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Phylogeny, species delimitation, and biogeographical history of Bredia.
Mol Phylogenet Evol
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School of Ecology, Sun Yat-sen University, Shenzhen 518107, China; State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou 510275, China. Electronic address:
Species delimitation in plants is sometimes challenging due to morphological convergence, interspecific gene flow, and historically limited sampling. Bredia Blume as currently defined comprises 27 species and has been resolved as monophyletic in previous phylogenomic studies. However, relationships among several major lineages in the genus remain elusive, and the species boundaries of some problematic taxa have not been tested.
View Article and Find Full Text PDFGenetic diversity assessment of cucumber landraces using molecular signatures.
BMC Genomics
November 2024
School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, 4072, Australia.
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- Genetic profiling of cucumber landraces is essential for preserving important traits in crop plants and enhancing breeding programs.
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Mitrani Department of Desert Ecology, Ben-Gurion University of the Negev, The Swiss Institute for Dryland Environmental & Energy Research, Midreshet Ben-Gurion, Israel.
A major challenge in analysing single-nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses and misinterpret ecological and evolutionary processes. Here, we present a comprehensive method to estimate and minimise genotyping error rates (deviations from the 'true' genotype) in any SNP datasets using triplicates (three repeats of the same sample) in a four-step filtration pipeline. The approach involves: (1) SNP filtering by missing data; (2) SNP filtering by error rates; (3) sample filtering by missing data and (4) detection of recaptured individuals by using estimated SNP error rates.
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Genome Biol
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State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
Background: Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution.
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Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits.
J Genet Genomics
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State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Techn
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