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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.

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Related in: MedlinePlus

Synteny maps between Chinese and Indian rhesus macaque reference sequences.The large-scale concordance serves to verify that the RSD algorithm is functioning to accurately map orthologous sequences. Each colored line maps an amino acid sequence in the Indian rhesus macaque draft sequence (top) to its corresponding ortholog on the Chinese rhesus macaque draft sequence (bottom). Diagonal lines illustrate transpositions; thin diagonal lines are indicative of single amino acid transposition, and thicker diagonal lines are indicative of block transpositions. The differing colors on each chromosome serve to illustrate the blocks in which synteny is fully conserved. Most chromosomes show almost fully conserved synteny, but chromosomes 15 and 16 show fairly large-scale rearrangement.
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pone.0123624.g001: Synteny maps between Chinese and Indian rhesus macaque reference sequences.The large-scale concordance serves to verify that the RSD algorithm is functioning to accurately map orthologous sequences. Each colored line maps an amino acid sequence in the Indian rhesus macaque draft sequence (top) to its corresponding ortholog on the Chinese rhesus macaque draft sequence (bottom). Diagonal lines illustrate transpositions; thin diagonal lines are indicative of single amino acid transposition, and thicker diagonal lines are indicative of block transpositions. The differing colors on each chromosome serve to illustrate the blocks in which synteny is fully conserved. Most chromosomes show almost fully conserved synteny, but chromosomes 15 and 16 show fairly large-scale rearrangement.

Mentions: Fig 1 plots the synteny maps implied by the ortholog classification of the RSD algorithm, dropping a small number of amino acid sequences that the RSD algorithm believes to have undergone inter-chromosomal transposition. These maps show that the vast majority of orthologous pairs are contained in expansive blocks of synteny. We observe only a small number of apparent intra-chromosomal transpositions per chromosome, the majority of which are inversions of neighboring amino acid sequences. On chromosomes 15, 16, and 19 we observed small intra-chromosomal block transpositions.


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)

Synteny maps between Chinese and Indian rhesus macaque reference sequences.The large-scale concordance serves to verify that the RSD algorithm is functioning to accurately map orthologous sequences. Each colored line maps an amino acid sequence in the Indian rhesus macaque draft sequence (top) to its corresponding ortholog on the Chinese rhesus macaque draft sequence (bottom). Diagonal lines illustrate transpositions; thin diagonal lines are indicative of single amino acid transposition, and thicker diagonal lines are indicative of block transpositions. The differing colors on each chromosome serve to illustrate the blocks in which synteny is fully conserved. Most chromosomes show almost fully conserved synteny, but chromosomes 15 and 16 show fairly large-scale rearrangement.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123624.g001: Synteny maps between Chinese and Indian rhesus macaque reference sequences.The large-scale concordance serves to verify that the RSD algorithm is functioning to accurately map orthologous sequences. Each colored line maps an amino acid sequence in the Indian rhesus macaque draft sequence (top) to its corresponding ortholog on the Chinese rhesus macaque draft sequence (bottom). Diagonal lines illustrate transpositions; thin diagonal lines are indicative of single amino acid transposition, and thicker diagonal lines are indicative of block transpositions. The differing colors on each chromosome serve to illustrate the blocks in which synteny is fully conserved. Most chromosomes show almost fully conserved synteny, but chromosomes 15 and 16 show fairly large-scale rearrangement.
Mentions: Fig 1 plots the synteny maps implied by the ortholog classification of the RSD algorithm, dropping a small number of amino acid sequences that the RSD algorithm believes to have undergone inter-chromosomal transposition. These maps show that the vast majority of orthologous pairs are contained in expansive blocks of synteny. We observe only a small number of apparent intra-chromosomal transpositions per chromosome, the majority of which are inversions of neighboring amino acid sequences. On chromosomes 15, 16, and 19 we observed small intra-chromosomal block transpositions.

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