Umeå University's logo

umu.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
The complete chloroplast genome of wild rice (Oryza minuta) and its comparison to related species
Show others and affiliations
2017 (English)In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 8, article id 304Article in journal (Refereed) Published
Abstract [en]

Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the Ominuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata. Thus, the complete Ominuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2017. Vol. 8, article id 304
Keywords [en]
wild rice (Oryza minuta), cp genome, repeat analysis, codon usage, phylogeny, sequence divergence, SSRs
National Category
Plant Biotechnology
Identifiers
URN: urn:nbn:se:umu:diva-176693DOI: 10.3389/fpls.2017.00304ISI: 000395517900001PubMedID: 28326093OAI: oai:DiVA.org:umu-176693DiVA, id: diva2:1500957
Available from: 2020-11-14 Created: 2020-11-14 Last updated: 2024-01-17Bibliographically approved

Open Access in DiVA

fulltext(5362 kB)197 downloads
File information
File name FULLTEXT01.pdfFile size 5362 kBChecksum SHA-512
9e864533a46c44f0ed03304f49c7d475aaa83b95a307d4c1d4179f08b73fcc94c4f0dae35de976e34761b8f9cdae32a70876dc6ee32ab0b907f1b513c4afa782
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Authority records

Imran, Qari Muhammad

Search in DiVA

By author/editor
Imran, Qari Muhammad
In the same journal
Frontiers in Plant Science
Plant Biotechnology

Search outside of DiVA

GoogleGoogle Scholar
Total: 197 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 264 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf