Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/68081707:_____/18:00502507 RIV/62156489:43110/18:43913803

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10600 - Biological sciences

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2018

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

BioMed research international

ISSN

2314-6133

e-ISSN

2314-6141

Svazek periodika

2018

Číslo periodika v rámci svazku

24 July 2018

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

10

Strana od-do

1-10

Kód UT WoS článku

000439627100001

EID výsledku v databázi Scopus

—