Codon-triplet context unveils unique features of the Candida albicans protein coding genome

Moura, Gabriela R; Lousado, José P; Pinheiro, Miguel; Carreto, Laura; Silva, Raquel M; Oliveira, José L; Santos, Manuel AS

doi:10.1186/1471-2164-8-444

BMC Genomics

Table 2 Ranking of the 10 most preferred codon-triplets in fungal ORFeomes

From: Codon-triplet context unveils unique features of the Candida albicans protein coding genome

	A.fum	C.alb	C.gla	D.han	E.gos	K.lac	S.bay	S.cer	S.mik	S.par	S.pom
1	AAG	CAA	GAA	GAA	CAG	GAA	GAA	GAA	GAA	CAA	GAA
	AAG	CAA	GAA	GAA	CAG	GAA	GAA	GAA	GAA	CAA	GAA
	AAG	CAA	GAA	GAA	CAG	GAA	GAA	GAA	GAA	CAA	GAA
2	GAG	GAA	AAG	GAT	GAG	CAA	CAA	GAT	GAT	GAA	ATT
	GAG	GAA	AAG	GAT	GAG	CAA	CAA	GAT	GAT	GAA	ACT
	GAG	GAA	AAG	GAT	GAG	CAA	CAA	GAT	GAT	GAA	AGT
3	GAG	AAT	GAT	CAA	AAG	GAT	AAC	CAA	CAA	GAT	ACA
	AAG	AAT	GAT	CAA	AAG	GAT	AAC	CAA	CAA	GAT	CCA
	AAG	AAT	GAT	CAA	AAG	GAT	AAC	CAA	CAA	GAT	ATT
4	CAG	GAT	GAT	GAT	GAC	AAG	CAG	GAT	CAG	AAT	CCA
	CAG	GAT	GAA	GAA	GAC	AAG	CAG	GAT	CAG	AAT	ATT
	CAG	GAT	GAA	GAA	GAC	AAG	CAG	GAA	CAG	AAT	ACT
5	GAA	AAC	GAT	GAA	GCG	CAA	CAA	AAT	CAA	CAA	GAT
	GAA	AAC	GAT	GAT	GCG	CAG	CAG	AAT	CAG	CAG	GAA
	GAA	AAC	GAA	GAA	GCG	CAA	CAA	AAT	CAA	CAA	GAA
6	GAG	CAA	GAT	GAT	GAG	GAT	GAT	CAA	AAT	GAT	TCC
	GAG	CAG	GAA	GAT	GAC	GAA	GAT	CAG	AAT	GAA	ACA
	GAA	CAA	GAT	GAA	GAG	GAT	GAT	CAA	AAT	GAA	CCA
7	GAA	GGT	AAG	AAG	GAG	CAG	AAG	GAT	GAT	CAG	GAA
	GAG	GGT	AAG	AAG	CTG	CAG	AAG	GAA	GAT	CAG	GAT
	GAG	GGT	AAA	AAG	CTG	CAG	AAG	GAA	GAA	CAG	GAA
8	AAG	CAA	CAA	GAT	GAC	CAG	AAT	GAA	GAT	GAT	GAT
	GAG	CAA	CAA	GAA	GAG	CAA	AAT	GAT	GAA	GAT	GAT
	AAG	CAG	CAA	GAT	GAC	CAA	AAT	GAA	GAA	GAA	GAT
9	GAA	GAT	GAA	GAC	GAC	CAA	GAA	GAT	GAA	GAA	TCT
	GAG	GAA	GAT	GAA	GAG	CAA	GAT	GAA	GAT	GAT	TCT
	GAA	GAA	GAA	GAA	GAG	CAG	GAA	GAT	GAA	GAA	TCT
10	GAG	CCA	GAA	AAT	CTG	GAT	GAA	CAG	CAG	AAG	AGT
	GAG	CCA	GAA	AAT	CTG	GAA	GAG	CAG	CAA	AAG	TCA
	AAG	CCA	GAG	AAT	CAG	GAA	GAA	CAG	CAG	AAG	ACT

The complete set of codon-triplets present in the 11 fungal ORFeomes studied were identified and the codon-triplets were ranked according to the difference between observed and expected values (bias). The 10 most preferred codon-triplets indicate that the codon-triplets with highest positive bias are common in all fungal ORFeomes. For example, the strongly biased GAA-GAA-GAA triplet was preferred in 10 out of 11 fungal ORFeomes (underscored). Also, codon-triplets containing identical codons were frequent (bold). Interestingly, the most common feature of these preferred codon-triplets was the presence of a guanosine (G) at position 4 and 7 of the triplet (X₁X₂X₃-Y₄Y₅Y₆-Z₇Z₈Z₉), a feature which was common to half of the codon-triplets indicated below.

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ISSN: 1471-2164

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