Research output: Contribution to journal › Article › peer-review
The Cytogenetic Map of the Nile Crocodile (Crocodylus niloticus, Crocodylidae, Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs. / Romanenko, Svetlana A.; Prokopov, Dmitry Yu; Proskuryakova, Anastasia A. et al.
In: International Journal of Molecular Sciences, Vol. 23, No. 21, 13063, 11.2022.Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - The Cytogenetic Map of the Nile Crocodile (Crocodylus niloticus, Crocodylidae, Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs
AU - Romanenko, Svetlana A.
AU - Prokopov, Dmitry Yu
AU - Proskuryakova, Anastasia A.
AU - Davletshina, Guzel I.
AU - Tupikin, Alexey E.
AU - Kasai, Fumio
AU - Ferguson-Smith, Malcolm A.
AU - Trifonov, Vladimir A.
N1 - Funding Information: This research was funded by RFBR grant No 19-54-26017 (V.A.T.). Publisher Copyright: © 2022 by the authors.
PY - 2022/11
Y1 - 2022/11
N2 - Tandemly arranged and dispersed repetitive DNA sequences are important structural and functional elements that make up a significant portion of vertebrate genomes. Using high throughput, low coverage whole genome sequencing followed by bioinformatics analysis, we have identified seven major tandem repetitive DNAs and two fragments of LTR retrotransposons in the genome of the Nile crocodile (Crocodylus niloticus, 2n = 32). The repeats showed great variability in structure, genomic organization, and chromosomal distribution as revealed by fluorescence in situ hybridization (FISH). We found that centromeric and pericentromeric heterochromatin of C. niloticus is composed of previously described in Crocodylus siamensis CSI-HindIII and CSI-DraI repetitive sequence families, a satellite revealed in Crocodylus porosus, and additionally contains at least three previously unannotated tandem repeats. Both LTR sequences identified here belong to the ERV1 family of endogenous retroviruses. Each pericentromeric region was characterized by a diverse set of repeats, with the exception of chromosome pair 4, in which we found only one type of satellite. Only a few repeats showed non-centromeric signals in addition to their centromeric localization. Mapping of 18S–28S ribosomal RNA genes and telomeric sequences (TTAGGG)n did not demonstrate any co-localization of these sequences with revealed centromeric and pericentromeric heterochromatic blocks.
AB - Tandemly arranged and dispersed repetitive DNA sequences are important structural and functional elements that make up a significant portion of vertebrate genomes. Using high throughput, low coverage whole genome sequencing followed by bioinformatics analysis, we have identified seven major tandem repetitive DNAs and two fragments of LTR retrotransposons in the genome of the Nile crocodile (Crocodylus niloticus, 2n = 32). The repeats showed great variability in structure, genomic organization, and chromosomal distribution as revealed by fluorescence in situ hybridization (FISH). We found that centromeric and pericentromeric heterochromatin of C. niloticus is composed of previously described in Crocodylus siamensis CSI-HindIII and CSI-DraI repetitive sequence families, a satellite revealed in Crocodylus porosus, and additionally contains at least three previously unannotated tandem repeats. Both LTR sequences identified here belong to the ERV1 family of endogenous retroviruses. Each pericentromeric region was characterized by a diverse set of repeats, with the exception of chromosome pair 4, in which we found only one type of satellite. Only a few repeats showed non-centromeric signals in addition to their centromeric localization. Mapping of 18S–28S ribosomal RNA genes and telomeric sequences (TTAGGG)n did not demonstrate any co-localization of these sequences with revealed centromeric and pericentromeric heterochromatic blocks.
KW - C-banding
KW - CDAG-banding
KW - FISH
KW - GTG-banding
KW - heterochromatin
KW - high-throughput sequencing
KW - karyotype
KW - repeats
KW - reptile
KW - ribosomal DNA
KW - tandem repeats
KW - telomeric DNA
KW - Alligators and Crocodiles/genetics
KW - In Situ Hybridization, Fluorescence
KW - Animals
KW - Repetitive Sequences, Nucleic Acid
KW - Centromere/genetics
KW - RNA, Ribosomal, 18S/genetics
UR - http://www.scopus.com/inward/record.url?scp=85141617778&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/e1f8a772-9a09-3ca3-8f5b-89d7d8ec4963/
U2 - 10.3390/ijms232113063
DO - 10.3390/ijms232113063
M3 - Article
C2 - 36361851
AN - SCOPUS:85141617778
VL - 23
JO - International Journal of Molecular Sciences
JF - International Journal of Molecular Sciences
SN - 1661-6596
IS - 21
M1 - 13063
ER -
ID: 39331744