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Comparative Genomics of Trypanosomatid Pathogens using Codon Usage Bias.

Rashmi M, Swati D - Bioinformation (2013)

Bottom Line: Translational selection is the dominant force selecting the preferred codon, and selection due to mutation is negligible.In contrast to an earlier study done on these pathogens, it is found in this work that CUB and CAI may be used to distinguish the Trypanosomatid genomes at the sub-genus level.Further, CUB may effectively be used as a signature of the species differentiation by using Principal Component Analysis (PCA).

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi-221005, India.

ABSTRACT

Unlabelled: It is well known that an amino acid can be encoded by more than one codon, called synonymous codons. The preferential use of one particular codon for coding an amino acid is referred to as codon usage bias (CUB). A quantitative analytical method, CUB and a related tool, Codon Adaptative Index have been applied to comparatively study whole genomes of a few pathogenic Trypanosomatid species. This quantitative attempt is of direct help in the comparison of qualitative features like mutational and translational selection. Pathogens of the Leishmania and Trypanosoma genus cause debilitating disease and suffering in human beings and animals. Of these, whole genome sequences are available for only five species. The complete coding sequences (CDS), highly expressed, essential and low expressed genes have all been studied for their CUB signature. The codon usage bias of essential genes and highly expressed genes show distribution similar to codon usage bias of all CDSs in Trypanosomatids. Translational selection is the dominant force selecting the preferred codon, and selection due to mutation is negligible. In contrast to an earlier study done on these pathogens, it is found in this work that CUB and CAI may be used to distinguish the Trypanosomatid genomes at the sub-genus level. Further, CUB may effectively be used as a signature of the species differentiation by using Principal Component Analysis (PCA).

Abbreviations: CUB - Codon Usage Bias, CAI - Codon Adaptative Index, CDS - Coding sequences, t-RNA - Transfer RNA, PCA - Principal Component Analysis.

No MeSH data available.


Related in: MedlinePlus

Plot of frequency of codon usage per thousand in all CDSs of length of less than ten thousands in L.major Freidlin(Orange), L.infantum JPCM5(Yellow), L.braziliensis MHOM(Green), T.brucei 927(Brown) and T.cruzi CL Brener (Blue).
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Figure 1: Plot of frequency of codon usage per thousand in all CDSs of length of less than ten thousands in L.major Freidlin(Orange), L.infantum JPCM5(Yellow), L.braziliensis MHOM(Green), T.brucei 927(Brown) and T.cruzi CL Brener (Blue).

Mentions: The genome size of Trypanosomatids is very large, average genome size in four species is 30 Mb but T.cruzi has a larger size of about 90 Mb Table 1 (see supplementary table) because 50% of its genome contains repetitive elements [11]. Overall codon frequencies of Trypanosomatids are listed in Table 2 (see supplementary table). The dominant codons referred to in Table 2 are those that are at least 1.25 times more frequent thanthe expected frequency of synonymous codons that code a specific amino acid. High codon usage bias in Leishmania species and comparatively lesser codon usage bias in Trypanosoma species are seen (Figure 1). Bias of cognate codon of the Trypanosoma species are not conserved as much as in the Leishmania species.


Comparative Genomics of Trypanosomatid Pathogens using Codon Usage Bias.

Rashmi M, Swati D - Bioinformation (2013)

Plot of frequency of codon usage per thousand in all CDSs of length of less than ten thousands in L.major Freidlin(Orange), L.infantum JPCM5(Yellow), L.braziliensis MHOM(Green), T.brucei 927(Brown) and T.cruzi CL Brener (Blue).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3842577&req=5

Figure 1: Plot of frequency of codon usage per thousand in all CDSs of length of less than ten thousands in L.major Freidlin(Orange), L.infantum JPCM5(Yellow), L.braziliensis MHOM(Green), T.brucei 927(Brown) and T.cruzi CL Brener (Blue).
Mentions: The genome size of Trypanosomatids is very large, average genome size in four species is 30 Mb but T.cruzi has a larger size of about 90 Mb Table 1 (see supplementary table) because 50% of its genome contains repetitive elements [11]. Overall codon frequencies of Trypanosomatids are listed in Table 2 (see supplementary table). The dominant codons referred to in Table 2 are those that are at least 1.25 times more frequent thanthe expected frequency of synonymous codons that code a specific amino acid. High codon usage bias in Leishmania species and comparatively lesser codon usage bias in Trypanosoma species are seen (Figure 1). Bias of cognate codon of the Trypanosoma species are not conserved as much as in the Leishmania species.

Bottom Line: Translational selection is the dominant force selecting the preferred codon, and selection due to mutation is negligible.In contrast to an earlier study done on these pathogens, it is found in this work that CUB and CAI may be used to distinguish the Trypanosomatid genomes at the sub-genus level.Further, CUB may effectively be used as a signature of the species differentiation by using Principal Component Analysis (PCA).

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi-221005, India.

ABSTRACT

Unlabelled: It is well known that an amino acid can be encoded by more than one codon, called synonymous codons. The preferential use of one particular codon for coding an amino acid is referred to as codon usage bias (CUB). A quantitative analytical method, CUB and a related tool, Codon Adaptative Index have been applied to comparatively study whole genomes of a few pathogenic Trypanosomatid species. This quantitative attempt is of direct help in the comparison of qualitative features like mutational and translational selection. Pathogens of the Leishmania and Trypanosoma genus cause debilitating disease and suffering in human beings and animals. Of these, whole genome sequences are available for only five species. The complete coding sequences (CDS), highly expressed, essential and low expressed genes have all been studied for their CUB signature. The codon usage bias of essential genes and highly expressed genes show distribution similar to codon usage bias of all CDSs in Trypanosomatids. Translational selection is the dominant force selecting the preferred codon, and selection due to mutation is negligible. In contrast to an earlier study done on these pathogens, it is found in this work that CUB and CAI may be used to distinguish the Trypanosomatid genomes at the sub-genus level. Further, CUB may effectively be used as a signature of the species differentiation by using Principal Component Analysis (PCA).

Abbreviations: CUB - Codon Usage Bias, CAI - Codon Adaptative Index, CDS - Coding sequences, t-RNA - Transfer RNA, PCA - Principal Component Analysis.

No MeSH data available.


Related in: MedlinePlus