Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61988987%3A17310%2F18%3AA1901WIB" target="_blank" >RIV/61988987:17310/18:A1901WIB - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/18:00502507 RIV/62156489:43110/18:43913803
Result on the web
<a href="https://www.hindawi.com/journals/bmri/2018/1097018/" target="_blank" >https://www.hindawi.com/journals/bmri/2018/1097018/</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1155/2018/1097018" target="_blank" >10.1155/2018/1097018</a>
Alternative languages
Result language
angličtina
Original language name
Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs
Original language description
Chloroplasts are key organelles in the management of oxygen in algae and plants and are therefore crucial for all living beingsthat consume oxygen. Chloroplasts typically contain a circular DNA molecule with nucleus-independent replication and heredity.Using ?palindrome analyser? we performed complete analyses of short inverted repeats (S-IRs) in all chloroplast DNAs (cpDNAs)available fromthe NCBI genome database. Our results provide basic parameters of cpDNAs including comparative information onlocalization, frequency, and differences in S-IR presence. In a total of 2,565 cpDNA sequences available, the average frequency ofS-IRs in cpDNA genomes is 45 S-IRs/per kbp, significantly higher than that found in mitochondrialDNA sequences.The frequencyof S-IRs in cpDNAs generally decreased with S-IR length, but not for S-IRs 15, 22, 24, or 27 bp long, which are significantly moreabundant than S-IRs with other lengths. These results point to the importance of specific S-IRs in cpDNA genomes. Moreover,comparison by Levenshtein distance of S-IR similarities showed that a limited number of S-IR sequences are shared in the majorityof cpDNAs. S-IRs are not located randomly in cpDNAs, but are length-dependently enriched in specific locations, including therepeat region, stem, introns, and tRNA regions. The highest enrichment was found for 12 bp and longer S-IRs in the stem-loopregion followed by 12 bp and longer S-IRs located before the repeat region. On the other hand, S-IRs are relatively rare in rRNAsequences and around introns.These data show nonrandom and conserved arrangements of S-IRs in chloroplast genomes.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10600 - Biological sciences
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
S - Specificky vyzkum na vysokych skolach
Others
Publication year
2018
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
BioMed research international
ISSN
2314-6133
e-ISSN
2314-6141
Volume of the periodical
2018
Issue of the periodical within the volume
24 July 2018
Country of publishing house
US - UNITED STATES
Number of pages
10
Pages from-to
1-10
UT code for WoS article
000439627100001
EID of the result in the Scopus database
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