Abstract
Synonymous codon usage bias (SCUB) is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons) are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes.
Highlights
IntroductionThe mitochondrion is a major double-membrane organelle found in most eukaryotic cells [1]
The mitochondrion is a major double-membrane organelle found in most eukaryotic cells [1].It is the site for supplying cellular energy as well as signaling, cellular differentiation, cell death and maintaining the control of the cell cycle and cell growth [2]
We found the amount of protein coding genes ranged from 30 in B. umbellatus to 156 in N. tabacum (Table 1)
Summary
The mitochondrion is a major double-membrane organelle found in most eukaryotic cells [1]. It is the site for supplying cellular energy as well as signaling, cellular differentiation, cell death and maintaining the control of the cell cycle and cell growth [2]. Unlike nuclear genome with a signal copy, there have many mitochondria, and each mitochondrion possesses multiple copies of a circular genome [3]. Eukaryotic mitochondria are believed to have originated from a symbiotic relationship with bacteria, and since their incorporation, most of their genetic content appears to have either been deleted or transferred into the nuclear genome during the whole evolution course of PLOS ONE | DOI:10.1371/journal.pone.0131508. Eukaryotic mitochondria are believed to have originated from a symbiotic relationship with bacteria, and since their incorporation, most of their genetic content appears to have either been deleted or transferred into the nuclear genome during the whole evolution course of PLOS ONE | DOI:10.1371/journal.pone.0131508 June 25, 2015
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