Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes
Chen L, Yang DY, Liu TF, Nong X, Huang X, Xie Y, Fu Y, Zheng WP, Zhang RH, Wu XH, Gu XB, Wang SX, Peng XR, Yang GY.
Abstract
We analyzedsynonymouscodonusagepatternsof themitochondrialgenomesof 43parasiticplatyhelminthspecies. The relativesynonymouscodonusage, the effective number of codons (NC) and the frequency of G+C at the third synonymously variable coding position were calculated. Correspondence analysis was used to determine the major variation trends shaping thecodonusagepatterns. Among themitochondrialgenomesof 19 trematode species, the GC content of thirdcodonpositions varied from 0.151 to 0.592, with a mean of 0.295 ± 0.116. In cestodes, the mean GC content of thirdcodonpositions was 0.254 ± 0.044. A comparison of the nucleotide composition at 4-foldsynonymoussites revealed that, on average, there was a greater abundance of codons ending on U (51.9%) or A (22.7%) than on C (6.3%) or G (19.14%). Twenty-two codons, including UUU, UUA and UUG, were frequently used. In the NC-plot, most of points were distributed well below or around the expected NC curve. In addition to compositional constraints, the degree of hydrophobicity and the aromatic amino acids also influencedcodonusagein themitochondrialgenomesof these 43parasiticplatyhelminthspecies.
Copyright © 2014 . Genetics and Molecular Research
Genet Mol Res.2013 Feb 27;12(1):587-96. doi: 10.4238/2013.February.27.8.
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