) Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biol 15:539 http://genomebiology.com/2014/15/12/539

    Article  PubMed  PubMed Central  Google Scholar 

  • Cunningham F, Amode MR, Barrell D et al (2015) Ensembl 2015. Nucleic Acids Res 43(Database issue):D662–D669. https://doi.org/10.1093/nar/gku1010

    Article  CAS  PubMed  Google Scholar 

  • Delany ME, Daniels LM, Swanberg SE, Taylor HA (2003) Telomeres in the chicken: genome stability and chromosome ends. Poult Sci 82:917–926

    Article  CAS  PubMed  Google Scholar 

  • Deryusheva S, Krasikova A, Kulikova T, Gaginskaya E (2007) Tandem 41-bp repeats in chicken and Japanese quail genomes: FISH mapping and transcription analysis on lampbrush chromosomes. Chromosoma 116:519–530

    Article  CAS  PubMed  Google Scholar 

  • Dobrynin P, Liu S, Tamazian G et al (2015) Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biol 16:277. https://doi.org/10.1186/s13059-015-0837-4

    Article  PubMed  PubMed Central  Google Scholar 

  • Enukashvily NI, Ponomartsev NV (2013) Mammalian satellite DNA: a speaking dumb. Adv Protein Chem Struct Biol 90:31–65

    Article  CAS  PubMed  Google Scholar 

  • Eöry L, Gilbert MTP, Li C, Li B, Archibald A, Aken BL, Zhang G, Jarvis E, Flicek P, Burt DW (2015) Avianbase: a community resource for bird genomics. Genome Biol 16:21. https://doi.org/10.1186/s13059-015-0588-2

    Article  PubMed  PubMed Central  Google Scholar 

  • Epplen JT, Engel W, Leipoldt M, Schmidtke J (1978) DNA-sequence organization in avian genomes. Chromosoma 69:307–321

    Article  CAS  PubMed  Google Scholar 

  • Ezaz T, Deakin JE (2014) Repetitive sequence and sex chromosome evolution in vertebrates. Adv Evol Biol 2014:ID104683 https://doi.org/10.1155/2014/104683

    Article  Google Scholar 

  • Galkina S, Fillon V, Saifitdinova A, Daks A, Kulak M, Dyomin A, Koshel E, Gaginskaya ER (2017) Chicken microchromosomes in the Lampbrush phase: a cytogenetic description. Cytogenet Genome Res 152:46–54. https://doi.org/10.1159/000475563

    Article  CAS  PubMed  Google Scholar 

  • Garrido-Ramos MA (2012) Repetitive DNA. Karger Medical and Scientific Publishers, p 238. https://www.karger.com/Book/Toc/256867

  • Graves JAM (2014) Avian sex, sex chromosomes, and dosage compensation in the age of genomics. Chromosom Res 22:45–57

    Article  Google Scholar 

  • Gregory TR (2012) Animal genome size database. Available from http://www.genomesize.com. Accessed 26 Oct 2016

  • Guizard S, Piégu B, Arensburger P, Guillou F, Bigot Y (2016) Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools. BMC Genomics 17:659. https://doi.org/10.1186/s12864-016-3015-5

    Article  PubMed  PubMed Central  Google Scholar 

  • Handley LJ, Ceplitis H, Ellegren H (2004) Evolutionary strata on the chicken Z chromosome: implications for sex chromosome evolution. Genetics 167:367–376

    Article  PubMed  PubMed Central  Google Scholar 

  • Hughes AL, Piontkivska H (2005) DNA repeat arrays in chicken and human genomes and the adaptive evolution of avian genome size. BMC Evol Biol 5:6

    Article  Google Scholar 

  • International Chicken Genome Sequencing Consortium (ICGSC) (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716

    Article  Google Scholar 

  • Itoh Y, Kampf K, Arnold AP (2008) Molecular cloning of zebra finch W chromosome repetitive sequences: evolution of the avian W chromosome. Chromosoma 117:111–121

    Article  CAS  PubMed  Google Scholar 

  • Itoh Y, Mizuno S (2002) Molecular and cytological characterization of SspI-family repetitive sequence on the chicken W chromosome. Chromosom Res 10:499–511

    Article  CAS  Google Scholar 

  • Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462–427

    Article  CAS  PubMed  Google Scholar 

  • Kasai F, O’Brien PCM, Ferguson-Smith MA (2012) Reassessment of genome size in turtle and crocodile based on chromosome measurement by flow karyotyping: close similarity to chicken. Biol Lett 8:631–635

    Article  PubMed  PubMed Central  Google Scholar 

  • Kodama H, Saitoh H, Tone M, Kuhara S, Sakaki Y, Mizuno S (1987) Nucleotide sequences and unusual electrophoretic behavior of the W chromosome-specific repeating DNA units of the domestic fowl, Gallus gallus domesticus. Chromosoma 96:18–25

    Article  CAS  PubMed  Google Scholar 

  • Komissarov AS, Gavrilova EV, Demin SJ, Ishov AM, Podgornaya OI (2011) Tandemly repeated DNA families in the mouse genome. BMC Genomics 12:531. https://doi.org/10.1186/1471-2164-12-531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Krasikova A, Derjusheva S, Galkina S, Kurganova A, Evteev A, Gaginskaya E (2006) On the positions of centromeres in chicken lampbrush chromosomes. Chromosom Res 14:777–789

    Article  CAS  Google Scholar 

  • Kuznetsova IS, Thevasagayam NM, Sridatta PSR, Komissarov AS, Saju JM, Ngoh SY, Jiang J, Shen X, Orban L (2014) Primary analysis of repeat elements of the Asian seabass (Lates Calcarifer) transcriptome and genome. Front Genet 5:223

    Article  PubMed  PubMed Central  Google Scholar 

  • Ladjali–Mohammedi K, Bitgood JJ, Tixier-Boichard M, Ponce De Leon FA (1999) International system for standardized avian karyotypes (ISSAK): standardized banded karyotypes of the domestic fowl (Gallus domesticus). Cytogenet Cell Genet 86:271–276

    Article  PubMed  Google Scholar 

  • Marcais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764–770

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maroteaux L, Heilig R, Dupret D, Mandel JL (1983) Repetitive satellite-like sequences are present within or upstream from 3 avian protein-coding genes. Nucleic Acids Res 11:1227–1243

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Masabanda JS, Burt DW, O’Brien PCM, Vignal A, Fillon V, Walsh PS, Cox H, Tempest HG, Smith J, Habermann F, Schmid M, Matsuda Y, Ferguson-Smith MA, Crooijmans R, Groenen MAM, Griffin DK (2004) Molecular cytogenetic definition of the chicken genome: the first complete avian karyotype. Genetics 166:1367–1373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mason AS, Fulton JE, Hocking PM, Burt DW (2016) A new look at the LTR retrotransposon content of the chicken genome. BMC Genomics 17:688. https://doi.org/10.1186/s12864-016-3043-1

    Article  PubMed  PubMed Central  Google Scholar 

  • Matzke MA, Varga F, Berger H, Schernthaner J, Schweizer D, Mayr B, Matzke AJM (1990) A 41-42 bp tandemly repeated sequence isolated from nuclear envelopes of chicken erythrocytes is located predominantly on microchromosomes. Chromosoma 99:131–137

    Article  CAS  PubMed  Google Scholar 

  • Mirkin SM, Frank-Kamenetskii MD (1994) H-DNA and related structures. Annu Rev Biophys Biomol Struct 23:541–576

    Article  CAS  PubMed  Google Scholar 

  • Mizuno S, Kunita R, Nakabayashi O, Kuroda Y, Arai N, Harata M, Ogawa A, Itoh Y, Teranishi M, Hori T (2002) Z and W chromosomes of chickens: studies on their gene functions in sex determination and sex differentiation. Cytogenet Genome Res 99:236–244

    Article  CAS  PubMed  Google Scholar 

  • Mizuno S, Macgregor H (1998) The ZW lampbrush chromosomes of birds: a unique opportunity to look at the molecular cytogenetics of sex chromosomes. Cytogenet Cell Genet 80:149–157

    Article  CAS  PubMed  Google Scholar 

  • Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA (2008) Database indexing for production MegaBLAST searches. Bioinformatics 24(16):1757–1764. https://doi.org/10.1093/bioinformatics/btn322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • O’Meally D, Patel HR, Stiglec R, Sarre SD, Georges A, Marshall Graves JA, Ezaz T (2010) Non-homologous sex chromosomes of birds and snakes share repetitive sequences. Chromosom Res 18:787–800

    Article  Google Scholar 

  • Ogawa A, Solovei I, Hutchison N, Saitoh Y, Ikeda JE, Macgregor H, Mizuno S (1997) Molecular characterization and cytological mapping of a non-repetitive DNA sequence region from the W chromosome of chicken and its use as a universal probe for sexing Carinatae birds. Chromosom Res 5:93–101

    Article  CAS  Google Scholar 

  • Pezer Z, Brajković J, Feliciello I, Ugarkovć D (2012) Satellite DNA-mediated effects on genome regulation. Genome Dyn 7:153–169

    Article  CAS  PubMed  Google Scholar 

  • Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y (2012) A tale of three next generation sequencing platforms: comparison of ion torrent, pacific biosciences and Illumina miseq sequencers. BMC Genomics 13:341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raghu G, Tevosian S, Anant S, Subramanian KN, George DL, Mirkin SM (1994) Transcriptional activity of the homopurine-homopyrimidine repeat of the c-Ki-ras promoter is independent of its H-forming potential. Nucleic Acids Res 22:3271–3279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rajagopal P, Feigon J (1989) Triple-strand formation in the homopurine: homopytimidine DNA oligonucleotides d(G-A)4 and d(T-C)4. Nature 339:637–640. https://doi.org/10.1038/339637a0

    Article  CAS  PubMed  Google Scholar 

  • Randsholt NB, Muller J-P, Loones M-T (1989) Transcription of dispersed repeated sequences during Pleurodeles Waltl oogenesis. Biol Cell 67:9–18

    Article  CAS  PubMed  Google Scholar 

  • Saifitdinova A, Derjusheva S, Krasikova A, Gaginskaya E (2003) Lampbrush chromosomes of the chaffinch (Fringilla coelebs L.) Chromosom Res 11:99–113

    Article  CAS  Google Scholar 

  • Saifitdinova AF, Derjusheva SE, Malykh AG, Zhurov VG, Andreeva TF, Gaginskaya ER (2001) Centromeric tandem repeat from the chaffinch genome: isolation and molecular characterization. Genome 44:96–103

    Article  CAS  PubMed  Google Scholar 

  • Saifitdinova AF, Galkina SA, Koshel EI, Gaginskaya ER (2016) The role of repetitive sequences in the evolution of sex chromosomes in birds. Tsitologiia 58:393–398

    Google Scholar 

  • Saitoh Y, Harata M, Mizuno S (1989) Presence of female-specific bent-repetitive DNA sequences in the genome of turkey and pheasant and their interactions with W-protein of chicken. Chromosoma 98:250–258

    Article  CAS  PubMed  Google Scholar 

  • Saitoh Y, Mizuno S (1992) Distribution of XhoI and EcoRI family repetitive DNA-sequences into separate domains in the chicken W-chromosome. Chromosoma 101:474–477

    Article  CAS  PubMed  Google Scholar 

  • Saitoh Y, Saitoh H, Ohtomo K, Mizuno S (1991) Occupancy of the majority of DNA in the chicken W chromosome by bent-repetitive sequences. Chromosoma 101:32–40

    Article  CAS  PubMed  Google Scholar 

  • Schmid M, Enderle E, Schindler D, Schempp W (1989) Chromosome-banding and DNA-replication patterns in bird karyotypes. Cytogenet Cell Genet 52:139–146

    Article  CAS  PubMed  Google Scholar 

  • Schmid M, Nanda I, Guttenbach M et al (2000) First report on chicken genes and chromosomes 2000. Cytogenet Cell Genet 90:169–218

    Article  CAS  PubMed  Google Scholar 

  • Schmid M, Smith J, Burt DW et al (2015) Third report on chicken genes and chromosomes. Cytogenet Genome Res 145:78–179

    Article  PubMed  Google Scholar 

  • Shang WH, Hori T, Toyoda A, Kato J, Popendorf K, Sakakibara Y, Fujiyama A, Fukagawa T (2010) Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences. Genome Res 20:1219–1228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shapiro JA, von Sternberg R (2005) Why repetitive DNA is essential to genome function. Biol Rev Camb Philos Soc 80:227–250

    Article  PubMed  Google Scholar 

  • Smeds L, Warmuth V, Bolivar P, Uebbing S, Burri R, Suh A, Nater A, Bureš S, Garamszegi LZ, Hogner S, Moreno J, Qvarnström A, Ružić M, Sæther SA, Sætre GP, Török J, Ellegren H (2015) Evolutionary analysis of the female-specific avian W chromosome. Nat Commun 6:7330

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smit AFA, Hubley R, Green P (2013) RepeatMasker Open-4.0. (2013–2015) Available from http://www.repeatmasker.org. Accessed 04 Aug 2015

  • Solovei I, Gaginskaya E, Hutchison N, Macgregor HC (1993) Avian sex chromosomes in the lampbrush form: ZW lampbrush bivalents from six species of bird. Chromosom Res 1:153–166

    Article  CAS  Google Scholar 

  • Solovei I, Gaginskaya ER, Macgregor HC (1994) The arrangement and transcription of telomere DNA sequences at the ends of lampbrush chromosomes of birds. Chromosom Res 2:460–470

    Article  CAS  Google Scholar 

  • Solovei I, Ogawa A, Naito M, Mizuno S, Macgregor H (1998) Specific chromomeres on the chicken W lampbrush chromosome contain specific repetitive DNA sequence families. Chromosom Res 6:323–327

    Article  CAS  Google Scholar 

  • Starostina E, Tamazian G, Dobrynin P, O’Brien S, Komissarov A (2015). Cookiecutter: a tool for kmer-based read filtering and extraction. bioRxiv 024679. doi: https://doi.org/10.1101/024679

  • Stepakov A, Galkina S, Bogomaz D, Gaginskaya E, Saifitdinova A (2015) Modified synthesis of 6-carboxyfluorescein (6-FAM): application to probe labeling for conventional Cytogenetics. Br J Appl Sci Technol 7:423–428

    Article  Google Scholar 

  • Stumph WE, Kristo P, Tsai MJ, Omalley BW (1981) A chicken middle-repetitive DNA-sequence which shares homology with mammalian ubiquitous repeats. Nucleic Acids Res 9:5383–5397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suka N, Shinohara Y, Saitoh Y, Saitoh H, Ohtomo K, Harata M, Shpigelman E, Mizuno S (1993) W-heterochromatin of chicken - its unusual DNA components, late replication, and chromatin structure. Genetica 88:93–105

    Article  CAS  PubMed  Google Scholar 

  • Szarski H (1976) Cell-size and nuclear-DNA content in vertebrates. Int Rev Cytol 44:93–111

    Article  CAS  PubMed  Google Scholar 

  • Tamazian G, Simonov S, Dobrynin P, Makunin A, Logachev A, Komissarov A, Shevchenko A, Brukhin V, Cherkasov N, Svitin A, Koepfli K, Pontius J, Driscoll C, Blackistone K, Barr C, Goldman D, Antunes A, Quilez J, Lorente-Galdos B, Alkan C, Marques-Bonet T, Menotti-Raymond M, David V, Narfström K, O’Brien S (2014) Annotated features of domestic cat – Felis Catus genome. Gigascience 3:13. https://doi.org/10.1186/2047-217X-3-13

    Article  PubMed  PubMed Central  Google Scholar 

  • Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryote genomes. Nucleic Acids Res 12:4127–4138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Treangen T, Salzberg S (2011) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13:36–46

    Article  PubMed  PubMed Central  Google Scholar 

  • Tripathi J, Brahmachari SK (1991) Distribution of simple repetitive (TG/GA)n and (CT/GA)n sequences in human and rodent genomes. J Biomol Struct Dyn 9:387–397

    Article  CAS  PubMed  Google Scholar 

  • Trofimova I, Krasikova A (2016) Transcription of highly repetitive tandemly organized DNA in amphibians and birds: a historical overview and modern concepts. RNA Biol 13:1246–1257. https://doi.org/10.1080/15476286.2016.1240142

    Article  PubMed  PubMed Central  Google Scholar 

  • Ugarkovic D (2005) Functional elements residing within satellite DNAs. EMBO Rep 6:1035–1039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Usdin K, Furano AV (1988) Rat L (long interspersed repeated DNA) elements contain guanine-rich homopurine sequences that induce unpairing of contiguous duplex DNA. Proc Natl Acad Sci 85:4416–4420

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Varley JM, Macgregor HC, Erba HP (1980) Satellite DNA is transcribed on lampbrush chromosomes. Nature 283:686–688

    Article  CAS  PubMed  Google Scholar 

  • Wang XF, Li J, Leung FC (2002) Partially inverted tandem repeat isolated from pericentric region of chicken chromosome 8. Chromosom Res 10:73–82

    Article  CAS  Google Scholar 

  • Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB, Cheng HH (2017) A new chicken genome assembly provides insight into avian genome structure. G3 (Bethesda) 7:109–117. https://doi.org/10.1534/g3.116.035923

    Article  Google Scholar 

  • Wells RD, Collier DA, Hanvey JC, Shimizu M, Wohlrab F (1988) The chemistry and biology of unusual DNA structures adopted by oligopurine-oligopyrimidine sequences. FASEB J 2:2939–2949

    Article  CAS  PubMed  Google Scholar 

  • Wicker T, Robertson JS, Schulze SR, Feltus FA, Magrini V, Morrison JA, Mardis ER, Wilson RK, Peterson DG, Paterson AH, Ivarie R (2005) The repetitive landscape of the chicken genome. Genome Res 15:126–136

    Article  PubMed  PubMed Central  Google Scholar 

  • Xiong Y, Sundaralingam M (2000) Crystal structure of a DNA·RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC). Nucleic Acids Res 28:2171–2176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang G, Li C, Li Q et al (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311–1320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou Q, Zhang J, Bachtrog D, An N, Huang Q, Jarvis ED, Gilbert MT, Zhang G (2014) Complex evolutionary trajectories of sex chromosomes across bird taxa. Science 346:1246338

    Article  PubMed  Google Scholar 

  • Zopl D, Dineva B, Betz H, Gundelfinger ED (1990) Isolation of the chicken middle-molecular weight neurofilament (NF-M) gene and characterization of its promoter. Nucleic Acids Res 18:521–529

    Article  Google Scholar 

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Acknowledgements

We are grateful to the anonymous Reviewers for their very useful comments and suggestions. The authors acknowledge Dr. Irina Solovei for providing plasmids pUGD0600 and pUGD1202. We would like to thank Dr. Denis Bogomaz for his assistance in oligonucleotide synthesis and Dr. Inna Kuznetsova for her fruitful discussion. This work was supported by the grant from Russian Foundation for Basic Research (16-04-01823). Aleksey Komissarov and Stephen O’Brien are financially supported by Russian Science Foundation (17-14-01138). The postdoctoral fellowship from St. Petersburg State University was provided for Elena I. Koshel (1.50.1043.2014). The equipment and software of Chromas Research Resource Center and Theodosius Dobzhansky Centre for Genome Bioinformatics of Saint Petersburg State University were used.

Funding

This study was funded by the grant from Russian Foundation for Basic Research (16–04-01823).

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Authors and Affiliations

  1. Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Sredniy av. 41, 199034, Saint Petersburg, Russia

    Aleksey S. Komissarov & Stephen J. O’Brien

  2. Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, Saint Petersburg, Russia

    Svetlana A. Galkina

  3. Saint Petersburg Association of Scientists and Scholars, Universitetskaya emb. 5, Saint Petersburg, 199034, Russia

    Svetlana A. Galkina & Aleksander G. Dyomin

  4. Department of Cytology and Histology, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, Saint Petersburg, Russia

    Elena I. Koshel, Maria M. Kulak & Elena R. Gaginskaya

  5. Chromas Research Resource Center, Saint Petersburg State University, Oranienbaumskoye sh. 2, 198504, Saint Petersburg, Russia

    Aleksander G. Dyomin & Alsu F. Saifitdinova

  6. Oceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida, 33004, USA

    Stephen J. O’Brien

  7. International Centre of Reproductive Medicine, Komendantskiy av. 53-1, Saint Petersburg, 197350, Russia

    Alsu F. Saifitdinova

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  1. Aleksey S. Komissarov
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  2. Svetlana A. Galkina
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  7. Elena R. Gaginskaya
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  8. Alsu F. Saifitdinova
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Correspondence to Alsu F. Saifitdinova.

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All procedures performed in studies involving animals were in accordance with International Guiding Principles for Biomedical Research Involving Animals established by Council for International Organizations of Medical Sciences (CIOMS) and approved by Saint-Petersburg State University Ethics Committee (statement # 131–03-2).

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Komissarov, A.S., Galkina, S.A., Koshel, E.I. et al. New high copy tandem repeat in the content of the chicken W chromosome. Chromosoma 127, 73–83 (2018). https://doi.org/10.1007/s00412-017-0646-5

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  • DOI: https://doi.org/10.1007/s00412-017-0646-5

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