title: Codon bias and gene expression of mitochondrial ND2 gene in chordates.
abstract: BACKGROUND
  Mitochondrial ND gene, which encodes NADH dehydrogenase, is the first enzyme of the mitochondrial electron transport chain. Leigh syndrome, a neurodegenerative disease caused by mutation in the ND2 gene (T4681C), is associated with bilateral symmetric lesions in basal ganglia and subcortical brain regions. Therefore, it is of interest to analyze mitochondrial DNA to glean information for evolutionary relationship. This study highlights on the analysis of compositional dynamics and selection pressure in shaping the codon usage patterns in the coding sequence of MT-ND2 gene across pisces, aves and mammals by using bioinformatics tools like effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU) etc.
  
  
  RESULTS
  We observed a low codon usage bias as reflected by high ENC values in MT-ND2 gene among pisces, aves and mammals. The most frequently used codons were ending with A/C at the 3(rd) position of codon and the gene was AT rich in all the three classes. The codons TCA, CTA, CGA and TGA were over represented in all three classes. The F1 correspondence showed significant positive correlation with G, T3 and CAI while the F2 axis showed significant negative correlation with A and T but significant positive correlation with G, C, G3, C3, ENC, GC, GC1, GC2 and GC3.
  
  
  CONCLUSIONS
  The codon usage bias in MTND2 gene is not associated with expression level. Mutation pressure and natural selection affect the codon usage pattern in MT-ND 2 gene.
authors.affiliation: Department of Biotechnology, Assam University, Silchar-788011, Assam, India.
authors.forename: Arif
authors.initials: A
authors.lastname: Uddin
authors.affiliation: Department of Biotechnology, Assam University, Silchar-788011, Assam, India.
authors.forename: Tarikul Huda
authors.initials: TH
authors.lastname: Mazumder
authors.affiliation: Department of Biotechnology, Assam University, Silchar-788011, Assam, India.
authors.forename: Monisha Nath
authors.initials: MN
authors.lastname: Choudhury
authors.affiliation: Department of Biotechnology, Assam University, Silchar-788011, Assam, India.
authors.forename: Supriyo
authors.initials: S
authors.lastname: Chakraborty
keywords: Codon usage; MT-ND2 gene; mutation pressure; natural selection