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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.


Hantavirus genomes are depleted for CpG dinucleotides and underlying evolutionary pressure is specific to CpG (not GpC) dinucleotides.(a) Among the 3 segments of hantaviruses the CpG dinucleotide O/E ratios for the M segment were significantly lower than that for the S segment (0.22±0.04 vs 0.28±0.06; P<0.0001) and that for the L segment (0.22±0.04 vs 0.29±0.05; P<0.0001). The differences in CpG O/E ratios of the S segment and the L segment were not significant (0.28±0.06 vs 0.29±0.05; P = 0.18). (b) The CpG/GpC O/E ratios were significantly lower for the M segment of hantaviruses as compared to those for the S segment (0.22±0.04 vs 0.29±0.07; P<0.0001) and for the L segment (0.22±0.04 vs 0.28±0.04; P<0.0001); clearly demonstrating that CpG dinucleotides but not GpC dinucleotides are susceptible to the underlying evolutionary pressures.
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pone.0133407.g002: Hantavirus genomes are depleted for CpG dinucleotides and underlying evolutionary pressure is specific to CpG (not GpC) dinucleotides.(a) Among the 3 segments of hantaviruses the CpG dinucleotide O/E ratios for the M segment were significantly lower than that for the S segment (0.22±0.04 vs 0.28±0.06; P<0.0001) and that for the L segment (0.22±0.04 vs 0.29±0.05; P<0.0001). The differences in CpG O/E ratios of the S segment and the L segment were not significant (0.28±0.06 vs 0.29±0.05; P = 0.18). (b) The CpG/GpC O/E ratios were significantly lower for the M segment of hantaviruses as compared to those for the S segment (0.22±0.04 vs 0.29±0.07; P<0.0001) and for the L segment (0.22±0.04 vs 0.28±0.04; P<0.0001); clearly demonstrating that CpG dinucleotides but not GpC dinucleotides are susceptible to the underlying evolutionary pressures.

Mentions: The depletion of CpG dinucleotides was common across all the three segments of hantaviruses (Fig 1A, 1B and 1C). Within the 3 segments of hantaviruses, the CpG dinucleotide O/E ratios for the M segment were significantly lower than that for the S segment (0.22±0.04 vs 0.28±0.06; P<0.0001; Fig 2A) and that for the L segment (0.22±0.04 vs 0.29±0.05; P<0.0001; Fig 2A). The differences in CpG O/E ratios of the S segment and the L segment were not significant (0.28±0.06 vs 0.29±0.05; P = 0.18; Fig 2A). CpG dinucleotide depletion is the most well-studied dinucleotide variation among vertebrate DNA viruses [35], RNA viruses [11] and single-stranded DNA viruses [2]. Nonetheless, this is the first report on CpG depletion among the three hantavirus segments.


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)

Hantavirus genomes are depleted for CpG dinucleotides and underlying evolutionary pressure is specific to CpG (not GpC) dinucleotides.(a) Among the 3 segments of hantaviruses the CpG dinucleotide O/E ratios for the M segment were significantly lower than that for the S segment (0.22±0.04 vs 0.28±0.06; P<0.0001) and that for the L segment (0.22±0.04 vs 0.29±0.05; P<0.0001). The differences in CpG O/E ratios of the S segment and the L segment were not significant (0.28±0.06 vs 0.29±0.05; P = 0.18). (b) The CpG/GpC O/E ratios were significantly lower for the M segment of hantaviruses as compared to those for the S segment (0.22±0.04 vs 0.29±0.07; P<0.0001) and for the L segment (0.22±0.04 vs 0.28±0.04; P<0.0001); clearly demonstrating that CpG dinucleotides but not GpC dinucleotides are susceptible to the underlying evolutionary pressures.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4508033&req=5

pone.0133407.g002: Hantavirus genomes are depleted for CpG dinucleotides and underlying evolutionary pressure is specific to CpG (not GpC) dinucleotides.(a) Among the 3 segments of hantaviruses the CpG dinucleotide O/E ratios for the M segment were significantly lower than that for the S segment (0.22±0.04 vs 0.28±0.06; P<0.0001) and that for the L segment (0.22±0.04 vs 0.29±0.05; P<0.0001). The differences in CpG O/E ratios of the S segment and the L segment were not significant (0.28±0.06 vs 0.29±0.05; P = 0.18). (b) The CpG/GpC O/E ratios were significantly lower for the M segment of hantaviruses as compared to those for the S segment (0.22±0.04 vs 0.29±0.07; P<0.0001) and for the L segment (0.22±0.04 vs 0.28±0.04; P<0.0001); clearly demonstrating that CpG dinucleotides but not GpC dinucleotides are susceptible to the underlying evolutionary pressures.
Mentions: The depletion of CpG dinucleotides was common across all the three segments of hantaviruses (Fig 1A, 1B and 1C). Within the 3 segments of hantaviruses, the CpG dinucleotide O/E ratios for the M segment were significantly lower than that for the S segment (0.22±0.04 vs 0.28±0.06; P<0.0001; Fig 2A) and that for the L segment (0.22±0.04 vs 0.29±0.05; P<0.0001; Fig 2A). The differences in CpG O/E ratios of the S segment and the L segment were not significant (0.28±0.06 vs 0.29±0.05; P = 0.18; Fig 2A). CpG dinucleotide depletion is the most well-studied dinucleotide variation among vertebrate DNA viruses [35], RNA viruses [11] and single-stranded DNA viruses [2]. Nonetheless, this is the first report on CpG depletion among the three hantavirus segments.

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.