The process of non-allelic gene conversion acts on homologous sequences during recombination, replacing parts of one with the other to make them uniform. Such concerted evolution is best described as paralogous ribosomal RNA gene unification that serves to preserve the essential house-keeping functions of the converted genes. Transposed elements (TE), especially short interspersed elements (SINE) that have more than a million copies in primate genomes, are a significant source of homologous units and a verified target of gene conversion. The consequences of such a recombination-based process are diverse, including multiplications of functional TE internal binding domains and, for evolutionists, confusing divergent annotations of orthologous transposable elements in related species. We systematically extracted and compared 68,097 insertions in various primates looking for potential events of TE gene conversion and discovered 98 clear cases of - gene conversion, including 64 cases for which the direction of conversion was identified (e.g., S conversion to Y). Gene conversion also does not necessarily affect the entire homologous sequence, and we detected 69 cases of partial gene conversion that resulted in virtual hybrids of two elements. Phylogenetic screening of gene-converted s revealed three clear hotspots of the process in the ancestors of Catarrhini, Hominoidea, and gibbons. In general, our systematic screening of orthologous primate loci for gene-converted TEs provides a new strategy and view of a post-integrative process that changes the identities of such elements.
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http://dx.doi.org/10.3390/genes12060905 | DOI Listing |
Am J Hum Genet
January 2025
UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA. Electronic address:
More than 50% of families with suspected rare monogenic diseases remain unsolved after whole-genome analysis by short-read sequencing (SRS). Long-read sequencing (LRS) could help bridge this diagnostic gap by capturing variants inaccessible to SRS, facilitating long-range mapping and phasing and providing haplotype-resolved methylation profiling. To evaluate LRS's additional diagnostic yield, we sequenced a rare-disease cohort of 98 samples from 41 families, using nanopore sequencing, achieving per sample ∼36× average coverage and 32-kb read N50 from a single flow cell.
View Article and Find Full Text PDFPlants (Basel)
January 2025
State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 311400, China.
Rice ( L.) is a staple crop for nearly half of the global population and one of China's most extensively cultivated cereals. Heading date, a critical agronomic trait, determines the regional and seasonal adaptability of rice varieties.
View Article and Find Full Text PDFPlants (Basel)
January 2025
Xinjiang Key Laboratory of Clean Conversion and High Value Utilization of Biomass Resources, Yili Normal University, Yining 835000, China.
The pervasive presence of microplastics (MPs) in agroecosystems poses a significant threat to soil health and plant growth. This study investigates the effects of varying concentrations and sizes of polystyrene microplastics (PS-MPs) on the L.'s height, dry weight, antioxidant enzyme activities, soil physicochemical properties, and rhizosphere microbial communities.
View Article and Find Full Text PDFNutrients
January 2025
Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, 4600 Wels, Austria.
Individuals with special metabolic demands are at risk of deficiencies in fat-soluble vitamins, which can be counteracted via supplementation. Here, we tested the ability of micellization alone or in combination with selected natural plant extracts to increase the intestinal absorption and bioefficacy of fat-soluble vitamins. Micellated and nonmicellated vitamins D3 (cholecalciferol), D2 (ergocalciferol), E (alpha tocopheryl acetate), and K2 (menaquionone-7) were tested in intestinal Caco-2 or buccal TR146 cells in combination with curcuma (), black pepper (), or ginger () plant extracts.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China.
Late-maturing hybrid citrus is a significant fruit that combines the best traits of both parents and is highly prized for its unique flavor. Not only can organic acids alter the flavor of citrus pulp, but they are also essential for cellular metabolism, energy conversion, and maintaining the acidbase balance in plant tissues. Although organic acids play a key role in the quality formation of citrus fruits, there is still insufficient research on the metabolic processes of organic acids in late-maturing hybrid citrus varieties.
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