TY - JOUR
T1 - Short tandem repeats in the human, cow, mouse, chicken, and lizard genomes are concentrated in the terminal regions of chromosomes
AU - Misawa, Kazuharu
N1 - Funding Information:
This study was funded through the national project titled “Next-Generation Integrated Living Matter Simulation” of the Ministry of Education, Culture, Sports, Science and Technology (MEXT) . Calculations were performed using RIKEN Integrated Cluster of Clusters (RICC) at the RIKEN Advanced Center for Computing and Communication and K computer at the Advanced Institute for Computational Science.
Publisher Copyright:
© 2016 Elsevier Inc.
PY - 2016/9/1
Y1 - 2016/9/1
N2 - Repetitive sequences in a genome cause mapping errors, especially in the case of short reads, because of the presence of similar or identical sequences. Distribution of repetitive sequences in a genome must be studied to distinguish between mappable and unmappable regions. Previous studies showed that short tandem repeats (STRs) are clustered in the terminal regions of chromosomes in the human genome. It is an open question whether formation of STRs in the terminal regions of chromosomes occurs only in humans. The present study investigated the distribution of STRs in the human, cow, mouse, chicken, and lizard genomes. In this study, it was shown that STRs were concentrated in the terminal regions of chromosomes not only in the human genome, but also in the mouse, cow, chicken, and lizard genomes. The results suggested the mechanism through which STRs are shared by amniotes in which mammals, birds and lizards are included. Thus, we must be careful with the genomic sequences at chromosome ends of amniotes by using the next generation sequencers.
AB - Repetitive sequences in a genome cause mapping errors, especially in the case of short reads, because of the presence of similar or identical sequences. Distribution of repetitive sequences in a genome must be studied to distinguish between mappable and unmappable regions. Previous studies showed that short tandem repeats (STRs) are clustered in the terminal regions of chromosomes in the human genome. It is an open question whether formation of STRs in the terminal regions of chromosomes occurs only in humans. The present study investigated the distribution of STRs in the human, cow, mouse, chicken, and lizard genomes. In this study, it was shown that STRs were concentrated in the terminal regions of chromosomes not only in the human genome, but also in the mouse, cow, chicken, and lizard genomes. The results suggested the mechanism through which STRs are shared by amniotes in which mammals, birds and lizards are included. Thus, we must be careful with the genomic sequences at chromosome ends of amniotes by using the next generation sequencers.
KW - Chromosome
KW - Evolution
KW - Mammalian genome
KW - Next generation sequencer
KW - Short tandem repeat
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U2 - 10.1016/j.genrep.2016.01.004
DO - 10.1016/j.genrep.2016.01.004
M3 - Article
AN - SCOPUS:84994494229
VL - 4
SP - 280
EP - 285
JO - Gene Reports
JF - Gene Reports
SN - 2452-0144
ER -