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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.


Relative abundance of dinucleotides in hantavirus genomes.(a) The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses S segment is 1.0±0.25. The O/E ratios for most of the dinucleotides lie inside the confidence interval of 0.75–1.25 with the exceptions of CpG and GpU dinucleotides (underrepresented) and CpA dinucleotides (overrepresented). (b) The mean±standard deviation of dinucleotide O/E ratios for hantaviruses M segment is 1.0±0.25. CpG dinucleotides were underrepresented and CpA and UpG dinucleotides were overrepresented as the O/E ratios for these dinucleotides were located outside the confidence interval of 0.75–1.25. (c) The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses L segment is 1.0±0.22. CpG and CpA dinucleotides were the most deviant dinucleotides as their O/E ratios were located outside the confidence interval of 0.78–1.22. (d) Comparison of the average dinucleotide O/E ratios for all three segments of hantaviruses. The depletion of CpG dinucleotides was common across all the three segments of hantaviruses.
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pone.0133407.g001: Relative abundance of dinucleotides in hantavirus genomes.(a) The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses S segment is 1.0±0.25. The O/E ratios for most of the dinucleotides lie inside the confidence interval of 0.75–1.25 with the exceptions of CpG and GpU dinucleotides (underrepresented) and CpA dinucleotides (overrepresented). (b) The mean±standard deviation of dinucleotide O/E ratios for hantaviruses M segment is 1.0±0.25. CpG dinucleotides were underrepresented and CpA and UpG dinucleotides were overrepresented as the O/E ratios for these dinucleotides were located outside the confidence interval of 0.75–1.25. (c) The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses L segment is 1.0±0.22. CpG and CpA dinucleotides were the most deviant dinucleotides as their O/E ratios were located outside the confidence interval of 0.78–1.22. (d) Comparison of the average dinucleotide O/E ratios for all three segments of hantaviruses. The depletion of CpG dinucleotides was common across all the three segments of hantaviruses.

Mentions: We analyzed the frequencies of all 16 dinucleotides for 51 S segments, 43 M segments and 24 L segments of hantaviruses. The relative abundance of dinucleotides in the three segments (S, M, L) of hantaviruses is shown in Fig 1. The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses S-, M- and L-segments are 1.0±0.25, 1.0±0.25, 1.0±0.22 respectively (Fig 1A, 1B and 1C). CpG dinucleotides were found to be the most depleted dinucleotides in all the three segments of hantaviruses as compared to any other dinucleotide (Fig 1D; P<0.0001). CpA and UpG over-representation and UpA depletion were seen in all three segments. CpA and UpG over-representation has been observed to occur concomitantly with CpG depletion in both DNA [2] and RNA virus genomes [11]. UpA depletion is a universal feature of animal [32] and microbial genomes [33]. Universal UpA depletion has been linked to increased sensitivity of the UpA dinucleotides to ribonucleases [34]. In addition we also found significant GpU depletion in 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)

Relative abundance of dinucleotides in hantavirus genomes.(a) The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses S segment is 1.0±0.25. The O/E ratios for most of the dinucleotides lie inside the confidence interval of 0.75–1.25 with the exceptions of CpG and GpU dinucleotides (underrepresented) and CpA dinucleotides (overrepresented). (b) The mean±standard deviation of dinucleotide O/E ratios for hantaviruses M segment is 1.0±0.25. CpG dinucleotides were underrepresented and CpA and UpG dinucleotides were overrepresented as the O/E ratios for these dinucleotides were located outside the confidence interval of 0.75–1.25. (c) The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses L segment is 1.0±0.22. CpG and CpA dinucleotides were the most deviant dinucleotides as their O/E ratios were located outside the confidence interval of 0.78–1.22. (d) Comparison of the average dinucleotide O/E ratios for all three segments of hantaviruses. The depletion of CpG dinucleotides was common across all the three segments of hantaviruses.
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Related In: Results  -  Collection

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pone.0133407.g001: Relative abundance of dinucleotides in hantavirus genomes.(a) The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses S segment is 1.0±0.25. The O/E ratios for most of the dinucleotides lie inside the confidence interval of 0.75–1.25 with the exceptions of CpG and GpU dinucleotides (underrepresented) and CpA dinucleotides (overrepresented). (b) The mean±standard deviation of dinucleotide O/E ratios for hantaviruses M segment is 1.0±0.25. CpG dinucleotides were underrepresented and CpA and UpG dinucleotides were overrepresented as the O/E ratios for these dinucleotides were located outside the confidence interval of 0.75–1.25. (c) The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses L segment is 1.0±0.22. CpG and CpA dinucleotides were the most deviant dinucleotides as their O/E ratios were located outside the confidence interval of 0.78–1.22. (d) Comparison of the average dinucleotide O/E ratios for all three segments of hantaviruses. The depletion of CpG dinucleotides was common across all the three segments of hantaviruses.
Mentions: We analyzed the frequencies of all 16 dinucleotides for 51 S segments, 43 M segments and 24 L segments of hantaviruses. The relative abundance of dinucleotides in the three segments (S, M, L) of hantaviruses is shown in Fig 1. The mean ±standard deviation of dinucleotide O/E ratios for hantaviruses S-, M- and L-segments are 1.0±0.25, 1.0±0.25, 1.0±0.22 respectively (Fig 1A, 1B and 1C). CpG dinucleotides were found to be the most depleted dinucleotides in all the three segments of hantaviruses as compared to any other dinucleotide (Fig 1D; P<0.0001). CpA and UpG over-representation and UpA depletion were seen in all three segments. CpA and UpG over-representation has been observed to occur concomitantly with CpG depletion in both DNA [2] and RNA virus genomes [11]. UpA depletion is a universal feature of animal [32] and microbial genomes [33]. Universal UpA depletion has been linked to increased sensitivity of the UpA dinucleotides to ribonucleases [34]. In addition we also found significant GpU depletion in 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.