Limits...
Evolutionary distance of amino acid sequence orthologs across macaque subspecies: identifying candidate genes for SIV resistance in Chinese rhesus macaques.

Ross CT, Roodgar M, Smith DG - PLoS ONE (2015)

Bottom Line: Four of the strongest candidate genes for SIVmac resistance in Chinese rhesus macaques identified in this study are CDK9, CXCL12, TRIM21, and TRIM32.Additionally, ANKRD30A, CTSZ, GORASP2, GTF2H1, IL13RA1, MUC16, NMDAR1, Notch1, NT5M, PDCD5, RAD50, and TM9SF2 were identified as possible candidates, among others.We failed to find many laboratory experiments contrasting the effects of Indian and Chinese orthologs at these sites on SIVmac pathogenesis, but future comparative studies might hold fertile ground for research into the biological mechanisms underlying innate resistance to SIVmac in Chinese rhesus macaques.

View Article: PubMed Central - PubMed

Affiliation: Department of Anthropology, University of California, Davis. Davis, United States of America; Molecular Anthropology Laboratory, University of California, Davis. Davis, United States of America.

ABSTRACT
We use the Reciprocal Smallest Distance (RSD) algorithm to identify amino acid sequence orthologs in the Chinese and Indian rhesus macaque draft sequences and estimate the evolutionary distance between such orthologs. We then use GOanna to map gene function annotations and human gene identifiers to the rhesus macaque amino acid sequences. We conclude methodologically by cross-tabulating a list of amino acid orthologs with large divergence scores with a list of genes known to be involved in SIV or HIV pathogenesis. We find that many of the amino acid sequences with large evolutionary divergence scores, as calculated by the RSD algorithm, have been shown to be related to HIV pathogenesis in previous laboratory studies. Four of the strongest candidate genes for SIVmac resistance in Chinese rhesus macaques identified in this study are CDK9, CXCL12, TRIM21, and TRIM32. Additionally, ANKRD30A, CTSZ, GORASP2, GTF2H1, IL13RA1, MUC16, NMDAR1, Notch1, NT5M, PDCD5, RAD50, and TM9SF2 were identified as possible candidates, among others. We failed to find many laboratory experiments contrasting the effects of Indian and Chinese orthologs at these sites on SIVmac pathogenesis, but future comparative studies might hold fertile ground for research into the biological mechanisms underlying innate resistance to SIVmac in Chinese rhesus macaques.

Show MeSH

Related in: MedlinePlus

The 90% posterior credibility intervals of the chromosomal random effects from the Bernoulli sub-model of the zero-inflated gamma regression.The value ‘Mu’ is the partially-pooled mean estimate across chromosomes. We see that there are no significant differences in the mean probabilty of non-zero divergence in amino acid sequences across chromosomes.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4401517&req=5

pone.0123624.g009: The 90% posterior credibility intervals of the chromosomal random effects from the Bernoulli sub-model of the zero-inflated gamma regression.The value ‘Mu’ is the partially-pooled mean estimate across chromosomes. We see that there are no significant differences in the mean probabilty of non-zero divergence in amino acid sequences across chromosomes.

Mentions: We did observe significant heterogeneity in mean evolutionary distance across chromosomes, with some (e.g. 5, 6, and 17) showing reduced amino acid sequence divergence and others (e.g. 8, 13, 19, and 20) showing increased evolutionary divergence. These results are plotted in Figs 9 and 10.


Evolutionary distance of amino acid sequence orthologs across macaque subspecies: identifying candidate genes for SIV resistance in Chinese rhesus macaques.

Ross CT, Roodgar M, Smith DG - PLoS ONE (2015)

The 90% posterior credibility intervals of the chromosomal random effects from the Bernoulli sub-model of the zero-inflated gamma regression.The value ‘Mu’ is the partially-pooled mean estimate across chromosomes. We see that there are no significant differences in the mean probabilty of non-zero divergence in amino acid sequences across chromosomes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401517&req=5

pone.0123624.g009: The 90% posterior credibility intervals of the chromosomal random effects from the Bernoulli sub-model of the zero-inflated gamma regression.The value ‘Mu’ is the partially-pooled mean estimate across chromosomes. We see that there are no significant differences in the mean probabilty of non-zero divergence in amino acid sequences across chromosomes.
Mentions: We did observe significant heterogeneity in mean evolutionary distance across chromosomes, with some (e.g. 5, 6, and 17) showing reduced amino acid sequence divergence and others (e.g. 8, 13, 19, and 20) showing increased evolutionary divergence. These results are plotted in Figs 9 and 10.

Bottom Line: Four of the strongest candidate genes for SIVmac resistance in Chinese rhesus macaques identified in this study are CDK9, CXCL12, TRIM21, and TRIM32.Additionally, ANKRD30A, CTSZ, GORASP2, GTF2H1, IL13RA1, MUC16, NMDAR1, Notch1, NT5M, PDCD5, RAD50, and TM9SF2 were identified as possible candidates, among others.We failed to find many laboratory experiments contrasting the effects of Indian and Chinese orthologs at these sites on SIVmac pathogenesis, but future comparative studies might hold fertile ground for research into the biological mechanisms underlying innate resistance to SIVmac in Chinese rhesus macaques.

View Article: PubMed Central - PubMed

Affiliation: Department of Anthropology, University of California, Davis. Davis, United States of America; Molecular Anthropology Laboratory, University of California, Davis. Davis, United States of America.

ABSTRACT
We use the Reciprocal Smallest Distance (RSD) algorithm to identify amino acid sequence orthologs in the Chinese and Indian rhesus macaque draft sequences and estimate the evolutionary distance between such orthologs. We then use GOanna to map gene function annotations and human gene identifiers to the rhesus macaque amino acid sequences. We conclude methodologically by cross-tabulating a list of amino acid orthologs with large divergence scores with a list of genes known to be involved in SIV or HIV pathogenesis. We find that many of the amino acid sequences with large evolutionary divergence scores, as calculated by the RSD algorithm, have been shown to be related to HIV pathogenesis in previous laboratory studies. Four of the strongest candidate genes for SIVmac resistance in Chinese rhesus macaques identified in this study are CDK9, CXCL12, TRIM21, and TRIM32. Additionally, ANKRD30A, CTSZ, GORASP2, GTF2H1, IL13RA1, MUC16, NMDAR1, Notch1, NT5M, PDCD5, RAD50, and TM9SF2 were identified as possible candidates, among others. We failed to find many laboratory experiments contrasting the effects of Indian and Chinese orthologs at these sites on SIVmac pathogenesis, but future comparative studies might hold fertile ground for research into the biological mechanisms underlying innate resistance to SIVmac in Chinese rhesus macaques.

Show MeSH
Related in: MedlinePlus