PMID- 36361851
OWN - NLM
STAT- MEDLINE
DCOM- 20221114
LR  - 20221117
IS  - 1422-0067 (Electronic)
IS  - 1422-0067 (Linking)
VI  - 23
IP  - 21
DP  - 2022 Oct 27
TI  - The Cytogenetic Map of the Nile Crocodile (Crocodylus niloticus, Crocodylidae, 
      Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs.
LID - 10.3390/ijms232113063 [doi]
LID - 13063
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.
FAU - Romanenko, Svetlana A
AU  - Romanenko SA
AUID- ORCID: 0000-0002-0951-5209
AD  - Institute of Molecular and Cellular Biology, Russian Academy of Sciences, 
      Siberian Branch, 630090 Novosibirsk, Russia.
FAU - Prokopov, Dmitry Yu
AU  - Prokopov DY
AUID- ORCID: 0000-0001-8420-5203
AD  - Institute of Molecular and Cellular Biology, Russian Academy of Sciences, 
      Siberian Branch, 630090 Novosibirsk, Russia.
FAU - Proskuryakova, Anastasia A
AU  - Proskuryakova AA
AUID- ORCID: 0000-0003-3812-4853
AD  - Institute of Molecular and Cellular Biology, Russian Academy of Sciences, 
      Siberian Branch, 630090 Novosibirsk, Russia.
FAU - Davletshina, Guzel I
AU  - Davletshina GI
AD  - Institute of Molecular and Cellular Biology, Russian Academy of Sciences, 
      Siberian Branch, 630090 Novosibirsk, Russia.
AD  - Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 
      630090 Novosibirsk, Russia.
FAU - Tupikin, Alexey E
AU  - Tupikin AE
AD  - Institute of Chemical Biology and Fundamental Medicine, Russian Academy of 
      Sciences, Siberian Branch, 630090 Novosibirsk, Russia.
FAU - Kasai, Fumio
AU  - Kasai F
AD  - Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell 
      Cultures, The National Institute of Biomedical Innovation, Health and Nutrition, 
      Saito-Asagi, Ibaraki 567-0085, Osaka, Japan.
AD  - Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, 
      UK.
FAU - Ferguson-Smith, Malcolm A
AU  - Ferguson-Smith MA
AUID- ORCID: 0000-0001-9372-1381
AD  - Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, 
      UK.
FAU - Trifonov, Vladimir A
AU  - Trifonov VA
AUID- ORCID: 0000-0003-0454-8359
AD  - Institute of Molecular and Cellular Biology, Russian Academy of Sciences, 
      Siberian Branch, 630090 Novosibirsk, Russia.
AD  - Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, 
      Russia.
LA  - eng
GR  - 19-54-26017/Russian Foundation for Basic Research/
PT  - Journal Article
DEP - 20221027
PL  - Switzerland
TA  - Int J Mol Sci
JT  - International journal of molecular sciences
JID - 101092791
RN  - 0 (RNA, Ribosomal, 18S)
SB  - IM
MH  - Animals
MH  - *Alligators and Crocodiles/genetics
MH  - In Situ Hybridization, Fluorescence
MH  - Centromere/genetics
MH  - Repetitive Sequences, Nucleic Acid
MH  - RNA, Ribosomal, 18S/genetics
PMC - PMC9656864
OTO - NOTNLM
OT  - C-banding
OT  - CDAG-banding
OT  - FISH
OT  - GTG-banding
OT  - heterochromatin
OT  - high-throughput sequencing
OT  - karyotype
OT  - repeats
OT  - reptile
OT  - ribosomal DNA
OT  - tandem repeats
OT  - telomeric DNA
COIS- The authors declare no conflict of interest.
EDAT- 2022/11/12 06:00
MHDA- 2022/11/15 06:00
PMCR- 2022/10/27
CRDT- 2022/11/11 01:26
PHST- 2022/08/31 00:00 [received]
PHST- 2022/10/21 00:00 [revised]
PHST- 2022/10/24 00:00 [accepted]
PHST- 2022/11/11 01:26 [entrez]
PHST- 2022/11/12 06:00 [pubmed]
PHST- 2022/11/15 06:00 [medline]
PHST- 2022/10/27 00:00 [pmc-release]
AID - ijms232113063 [pii]
AID - ijms-23-13063 [pii]
AID - 10.3390/ijms232113063 [doi]
PST - epublish
SO  - Int J Mol Sci. 2022 Oct 27;23(21):13063. doi: 10.3390/ijms232113063.