Limits...
Novel Insights on Hantavirus Evolution: The Dichotomy in Evolutionary Pressures Acting on Different Hantavirus Segments.

Sankar S, Upadhyay M, Ramamurthy M, Vadivel K, Sagadevan K, Nandagopal B, Vivekanandan P, Sridharan G - PLoS ONE (2015)

Bottom Line: The relative abundance of dinucleotides, effective codon number (ENC), codon usage biases were analyzed.These findings provide new insights on the current understanding of hantavirus evolution.There is a dichotomy among evolutionary pressures shaping a) the relative abundance of different dinucleotides in hantavirus genomes b) the evolution of the three hantavirus segments.

View Article: PubMed Central - PubMed

Affiliation: Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India.

ABSTRACT

Background: Hantaviruses are important emerging zoonotic pathogens. The current understanding of hantavirus evolution is complicated by the lack of consensus on co-divergence of hantaviruses with their animal hosts. In addition, hantaviruses have long-term associations with their reservoir hosts. Analyzing the relative abundance of dinucleotides may shed new light on hantavirus evolution. We studied the relative abundance of dinucleotides and the evolutionary pressures shaping different hantavirus segments.

Methods: A total of 118 sequences were analyzed; this includes 51 sequences of the S segment, 43 sequences of the M segment and 23 sequences of the L segment. The relative abundance of dinucleotides, effective codon number (ENC), codon usage biases were analyzed. Standard methods were used to investigate the relative roles of mutational pressure and translational selection on the three hantavirus segments.

Results: All three segments of hantaviruses are CpG depleted. Mutational pressure is the predominant evolutionary force leading to CpG depletion among hantaviruses. Interestingly, the S segment of hantaviruses is GpU depleted and in contrast to CpG depletion, the depletion of GpU dinucleotides from the S segment is driven by translational selection. Our findings also suggest that mutational pressure is the primary evolutionary pressure acting on the S and the M segments of hantaviruses. While translational selection plays a key role in shaping the evolution of the L segment. Our findings highlight how different evolutionary pressures may contribute disproportionally to the evolution of the three hantavirus segments. These findings provide new insights on the current understanding of hantavirus evolution.

Conclusions: There is a dichotomy among evolutionary pressures shaping a) the relative abundance of different dinucleotides in hantavirus genomes b) the evolution of the three hantavirus segments.

No MeSH data available.


GpU dinucleotide depletion in the S segment is linked to translational selection.The intracodon GpU O/E ratio for the S segment was significantly lower than that for the non-coding region of this segment (0.70±0.07 vs 0.95±0.14; P< 0.0001); clearly supporting translational selection as the major driver of GpU depletion in the S segment of hantaviruses.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4508033&req=5

pone.0133407.g007: GpU dinucleotide depletion in the S segment is linked to translational selection.The intracodon GpU O/E ratio for the S segment was significantly lower than that for the non-coding region of this segment (0.70±0.07 vs 0.95±0.14; P< 0.0001); clearly supporting translational selection as the major driver of GpU depletion in the S segment of hantaviruses.

Mentions: We analyzed the GpU O/E ratios for the non-coding region and the coding region (intracodon O/E ratio) of the S segment. We found that the intracodon GpU O/E ratio for the S segment was significantly lower than that for the non-coding region of this segment (0.70±0.07 vs 0.95±0.14; P<0.0001; Fig 7); clearly supporting translational selection as the major driver of GpU depletion in the S segment of hantaviruses. This finding is in contrast to our findings that mutational pressure is the primary evolutionary force leading to the depletion of CpG dinucleotides in all the three segments of hantaviruses. Our results suggest that the relative abundance of different dinucleotides within the S segment may be driven by different evolutionary forces. Nonetheless, it is not clear why GpU depletion is restricted to the S segment of hantaviruses.


Novel Insights on Hantavirus Evolution: The Dichotomy in Evolutionary Pressures Acting on Different Hantavirus Segments.

Sankar S, Upadhyay M, Ramamurthy M, Vadivel K, Sagadevan K, Nandagopal B, Vivekanandan P, Sridharan G - PLoS ONE (2015)

GpU dinucleotide depletion in the S segment is linked to translational selection.The intracodon GpU O/E ratio for the S segment was significantly lower than that for the non-coding region of this segment (0.70±0.07 vs 0.95±0.14; P< 0.0001); clearly supporting translational selection as the major driver of GpU depletion in the S segment of hantaviruses.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4508033&req=5

pone.0133407.g007: GpU dinucleotide depletion in the S segment is linked to translational selection.The intracodon GpU O/E ratio for the S segment was significantly lower than that for the non-coding region of this segment (0.70±0.07 vs 0.95±0.14; P< 0.0001); clearly supporting translational selection as the major driver of GpU depletion in the S segment of hantaviruses.
Mentions: We analyzed the GpU O/E ratios for the non-coding region and the coding region (intracodon O/E ratio) of the S segment. We found that the intracodon GpU O/E ratio for the S segment was significantly lower than that for the non-coding region of this segment (0.70±0.07 vs 0.95±0.14; P<0.0001; Fig 7); clearly supporting translational selection as the major driver of GpU depletion in the S segment of hantaviruses. This finding is in contrast to our findings that mutational pressure is the primary evolutionary force leading to the depletion of CpG dinucleotides in all the three segments of hantaviruses. Our results suggest that the relative abundance of different dinucleotides within the S segment may be driven by different evolutionary forces. Nonetheless, it is not clear why GpU depletion is restricted to the S segment of hantaviruses.

Bottom Line: The relative abundance of dinucleotides, effective codon number (ENC), codon usage biases were analyzed.These findings provide new insights on the current understanding of hantavirus evolution.There is a dichotomy among evolutionary pressures shaping a) the relative abundance of different dinucleotides in hantavirus genomes b) the evolution of the three hantavirus segments.

View Article: PubMed Central - PubMed

Affiliation: Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India.

ABSTRACT

Background: Hantaviruses are important emerging zoonotic pathogens. The current understanding of hantavirus evolution is complicated by the lack of consensus on co-divergence of hantaviruses with their animal hosts. In addition, hantaviruses have long-term associations with their reservoir hosts. Analyzing the relative abundance of dinucleotides may shed new light on hantavirus evolution. We studied the relative abundance of dinucleotides and the evolutionary pressures shaping different hantavirus segments.

Methods: A total of 118 sequences were analyzed; this includes 51 sequences of the S segment, 43 sequences of the M segment and 23 sequences of the L segment. The relative abundance of dinucleotides, effective codon number (ENC), codon usage biases were analyzed. Standard methods were used to investigate the relative roles of mutational pressure and translational selection on the three hantavirus segments.

Results: All three segments of hantaviruses are CpG depleted. Mutational pressure is the predominant evolutionary force leading to CpG depletion among hantaviruses. Interestingly, the S segment of hantaviruses is GpU depleted and in contrast to CpG depletion, the depletion of GpU dinucleotides from the S segment is driven by translational selection. Our findings also suggest that mutational pressure is the primary evolutionary pressure acting on the S and the M segments of hantaviruses. While translational selection plays a key role in shaping the evolution of the L segment. Our findings highlight how different evolutionary pressures may contribute disproportionally to the evolution of the three hantavirus segments. These findings provide new insights on the current understanding of hantavirus evolution.

Conclusions: There is a dichotomy among evolutionary pressures shaping a) the relative abundance of different dinucleotides in hantavirus genomes b) the evolution of the three hantavirus segments.

No MeSH data available.