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

Aleksey S. Komissarov; Svetlana A. Galkina; Elena I. Koshel; Maria M. Kulak; Aleksander G. Dyomin; Stephen J. O’Brien; Elena R. Gaginskaya; Alsu F. Saifitdinova; Stephen James O'Brien

doi:10.1007/s00412-017-0646-5

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

Aleksey S. Komissarov
, Svetlana A. Galkina
, Elena I. Koshel
, Maria M. Kulak
, Aleksander G. Dyomin
, Stephen J. O’Brien
, Elena R. Gaginskaya
, Alsu F. Saifitdinova
, Stephen James O'Brien

Research output: Contribution to journal › Article › peer-review

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.

Original language	American English
Pages (from-to)	73-83
Number of pages	11
Journal	Chromosoma
Volume	127
Issue number	1
DOIs	https://doi.org/10.1007/s00412-017-0646-5
State	Published - Mar 1 2018

Bibliographical note

Publisher Copyright:
© 2017, Springer-Verlag GmbH Germany.

Funding

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

Funders	Funder number
Russian Foundation for Basic Research	16–04-01823
Russian Science Foundation	17-14-01138, 1.50.1043.2014

ASJC Scopus Subject Areas

Genetics(clinical)
Genetics

Keywords

Gallus gallus Domesticus
Kmer analysis
Lampbrush chromosomes
Raw reads analysis
Satellite DNA
Tandem repeats

Disciplines

Genetics and Genomics
Life Sciences

Access to Document

10.1007/s00412-017-0646-5

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

Cite this

@article{d5c588b4b499428687dbff19bb5a8cf6,

title = "New high copy tandem repeat in the content of the chicken W chromosome",

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.",

keywords = "Gallus gallus Domesticus, Kmer analysis, Lampbrush chromosomes, Raw reads analysis, Satellite DNA, Tandem repeats",

author = "Komissarov, \{Aleksey S.\} and Galkina, \{Svetlana A.\} and Koshel, \{Elena I.\} and Kulak, \{Maria M.\} and Dyomin, \{Aleksander G.\} and O{\textquoteright}Brien, \{Stephen J.\} and Gaginskaya, \{Elena R.\} and Saifitdinova, \{Alsu F.\} and O'Brien, \{Stephen James\}",

note = "Publisher Copyright: {\textcopyright} 2017, Springer-Verlag GmbH Germany.",

year = "2018",

month = mar,

day = "1",

doi = "10.1007/s00412-017-0646-5",

language = "American English",

volume = "127",

pages = "73--83",

journal = "Chromosoma",

issn = "0009-5915",

number = "1",

}

TY - JOUR

T1 - New high copy tandem repeat in the content of the chicken W chromosome

AU - Komissarov, Aleksey S.

AU - Galkina, Svetlana A.

AU - Koshel, Elena I.

AU - Kulak, Maria M.

AU - Dyomin, Aleksander G.

AU - O’Brien, Stephen J.

AU - Gaginskaya, Elena R.

AU - Saifitdinova, Alsu F.

AU - O'Brien, Stephen James

PY - 2018/3/1

Y1 - 2018/3/1

N2 - 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.

AB - 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.

KW - Gallus gallus Domesticus

KW - Kmer analysis

KW - Lampbrush chromosomes

KW - Raw reads analysis

KW - Satellite DNA

KW - Tandem repeats

UR - https://nsuworks.nova.edu/cnso_bio_facarticles/1091

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

UR - https://www.scopus.com/pages/publications/85029898350

UR - https://www.scopus.com/pages/publications/85029898350#tab=citedBy

U2 - 10.1007/s00412-017-0646-5

DO - 10.1007/s00412-017-0646-5

M3 - Article

SN - 0009-5915

VL - 127

SP - 73

EP - 83

JO - Chromosoma

JF - Chromosoma

IS - 1

ER -

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

Abstract

Bibliographical note

Funding

ASJC Scopus Subject Areas

Keywords

Disciplines

Access to Document

Other files and links

Fingerprint

Cite this