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Consistent with these findings, we detected reduced sequence variation around gp60 in virulent subtype IbA10G2, suggesting that the 129-kb region surrounding gp60 in chromosome 6, perhaps gp60 itself, might be involved in selection for virulent gp60 subtype IbA10G2 in C. hominis.
The prediction of reduced sequence variation around selected polymorphisms is much stronger for hard than soft sweeps, particularly when considering quantitative traits where sweeps are likely to be incomplete.
Native individuals assembled slightly higher numbers of both unigenes and contigs than invading individuals, potentially indicating reduced sequence variation in introduced genotypes, but these differences were not significant in either case (analysis of covariance on Ln-transformed data: unigenes, P = 0.06; contigs, P = 0.23).
Since our Miscanthus markers were derived from (1) transcribed regions with reduced sequence variation (SNPs) and (2) sequences from conserved ESTs and intergenic regions (SSRs), many of them could be unambiguously assigned to orthologous (i.e., evolutionarily homologous) positions on the Sorghum bicolor genome sequence by straightforward sequence alignment.
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One of these regions contains a repeat present in multiple copies in 16 M, but apparently single or at least fewer copies in REO198, causing reduced sequence dosage and apparent variation (unpublished observations).
With vast germplasm resources and reduced sequencing cost, genome-wide association study (GWAS) has been feasible to explore the allelic variation underlying agronomic traits in rice.
SNP assays directly interrogate the sequence variation, reducing genotyping errors compared to assays based on size discrimination or hybridization.
Under conditions of partial heat denaturation within a linear acetonitrile gradient, heteroduplexes that form in PCR samples having internal sequence variation display reduced column retention time relative to their homoduplex counterparts.
To reduce the number of parameters while keeping the majority of sequence variation, we used reduced data sets for model determination.
More recent, large-scale studies show similar trends; sequence variation is markedly reduced on the X chromosome in derived strains while reductions in diversity at autosomal regions are less uniform across loci [ 22, 23].
Compared to markers based on size discrimination or hybridization, SNPs directly interrogate sequence variation and can reduce genotyping errors [ 12].
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