Publication detail

The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation

DOBROVOLNÁ, M. BRÁZDA, V.

Original Title

The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation

Type

journal article in Web of Science

Language

English

Original Abstract

G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional relevance in bacteria and animals, including humans, their importance has been recently demonstrated in evolutionarily distinct plant species. In this study, we analyzed the genome of Pisum sativum (garden pea, or the so-called green pea), a unique member of the Fabaceae family. Our results showed that this genome contained putative G4 sequences (PQSs). Interestingly, these PQSs were located nonrandomly in the nuclear genome. We also found PQSs in mitochondrial (mt) and chloroplast (cp) DNA, and we experimentally confirmed G4 formation for sequences found in these two organelles. The frequency of PQSs for nuclear DNA was 0.42 PQSs per thousand base pairs (kbp), in the same range as for cpDNA (0.53/kbp), but significantly lower than what was found for mitochondrial DNA (1.58/kbp). In the nuclear genome, PQSs were mainly associated with regulatory regions, including 5 ' UTRs, and upstream of the rRNA region. In contrast to genomic DNA, PQSs were located around RNA genes in cpDNA and mtDNA. Interestingly, PQSs were also associated with specific transposable elements such as TIR and LTR and around them, pointing to their role in their spreading in nuclear DNA. The nonrandom localization of PQSs uncovered their evolutionary and functional significance in the Pisum sativum genome.

Keywords

G-quadruplex; G4 propensity; chloroplast DNA; sequence prediction

Authors

DOBROVOLNÁ, M.; BRÁZDA, V.

Released

30. 7. 2022

Publisher

MDPI

Location

BASEL

ISBN

1661-6596

Periodical

International Journal of Molecular Sciences

Year of study

23

Number

15

State

United States of America

Pages count

12

URL

https://www.mdpi.com/1422-0067/23/15/8482

BibTex

@article{BUT187727,
  author="Michaela {Dobrovolná} and Václav {Brázda}",
  title="The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation",
  journal="International Journal of Molecular Sciences",
  year="2022",
  volume="23",
  number="15",
  pages="12",
  doi="10.3390/ijms23158482",
  issn="1661-6596",
  url="https://www.mdpi.com/1422-0067/23/15/8482"
}