scholarly journals Dynamics of genetic diversity among Indian Sugarcane bacilliform virus species and implications of associated recombination events in the virus

2021 ◽  
Author(s):  
PK Janiga ◽  
K. Nithya ◽  
Rasappa Viswanathan
Keyword(s):  
Protein Sequence ◽  
Low Frequency ◽  
Purifying Selection ◽  
Virus Species ◽  
Efficient Tool ◽  
Over Expression ◽  
Evolutionary Changes ◽  
Sugarcane Bacilliform Virus ◽  
Neutrality Tests ◽  
Virus Isolates

Abstract Sugarcane bacilliform virus (SCBV), a plant pararetrovirus causing leaf fleck disease in sugarcane across the globe. Since the virus occurs throughout the sugarcane growing areas and germplasm in India, we have assessed the genetic divergences among the virus isolates from 104 isolates infecting germplasm and Saccharum hybrid varieties. With the evidence gathered from phylogenetic analysis and sequence demarcation tool, five novel genotypes are being proposed: SCBV-U, SCBV-V, SCBV-W, SCBV-X and SCBV-Y. SCBV-W: CBJ 46, due to the divergence in the nucleotide and protein sequence with existing isolates, established itself as a novel candidate in SCBV species. In comparison with the existing database of SCBV and conclusion from the present study, SCBV isolates from India exhibited maximum diversity in comparison with other regions. SCBV-U, SCBV-W, SCBV-X which turned out as potent recombinants along with other six recombinants in the study, directs at the plausible heterogeneity and genetic exchange happened within SCBV species over time which lead to the evolution of new variants. Neutrality tests indicate the existence of low-frequency polymorphism and Selection pressure of < 1 pointed out at purifying selection. Codon usage bias acted as an efficient tool for identifying patterns in SCBV, in which non-randomness in mutational events might lead to the over expression of codon AGA. The current study on characterization and evidence of nucleotidal variation within SCBV species will lead to devising robust diagnostics of the virus in quarantine and improving the knowledge on the evolutionary changes in SCBV species.

scholarly journals Dynamics of Genetic Diversity Among Indian Sugarcane Bacilliform Virus Species and Implications of Associated Recombination Events in the Virus

2021 ◽  
Author(s):  
PK Janiga ◽  
K. Nithya ◽  
Rasappa Viswanathan
Keyword(s):  
Protein Sequence ◽  
Low Frequency ◽  
Purifying Selection ◽  
Virus Species ◽  
Efficient Tool ◽  
Over Expression ◽  
Evolutionary Changes ◽  
Sugarcane Bacilliform Virus ◽  
Neutrality Tests ◽  
Virus Isolates

Abstract Sugarcane bacilliform virus (SCBV), a plant pararetrovirus causing leaf fleck disease in sugarcane across the globe. Since the virus occurs throughout the sugarcane growing areas and germplasm in India, we have assessed the genetic divergences among the virus isolates from 104 isolates infecting germplasm and Saccharum hybrid varieties. With the evidence gathered from phylogenetic analysis and sequence demarcation tool, five novel genotypes are being proposed: SCBV-U, SCBV-V, SCBV-W, SCBV-X and SCBV-Y. SCBV-W: CBJ 46, due to the divergence in the nucleotide and protein sequence with existing isolates, established itself as a novel candidate in SCBV species. In comparison with the existing database of SCBV and conclusion from the present study, SCBV isolates from India exhibited maximum diversity in comparison with other regions. SCBV-U, SCBV-W, SCBV-X which turned out as potent recombinants along with other six recombinants in the study, directs at the plausible heterogeneity and genetic exchange happened within SCBV species over time which lead to the evolution of new variants. Neutrality tests indicate the existence of low-frequency polymorphism and Selection pressure of < 1 pointed out at purifying selection. Codon usage bias acted as an efficient tool for identifying patterns in SCBV, in which non-randomness in mutational events might lead to the over expression of codon AGA. The current study on characterization and evidence of nucleotidal variation within SCBV species will lead to devising robust diagnostics of the virus in quarantine and improving the knowledge on the evolutionary changes in SCBV species.

scholarly journals Diversity of and Selection Acting on CylindrospermopsincyrBGene Adenylation Domain Sequences in Florida

2011 ◽  
Vol 77 (7) ◽  
pp. 2502-2507 ◽  
Author(s):  
Mete Yilmaz ◽  
Edward J. Phlips
Keyword(s):  
United States ◽  
Low Frequency ◽  
Purifying Selection ◽  
The United States ◽  
The Other ◽  
Cylindrospermopsis Raciborskii ◽  
Adenylation Domain ◽  
Other Hand ◽  
Neutrality Tests ◽  
The One

ABSTRACTAphanizomenon ovalisporumis the only confirmed cylindrospermopsin producer identified in the United States to date. On the other hand,Cylindrospermopsis raciborskiiis a prominent feature of many lakes in Florida and other regions of the United States. To see the variation in cylindrospermopsincyrBgene adenylation domain sequences and possibly discover new cylindrospermopsin producers, we collected water samples for a 3-year period from 17 different systems in Florida. Positive amplicons were cloned and sequenced, revealing that approximately 92% of sequences wereA. ovalisporum-like (>99% identity). Interestingly, 6% of sequences were very similar (>99% identity) tocyrBsequences ofC. raciborskiifrom Australia and ofAphanizomenonsp. from Germany. Neutrality tests suggest thatA. ovalisporum-likecyrBadenylation domain sequences are under purifying selection, with abundant low-frequency polymorphisms within the population. On the other hand, when compared between species by codon-based methods, amino acids of CyrB also seem to be under purifying selection, in accordance with the one proposed amino acid thought to be activated by the CyrB adenylation domain.

scholarly journals High Polymorphism at the Human Melanocortin 1 Receptor Locus

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1547-1557 ◽  
Author(s):  
Brinda K Rana ◽  
David Hewett-Emmett ◽  
Li Jin ◽  
Benny H-J Chang ◽  
Naymkhishing Sambuughin ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Nucleotide Diversity ◽  
Coat Color ◽  
Low Frequency ◽  
Melanocortin Receptor ◽  
Human Populations ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene ◽  
Southeast Asians ◽  
Color Changes

Abstract Variation in human skin/hair pigmentation is due to varied amounts of eumelanin (brown/black melanins) and phaeomelanin (red/yellow melanins) produced by the melanocytes. The melanocortin 1 receptor (MC1R) is a regulator of eu- and phaeomelanin production in the melanocytes, and MC1R mutations causing coat color changes are known in many mammals. We have sequenced the MC1R gene in 121 individuals sampled from world populations with an emphasis on Asian populations. We found variation at five nonsynonymous sites (resulting in the variants Arg67Gln, Asp84Glu, Val92Met, Arg151Cys, and Arg163Gln), but at only one synonymous site (A942G). Interestingly, the human consensus protein sequence is observed in all 25 African individuals studied, but at lower frequencies in the other populations examined, especially in East and Southeast Asians. The Arg163Gln variant is absent in the Africans studied, almost absent in Europeans, and at a low frequency (7%) in Indians, but is at an exceptionally high frequency (70%) in East and Southeast Asians. The MC1R gene in common and pygmy chimpanzees, gorilla, orangutan, and baboon was sequenced to study the evolution of MC1R. The ancestral human MC1R sequence is identical to the human consensus protein sequence, while MC1R varies considerably among higher primates. A comparison of the rates of substitution in genes in the melanocortin receptor family indicates that MC1R has evolved the fastest. In addition, the nucleotide diversity at the MC1R locus is shown to be several times higher than the average nucleotide diversity in human populations, possibly due to diversifying selection.

Calreticulin molecular evolution: a strong purifying and episodic diversifying selection result

Biologia ◽  
2014 ◽  
Vol 69 (3) ◽  
Author(s):  
Rigers Bakiu
Keyword(s):  
Molecular Evolution ◽  
Higher Plants ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Amino Acid Sequences ◽  
Over Expression ◽  
Diversifying Selection ◽  
Pathological Conditions ◽  
Weight Protein ◽  
Low Molecular Weight Protein

AbstractCalreticulin (CRT) is a low molecular weight protein present in vertebrates, invertebrates and higher plants. Its multiple functions have been demonstrated. It plays an important role as a chaperone and Ca2+ buffer inside sarcoplasmic/endoplasmic reticulum (SR/ER), and outside the ER in many physiological/pathological processes. Recently it has been observed that CRT over-expression or its absence is linked to various pathological conditions, such as malignant evolution and progression, and these facts really increased its study interests. Using an evolution approach CRT was further characterized. Several Bayesian phylogenetic analyses were performed using coding and amino acid sequences. CRT molecular evolution was investigated for the presence of negative or/and positive selection using HyPhy package. The results indicated that the purifying selection might have operated over the whole CRT primary structure. Although, an episodic diversifying selection was also found on the analyzed CRT sequences.

scholarly journals Inter- and Intraspecific Variation in Drosophila Genes with Sex-Biased Expression

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Lena Müller ◽  
Sonja Grath ◽  
Korbinian von Heckel ◽  
John Parsch
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Protein Sequence ◽  
Sequence Variation ◽  
Purifying Selection ◽  
Sexually Dimorphic ◽  
Expression Divergence ◽  
Sexually Dimorphic Expression ◽  
Dimorphic Expression

Genes with sexually dimorphic expression (sex-biased genes) often evolve rapidly and are thought to make an important contribution to reproductive isolation between species. We examined the molecular evolution of sex-biased genes in Drosophila melanogaster and D. ananassae, which represent two independent lineages within the melanogaster group. We find that strong purifying selection limits protein sequence variation within species, but that a considerable fraction of divergence between species can be attributed to positive selection. In D. melanogaster, the proportion of adaptive substitutions between species is greatest for male-biased genes and is especially high for those on the X chromosome. In contrast, male-biased genes do not show unusually high variation within or between populations. A similar pattern is seen at the level of gene expression, where sex-biased genes show high expression divergence between species, but low divergence between populations. In D. ananassae, there is no increased rate of adaptation of male-biased genes, suggesting that the type or strength of selection acting on sex-biased genes differs between lineages.

Mistranslation in IGF-1 during over-expression of the protein in Escherichia coli using a synthetic gene containing low frequency codons

1988 ◽  
Vol 155 (1) ◽  
pp. 518-523 ◽  
Author(s):  
Ramnath Seetharam ◽  
Robert A. Heeren ◽  
Edith Y. Wong ◽  
Sarah R. Braford ◽  
Barbara K. Klein ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Low Frequency ◽  
Synthetic Gene ◽  
Over Expression

Genetic diversity of Sugarcane bacilliform virus isolates infecting Saccharum spp. in India

Virus Genes ◽  
2013 ◽  
Vol 46 (3) ◽  
pp. 505-516 ◽  
Author(s):  
R. Karuppaiah ◽  
R. Viswanathan ◽  
V. Ganesh Kumar
Keyword(s):  
Genetic Diversity ◽  
Saccharum Spp ◽  
Sugarcane Bacilliform Virus ◽  
Virus Isolates

scholarly journals Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

2017 ◽  
Author(s):  
Nandita R. Garud ◽  
Benjamin H. Good ◽  
Oskar Hallatschek ◽  
Katherine S. Pollard
Keyword(s):  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Gut Bacteria ◽  
Fundamental Limits ◽  
Evolutionary Forces ◽  
Standard Population ◽  
Evolutionary Changes ◽  
Or Gene ◽  
Adult Twins ◽  
Long Timescales

AbstractGut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in ∼30 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over ∼6 month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps are seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.

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