Convergent evolution through independent rearrangements in the primate amylase locus [Rhesus]
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PROVIDER: PRJNA1304929 | ENA |
REPOSITORIES: ENA
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Project description:Structurally complex regions of the genome are increasingly recognized as engines of evolutionary convergence due to their propensity to generate recurrent gene duplications that give rise to similar gene expression patterns and traits across lineages. However the mutational mechanisms driving these duplications and the regulatory changes enabling novel expression patterns remain poorly understood. The primate amylase locus, marked by independent gene duplications, provides an ideal model to investigate these dynamics. Leveraging high-quality genome assemblies from 53 primates and multi-tissue transcriptomes from Old World monkeys, we reconstructed the evolutionary history of the recurrent gene duplications across the primate phylogeny. Our data suggest that lineage-specific LTR retrotransposon insertions are associated with initial structural instability, while subsequent duplications are primarily driven by non-allelic homologous recombination. Recurrent independent duplications in rhesus macaques, olive baboons, and great apes gave rise to distinct amylase gene copies with convergent expression in the pancreas and salivary glands. We found that these independent gene duplications are accompanied by episodic diversifying selection on lineage-specific copies, likely driving the emergence of functional divergence. Our comparative analyses in primates indicate that the gene ancestral to great ape AMY1 and AMY2A was expressed in both salivary glands and pancreas in the Catarrhini ancestor. The great ape–specific duplication of this ancestral gene likely facilitated subfunctionalization into salivary gland- and pancreas-specific expression, respectively. Comparative analysis of primate amylase promoter regions reveals regulatory rewiring, driven by motif turnover mediated by structural rearrangements, and partially explaining evolutionary shifts in expression. Together, our findings highlight how structural and regulatory modularity in complex genomic regions drives evolutionary innovation and molecular convergence, and we provide a genomic framework for dissecting these processes across diverse lineages.
2025-08-27 | GSE305255 | GEO
Project description:Structurally complex regions of the genome are increasingly recognized as engines of evolutionary convergence due to their propensity to generate recurrent gene duplications that give rise to similar gene expression patterns and traits across lineages. However the mutational mechanisms driving these duplications and the regulatory changes enabling novel expression patterns remain poorly understood. The primate amylase locus, marked by independent gene duplications, provides an ideal model to investigate these dynamics. Leveraging high-quality genome assemblies from 53 primates and multi-tissue transcriptomes from Old World monkeys, we reconstructed the evolutionary history of the recurrent gene duplications across the primate phylogeny. Our data suggest that lineage-specific LTR retrotransposon insertions are associated with initial structural instability, while subsequent duplications are primarily driven by non-allelic homologous recombination. Recurrent independent duplications in rhesus macaques, olive baboons, and great apes gave rise to distinct amylase gene copies with convergent expression in the pancreas and salivary glands. We found that these independent gene duplications are accompanied by episodic diversifying selection on lineage-specific copies, likely driving the emergence of functional divergence. Our comparative analyses in primates indicate that the gene ancestral to great ape AMY1 and AMY2A was expressed in both salivary glands and pancreas in the Catarrhini ancestor. The great ape–specific duplication of this ancestral gene likely facilitated subfunctionalization into salivary gland- and pancreas-specific expression, respectively. Comparative analysis of primate amylase promoter regions reveals regulatory rewiring, driven by motif turnover mediated by structural rearrangements, and partially explaining evolutionary shifts in expression. Together, our findings highlight how structural and regulatory modularity in complex genomic regions drives evolutionary innovation and molecular convergence, and we provide a genomic framework for dissecting these processes across diverse lineages.
2025-08-27 | GSE305241 | GEO
Project description:Convergent evolution through independent rearrangements in the primate amylase locus [Baboon]
| PRJNA1304902 | ENA
Project description:Though the rhesus monkey is one of the most valuable non-human primate animal models for various human diseases because of its manageable size and genetic and proteomic similarities with humans, proteomic research using rhesus monkeys still remains challenging due to the lack of a complete protein sequence database and sufficient proteomic information. In this project, proteomic profiling of multiple organ tissues, 9 male and 11 female were performed in an automated, high-throughput manner employing annotated UniProtKB human database. Based on the success of this alternative interpretation of MS data, the list of proteins identified from total 12 organs of male and female subjects will benefit future rhesus monkey proteome research.
2015-05-19 | PXD001972 | Pride
Project description:Aging of population is a great challenge of healthcare. In china, the number of the elderly is rapidly growing, and it was estimated that there will be approximately 400 million citizens above 65 years old in 2050.Study on the changes of brain during aging may help elucidate the mechanism of the pathological process, and hence prevent or treat these neurological diseases.Rhesus macaque (Macaca mulatta) and human have a genetic homology of 95%, and their anatomy structures or physiological process are highly similar, which make rhesus macaque one of the most important nonhuman primate models.Thus, the comparison between the change of protein profile during aging in human and rhesus macaque is still necessary, and the characteristics of proteins that are conservative or divergent are of interest.The aim of the(our) study is to identify the conservative changes of pathways during aging, and to reveal the potential difference between human and rhesus macaque so that relevant studies based on primate models can be interpreted more accurately.
2020-06-25 | PXD013597 | Pride
Project description:Novel approaches were used to generate the DNA sequence information for the rhesus GeneChip (2005). The purpose of this experiment was to test its reliability and validity of the rhesus macaque GeneChip across different tissues and centers. Keywords: reliability To test the reliability of the rhesus GeneChip across different centers, RNA was isolated from five sources: cerebral cortex, pancreas, thymus, testis, and an immortalized fibroblast cell line. Aliquots of this RNA were sent to each of three centers: Yerkes National Primate Research Center, Oregon National Primate Research Center and the University of Nebraska Medical Center. Each center labeled the samples and hybridized them to two rhesus macaque GeneChips.
2010-06-11 | E-GEOD-7094 | biostudies-arrayexpress
Project description:Rhesus Monkey is one of the important primate models widely used in the fields of disease mechanism study, pre-clinical test in drug discovery and molecular evolution. However, the majority of rhesus gene annotations were putatively mapped from human genome, with only 10% supported by rhesus EST data.So, to better study the transcriptome, paired-end, strand-specific, poly(A)-positive RNA-Seq were performed in 5 rhesus monkey tissues. 5 tissue samples examined: prefrontal cortex, liver, skeletal muscle, adipose, testis
2012-10-10 | E-GEOD-34426 | biostudies-arrayexpress
Project description:Amylase study hifiasm assemblies
| PRJEB78558 | ENA
Project description:Derivation of embryonic stem cells (ESC) genetically identical to a patient by somatic cell nuclear transfer (SCNT) holds the potential to cure or alleviate the symptoms of many degenerative diseases while circumventing any immunorejection issues. However, no primate nuclear transfer embryonic stem (ntES) cell lines have been derived to date. Here, we used a modified SCNT technique to produce rhesus macaque SCNT blastocysts at a relatively high efficiency from adult donor cells and we successfully derived two primate ntES cell lines from 304 oocytes (an overall efficiency of 0.7%). Nuclear and mitochondrial DNA analysis confirmed the ntES cell lines were derived from rhesus monkey SCNT blastocysts and both rhesus monkey ntES cell lines exhibited a normal ESC morphology, expressed key stemness markers, were transcriptionally indistinguishable from control ESC lines and differentiated into multiple cell types. This is, to our knowledge, the first confirmed derivation of primate ntES cell lines. Keywords: rhesus monkey somatic cell nuclear transfer embryonic stem cells
2007-08-29 | GSE7748 | GEO
Project description:Streptococcus gordonii, an important primary colonizer of dental plaque biofilm, specifically binds to salivary amylase via the surface-associated amylase-binding protein A (AbpA). We hypothesized that amylase binding to S. gordonii modulates expression of chromosomal genes, which could influence bacterial survival and persistence in the oral cavity. Gene expression profiling by microarray analysis was performed to detect differentially expressed genes in S. gordonii strain CH1 in response to the binding of purified human salivary amylase as compared to exposure to heat-denatured amylase. Selected genes found to be differentially expressed were validated by qRT-PCR. Five genes from the fatty acid synthesis (FAS) cluster were highly (10-35 fold) up-regulated in amylase treated S. gordonii CH1 cells compared to the denatured-amylase treated cells. An abpA-deficient strain of S. gordonii exposed to amylase did not show a similar response in FAS gene expression as observed in the parental strain. Predicted phenotypic effects of amylase binding to S. gordonii strain CH1 associated with increased expression of FAS genes leading to changes in fatty acid synthesis were noted, as evidenced by increased bacterial growth, survival at low pH, and resistance to triclosan. These changes were not observed in the amylase exposed abpA-deficient strain, suggesting for the role of AbpA in amylase-induced phenotype. These results provide evidence that the binding of salivary amylase elicits a differential gene response in S. gordonii, resulting in a phenotype adjustment that is potentially advantageous for bacterial survival in the oral environment.
2011-09-03 | GSE31830 | GEO