Compositional properties of green-plant plastid genomes

Junko Kusumi, Hidenori Tachida

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

We studied variation of GC contents among plastid (Pt) genomes of green plants. In the green plants, the GC contents of the whole Pt genomes range from 42.14 to 28.81%. These values are similar to those observed in the mitochondrial (Mt) genomes of the green plants, however, the GC contents in the Pt genomes are not related to those in the Mt genomes or the nuclear (Nc) genomes. In addition, some compositional properties of the three types of genomes are different. Thus, it is suggested that the GC contents of the Pt genomes are maintained independently of the other genomes within a cell. We found that the compositional bias toward AT is strong at the third codon position and in intergenic spacer (IGS) regions in the Pt genomes, and the GC contents (GC3 and GCIGS) at these sites are generally similar within each genome. Additionally, the GC3 and GCIGS are strongly related to the whole-genome GC content. Therefore, the interspecific variation of the GC contents in the Pt genomes is suggested to be mainly caused by the variation of the GC3 and GCIGS, both of which are considered to be under weak selective constraints. Using a maximum likelihood approach, we estimated equilibrium GC3 (eqGC3) of 12 genes in the land-plant Pt genomes. We found an increase in eqGC3 after the divergence of liverworts. These results suggest that genome-wide factors such as GC mutational bias are important for the biased base composition in the Pt genomes.

Original languageEnglish
Pages (from-to)417-425
Number of pages9
JournalJournal of Molecular Evolution
Volume60
Issue number4
DOIs
Publication statusPublished - Apr 1 2005

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Plastid Genomes
Viridiplantae
Plant Genome
plastid
Base Composition
genome
Genes
Genome
Mitochondrial Genome
Hepatophyta
Embryophyta
Intergenic DNA
plastid genome
embryophytes
intergenic DNA
interspecific variation
codons
Codon
nuclear genome
mosses and liverworts

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Compositional properties of green-plant plastid genomes. / Kusumi, Junko; Tachida, Hidenori.

In: Journal of Molecular Evolution, Vol. 60, No. 4, 01.04.2005, p. 417-425.

Research output: Contribution to journalArticle

Kusumi, Junko ; Tachida, Hidenori. / Compositional properties of green-plant plastid genomes. In: Journal of Molecular Evolution. 2005 ; Vol. 60, No. 4. pp. 417-425.
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