Research output: Contribution to journal › Article › peer-review
New high copy tandem repeat in the content of the chicken W chromosome. / Komissarov, Aleksey S.; Galkina, Svetlana A.; Koshel, Elena I.; Kulak, Maria M.; Dyomin, Aleksander G.; O’Brien, Stephen J.; Gaginskaya, Elena R.; Saifitdinova, Alsu F.
In: Chromosoma, Vol. 127, No. 1, 01.03.2018, p. 73-83.Research output: Contribution to journal › Article › peer-review
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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.
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
KW - EUKARYOTIC GENOMES
KW - MOLECULAR CHARACTERIZATION
KW - LAMPBRUSH CHROMOSOMES
KW - SATELLITE DNA
KW - GALLUS-DOMESTICUS
KW - SEX-CHROMOSOMES
KW - Y-CHROMOSOMES
KW - AVIAN SEX
KW - DNA-SEQUENCE ORGANIZATION
KW - REPETITIVE DNA
UR - http://www.scopus.com/inward/record.url?scp=85029898350&partnerID=8YFLogxK
UR - http://www.mendeley.com/research/new-high-copy-tandem-repeat-content-chicken-w-chromosome
U2 - 10.1007/s00412-017-0646-5
DO - 10.1007/s00412-017-0646-5
M3 - Article
C2 - 28951974
AN - SCOPUS:85029898350
VL - 127
SP - 73
EP - 83
JO - Chromosoma
JF - Chromosoma
SN - 0009-5915
IS - 1
ER -
ID: 9315666