title: Synonymous codon usage bias in plant mitochondrial genes is associated with intron number and mirrors species evolution.
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.
authors.affiliation: The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China.
authors.forename: Wenjing
authors.initials: W
authors.lastname: Xu
authors.affiliation: The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China.
authors.forename: Tian
authors.initials: T
authors.lastname: Xing
authors.affiliation: The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China.
authors.forename: Mingming
authors.initials: M
authors.lastname: Zhao
authors.affiliation: The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China.
authors.forename: Xunhao
authors.initials: X
authors.lastname: Yin
authors.affiliation: The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China.
authors.forename: Guangmin
authors.initials: G
authors.lastname: Xia
authors.affiliation: The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China.
authors.forename: Mengcheng
authors.initials: M
authors.lastname: Wang
mesh_terms: D005075:Biological Evolution; D002736:Chloroplasts / Q000235:genetics; D003062:Codon; D018388:Codon, Terminator; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D005091:Exons; D005787:Gene Frequency; D050259:Genes, Mitochondrial; D017343:Genes, Plant; D007438:Introns; D010802:Phylogeny; D010944:Plants / Q000235:genetics*; D018087:Plastids / Q000235:genetics; D013045:Species Specificity
chemical_list: D003062:Codon; D018388:Codon, Terminator; D004272:DNA, Mitochondrial