We tested the opposing views concerning evolution of genes of the innate immune system that (i) being evolutionary ancient, the system may have been highly optimized by natural selection and therefore should be under purifying selection, and (ii) the system may be plastic and continuing to evolve under balancing selection. We have resequenced 12 important innate-immunity genes (CAMP, DEFA4, DEFA5, DEFA6, DEFB1, MBL2, and TLRs 1, 2, 4, 5, 6, and 9) in healthy volunteers (n = 171) recruited from a region of India with high microbial load. We have compared these data with those of European-Americans (EUR) and African-Americans (AFR). We have found that most of the human haplotypes are many mutational steps away from the ancestral (chimpanzee) haplotypes, indicating that humans may have had to adapt to new pathogens. The haplotype structures in India are significantly different from those of EUR and AFR populations, indicating local adaptation to pathogens. In these genes, there is (i) generally an excess of rare variants, (ii) high, but variable, degrees of extended haplotype homozygosity, (iii) low tolerance to nonsynonymous changes, (iv) essentially one or a few high-frequency haplotypes, with star-like phylogenies of other infrequent haplotypes radiating from the modal haplotypes. Purifying selection is the most parsimonious explanation operating on these innate immunity genes. This genetic surveillance system recognizes motifs in pathogens that are perhaps conserved across a broad range of pathogens. Hence, functional constraints are imposed on mutations that diminish the ablility of these proteins to detect pathogens.
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http://dx.doi.org/10.1073/pnas.0811357106 | DOI Listing |
Front Plant Sci
December 2024
College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou, China.
Roses () are among the most cherished ornamental plants globally, yet they are highly susceptible to infections by , the causative agent of gray mold disease. Here we inoculated the resistant rose variety 'Yellow Leisure Liness' with to investigate its resistance mechanisms against gray mold disease. Through transcriptome sequencing, we identified 578 differentially expressed genes (DEGs) that were significantly upregulated at 24, 48, and 72 hours post-inoculation, with these genes significantly enriched for three defense response-related GO terms.
View Article and Find Full Text PDFMol Phylogenet Evol
December 2024
Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
In plants, cellular function is orchestrated by three distinct genomes located within the nucleus, mitochondrion, and plastid. These genomes are interdependent, requiring tightly coordinated maintenance and expression. Plastids host several multisubunit protein complexes encoded by both the plastid and nuclear genomes.
View Article and Find Full Text PDFSci Rep
December 2024
Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
The development of management strategies for the promotion of sustainable fisheries relies on a deep knowledge of ecological and evolutionary processes driving the diversification and genetic variation of marine organisms. Sustainability strategies are especially relevant for marine species such as the European sardine (Sardina pilchardus), a small pelagic fish with high ecological and socioeconomic importance, especially in Southern Europe, whose stock has declined since 2006, possibly due to environmental factors. Here, we generated sequences for 139 mitochondrial genomes from individuals from 19 different geographical locations across most of the species distribution range, which was used to assess genetic diversity, diversification history and genomic signatures of selection.
View Article and Find Full Text PDFBMC Plant Biol
December 2024
College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China.
Late Embryogenesis Abundant (LEA) proteins are extensively distributed among higher plants and are crucial for regulating growth, development, and abiotic stress resistance. However, comprehensive data regarding the LEA gene family in Ipomoea species remains limited. In this study, we conducted a genome-wide comparative analysis across seven Ipomoea species, including sweet potato (I.
View Article and Find Full Text PDFFront Cell Dev Biol
December 2024
Proteomics, Lipidomics and Metabolomics Core Facility, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia.
Introduction: The identification of effective, selective biomarkers and therapeutics is dependent on truly deep, comprehensive analysis of proteomes at the proteoform level.
Methods: Bovine serum albumin (BSA) isolated by two different protocols, cold ethanol fractionation and heat shock fractionation, was resolved and identified using Integrative Top-down Proteomics, the tight coupling of two-dimensional gel electrophoresis (2DE) with liquid chromatography and tandem mass spectrometry (LC-MS/MS).
Results And Discussion: Numerous proteoforms were identified in both "purified" samples, across a broad range of isoelectric points and molecular weights.
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