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370 results for “Diploidization”
Data from: Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia
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Data from: Insights into the genetic basis of blueberry fruit-related traits using diploid and polyploid models in a GWAS context
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Data from: Evolution and phylogeography analysis of diploid and polyploid Misgurnus anguillicaudatus populations across China
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Data from: Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe
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Data from: Invasion success in polyploids: the role of inbreeding in the contrasting colonization abilities of diploid versus tetraploid populations of Centaurea stoebe s.l
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Uptake of nitrogen forms by diploid and triploid white poplar depends on seasonal carbon use strategy and elevated summer ozone
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Data from: The effects of quantitative fecundity in the haploid stage on reproductive success and diploid fitness in the aquatic peat moss Sphagnum macrophyllum
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Data from: Diploid males support a two-step mechanism of endosymbiont-induced thelytoky in a parasitoid wasp
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Data from: Adaptation of diploid and tetraploid Chamerion angustifolium to elevation but not local environment
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Fig. 1 in First chromosomal analysis of Gymnorhamphichthys britskii: the remarkable lowest diploid value within the family Rhamphichthyidae (Gymnotiformes)
Fig. 1. Location of Dourado stream in the upper Paraná River basin where Gymnorhamphichthys britskii individuals were captured. The dark circle indicates the sampling spots.
Fig. 2 in First chromosomal analysis of Gymnorhamphichthys britskii: the remarkable lowest diploid value within the family Rhamphichthyidae (Gymnotiformes)
Fig. 2. Gymnorhamphichthys britskii sampled in the Dourado stream, Mato Grosso do Sul State, Brazil.
Haplotype-resolved genome analyses of a heterozygous diploid potato
<p>Potato (<i>Solanum tuberosum</i> L.) is the most important tuber crop worldwide. An effort is underway to transform the crop from a clonally propagated tetraploid into a diploid seed-propagated, inbred line-based hybrid, which requires a better understanding of its highly heterozygous genome of potato. Here, we report the 1.67 Gb haplotype-resolved assembly of a diploid potato, RH89-039-16, using the combination of multiple sequencing and mapping strategies, including circular consensus sequencing. Comparison of the two haplotypes revealed ~2.1% intra-genome diversity, including 22,134 predicted deleterious mutations in 10,642 annotated genes. In a total of 20,583 pairs of allelic genes, 16.6% and 30.8% exhibited differential expression and methylation between alleles, respectively. Deleterious mutations and differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies to eradicate deleterious alleles or stacking of beneficial alleles, via meiotic recombination. Further cataloguing of functional haplotypes, in diploid potato, could enable exploitation of heterosis using genotypes with complementary haplotypes. This study offers a holistic view of the genome organization of a clonally propagated diploid species, as well as provides insights into technological evolution in resolving complex genomes.</p>
Diploid VCF files used for publication "Haplotype Threading: Accurate Polyploid Phasing from Long Reads"
<p>Diploid VCF files for three human samples, from which polyploid datasets were generated as evaluation data for the publication given in the title. Files contain gold standard haplotypes, which have been conducted by trio phasing from the samples themselves and their respective parents.</p>
Data from: Queen execution, diploid males, and selection for and against polyandry in the Brazilian stingless bee Scaptotrigona depilis
Female mating frequency varies. Determining the causes of this variation is an active research area. We tested the hypothesis that in stingless bees, Meliponini, single mating is due to the execution of queens that make a matched mating at the CSD (complementary sex determination) locus and have diploid male offspring. We studied the Brazilian species Scaptotrigona depilis. We made up 70 test colonies so that 50% (single matched mating), 25% (double mating), 12.5% (4-mating), or 0% (single non-matched mating) emerging brood were diploid males. Queen execution following diploid male emergence was equal and high in colonies producing 50% (77% executed) and 25% (75%) diploid males, versus equal and low in colonies producing 12.5% (7%) and 0% (0%) diploid males. These results show that queens that mate with two males with similar paternity suffer an increased chance of being executed, which selects against double mating. However, double mating with unequal paternity (e.g., 25:75), which occasionally occurs in S. depilis, is selectively neutral. Single mating and double mating with unequal paternity form one adaptive peak. The results show a second adaptive peak at 4-mating. However, this is inaccessible via gradual evolutionary change in a selective landscape with reduced fitness at double mating.
Data from: Extensive recombination of a yeast diploid hybrid through meiotic reversion
In somatic cells, recombination between the homologous chromosomes followed by equational segregation leads to loss of heterozygosity events (LOH), allowing the expression of recessive alleles and the production of novel allele combinations that are potentially beneficial upon Darwinian selection. However, inter-homolog recombination in somatic cells is rare, thus reducing potential genetic variation. Here, we explored the property of S. cerevisiae to enter the meiotic developmental program, induce meiotic Spo11-dependent double-strand breaks genome-wide and return to mitotic growth, a process known as Return To Growth (RTG). Whole genome sequencing of 36 RTG strains derived from the hybrid S288c/SK1 diploid strain demonstrates that the RTGs are bona fide diploids with mosaic recombined genome, derived from either parental origin. Individual RTG genome-wide genotypes are comprised of 5 to 87 homozygous regions due to the loss of heterozygous (LOH) events of various lengths, varying between a few nucleotides up to several hundred kilobases. Furthermore, we show that reiteration of the RTG process shows incremental increases of homozygosity. Phenotype/genotype analysis of the RTG strains for the auxotrophic and arsenate resistance traits validates the potential of this procedure of genome diversification to rapidly map complex traits loci (QTLs) in diploid strains without undergoing sexual reproduction.
Data from: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity
Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825,767,562 bp in 8,260 scaffolds with an N50 scaffold size of 713,602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49,124 high confidence gene models representing 37,740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158,367 Solanaceae genes and 1,897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding.
Data from: Haploids adapt faster than diploids across a range of environments
Despite a great deal of theoretical attention, we have limited empirical data about how ploidy influences the rate of adaptation. We evolved isogenic haploid and diploid populations of Saccharomyces cerevisiae for 200 generations in seven different environments. We measured the competitive fitness of all ancestral and evolved lines against a common competitor and find that in all seven environments haploid lines adapted faster than diploids, significantly so in three environments. We apply theory that relates the rates of adaptation and measured effective population sizes to the properties of beneficial mutations. We obtained rough estimates of the average selection coefficients in haploids between 2-10% for these first selected mutations. Results were consistent with semi-dominant to dominant mutations in four environments and recessive to additive mutations in two other environments. These results are consistent with theory that predicts haploids should evolve faster than diploids at large population sizes.
Data from: Comparisons of reproductive function and fatty acid fillet quality between triploid and diploid farm Atlantic salmon (Salmo salar)
Triploidy could prevent escaped farm salmon breeding in the wild, while also improving nutrient quality within farmed fillets. Despite these potential advantages, triploid Atlantic salmon have not been widely used in aquaculture, and their reproductive function has yet to be fully evaluated. Here, we compare reproductive function and fillet composition between triploid and diploid farm salmon under standard aquaculture rearing conditions. We show that female triploids are sterile and do not develop gonads. In contrast, males produce large numbers of motile spermatozoa capable of fertilising wild salmon eggs. However, compared with diploids, reproductive development and survival rates of eggs fertilised by triploid males were significantly reduced, with less than 1% of eggs sired by triploid males reaching late eyed stages of development. Analyses of fillets showed that total lipid and fatty acid quantities were significantly lower in triploid compared to diploid Atlantic salmon fillets. However, when fatty acids were normalized to total lipid content, triploid fillets had significantly higher relative levels of important omega-3 Long Chain Polyunsaturated Fatty Acids. Our results show that: (1) escaped triploid farm salmon are very unlikely to reproduce in the wild; and (2) if able to match diploid fillet lipid content, triploid farm salmon could achieve better fillet quality in terms of essential fatty acids.
Supplementary material 3 from: Zuo Z-Y, Lu J-M, Li C-F, Li D-Z (2024) Dryopteris jinpingensis, a critically endangered diploid new species of Dryopteridaceae from Yunnan, China. PhytoKeys 239: 195-204. https://doi.org/10.3897/phytokeys.239.118655
The voucher information and GenBank accession numbers of plastid regions used in this study
Supplementary material 1 from: Zuo Z-Y, Lu J-M, Li C-F, Li D-Z (2024) Dryopteris jinpingensis, a critically endangered diploid new species of Dryopteridaceae from Yunnan, China. PhytoKeys 239: 195-204. https://doi.org/10.3897/phytokeys.239.118655
The voucher information and GenBank accession numbers of complete plastid genome used in this study
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Allen Brain Atlas
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