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Nucleotide diversity

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Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

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When comparing nucleotide diversity per gene class in species pairs, mean MHC nucleotide diversity did not differ significantly for domestic Bactrian camels and dromedaries, as well as for wild camels and dromedaries, but differed between wild and do- mestic Bactrian camels, with the latter showing higher nucleotide mean diversity (Supplemental Fig.

Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

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Genetic diversity. Inbreeding coefficient for the Capsicum population was 0.54. Expected nucleotide diversity (θ) for the whole Capsicum panel was 0.18. baccatum and C.chacoense complex (0.55) (Additional file 2, Table S1). Table 1 Analysis of molecular variance using genome wide SNP markers for the Capsicum populations. chacoense) and 0.12 (C. Tajima’s D statistic for the Capsicum population across all chromosomes was D = 2.85 (Fig.

Mitogenomic diversity and phylogeny analysis of yak (Bos grunniens)

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Genetic diversity analysis of yak mtDNA. The genetic diversity analysis showed that the mitotype diversity of the five yak populations was and the nucleotide diversity was . These data showed that the genetic diversity of five yak populations was high. The nucleotide diversity value of the Pamir yak population was higher than that of the other four populations. The mitotype di- versity reached a maximum in the Xueduo yak popula- tion and a minimum in the Huanhu yak population .

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

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Jiaxian Red (mean θπ = 0.0029) and Qinchuan cattle (mean θπ = 0.0026) showed a similar level of nucleotide diversity (Fig. We also analyzed the ROH distribution pattern of Jiaxian Red by comparing with other cattle breeds.

Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

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The color of the vertical bar on the x-axis represents the proportion of membership of each inbred line in each subgroup. low nucleotide diversity [15], and decreased natural and arti- ficial selection for alleles located in this part of the genome are both additional plausible reasons for lower marker numbers..

Contrasting genetic variation and positive selection followed the divergence of NBSencoding genes in Asian and European pears

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In contrast, the higher nucleotide diversity in NBS-encoding genes of cultivated groups in Europe might have occurred due to distinct selection pressure imposed by the cultivated habitats [41]. A recent study has shown that several regions with NBS-encoding genes had higher nucleotide diversity in landraces than the wild pear group [42].

Population analysis of the Korean native duck using whole-genome sequencing data

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The mean nucleotide diversity (π) of duck breeds was between 0.1028 to 0.1384, and MD showed exceptionally higher nucleotide diversity than domesticated breeds.. We also performed population ana- lyses of 15 duck breeds including KD, and found similar patterns for duck breeds used in the previous study [23].. In the highly differentiated regions.

Chloroplast genome variation and phylogenetic relationships of Atractylodes species

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Additionally, we compared single nucleotide substi- tutions and nucleotide diversity in the total, LSC, SSC and IR regions of the chloroplast genomes (Table 3).. The Table 2 The basic chloroplast genome information of six Atractylodes species. 3 Analyses of indels in the Atractylodes chloroplast genomes. (B) Number and size of non-SSR- related indels in the six Atractylodes chloroplast genomes.

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: Insights into evolutionary divergence and phylogenomic implications

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Of particular interest, accD, encoding the beta-carboxyl transferase subunit of acetyl-CoA carboxylase, and ycf1, encoding Tic214 of the TIC complex, showed lower sequence identity, higher nucleotide diversity, and a larger number of PI sites than the other genes, indicating a high level of sequence divergence. protein-coding genes, accD and ycf1, were identified as nucleotide diversity hotspots of the Artemisia chloroplast protein-coding genes, and have potential as candidate regions for the development

The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China

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Heatmap shows pairwise Ka/Ks ratios between every concatenated single-copy CDs sequence in the multigene nucleotide alignment. our study, both genome-scale level alignments and nucleotide diversity analyses of the eight Lardizabaloi- deae chloroplast genomes revealed common variable sites, including eleven intergenic regions and eight coding genes (Figs.

Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)

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However, due to rapid radiation, sampling of additional individuals from each species and extending more nuclear genes would provide additional evidence of the evolutionary history of Distylium.. 4 Nucleotide diversity ( π ) in the Distylium plastomes using sliding window method. Table 4 Variability of the four highly mutation hotspot regions and the universal chloroplast DNA barcodes in Distylium.

Analysis of six chloroplast genomes provides insight into the evolution of Chrysosplenium (Saxifragaceae)

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The best-fitting nucleotide substi- tution model was determined using the Akaike Informa- tion Criterion in the model-finder IQ-TREE [63]. Additional File 3 Comparison of nucleotide diversity (Pi) between the chloroplast genomes of Chrysosplenium. Analyses of repeat sequences in the ten species of Saxifragaceae. (A) The analysis of simple sequence repeats (SSRs) in chloroplast genomes of Saxifragaceae.

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

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Thus, a few animals that are selected based on their marginal genetic contribution to the active breeding population, account for a large fraction of the population’s haplotype diversity. In spite of the low effective population size, the nucleotide diversity (π) was high in both lines (π dam . Although our sequencing cohort contained more ani- mals from the sire line, we detected somewhat more autosomal variants in the dam line (N sire .

Comparison of chloroplast genomes of Gynura species: Sequence variation, genome rearrangement and divergence studies

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The Pi value (nucleotide diversity) of chloroplast genome sequences between four Gynura species and five Ligularia species.. WL and JC designed the idea of the article. Hassan Z, Yam MF, Ahmad M, et al. Deng YX, Chen YS, Zhang WR, et al. Rosidah, Yam MF, Sadikun A, et al. Palmer JD, Jansen RK, Michaels HJ, et al. Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae.

Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928–2013): Antimicrobial use/misuse selects for resistance and drives evolution

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Fur- thermore, the nucleotide diversity of the common core genome of the isolates decreased over time and was polymorphisms poly- morphisms), and polymorphisms) for the preantibiotic, golden, and postmodern era, respect- ively.

Impacts of local population history and ecology on the evolution of a globally dispersed pathogen

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Nucleotide diversity (Tajima ’ s D) and recombinant events across the length of the core genome alignment. fastidiosa in Costa Rica (orange), subsp. fastidiosa : Line plot showing Tajima ’ s D values across the length of the core genome alignment and fastGEAR output showing the location of recombination events among identified clusters. pauca : Line plot showing Tajima ’ s D values across the length of the core genome alignment and fastGEAR output showing the location of recombination events among

Population and subspecies diversity at mouse centromere satellites

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Despite its smaller size, the minor satellite harbors more sites with at least 20% non-consensus nucleotide usage than the major sat- ellite (107 versus 79. Estimated centromere satellite copy number and centromere diversity index for the (a) minor or (b) major satellite sequence. In addition, position 78 exhibits more variability in the proportion of non-consensus nucleotide usage than any other minor satellite position in both inbred strains and wild-caught mice.

Molecular genetic diversity and population structure analyses of rutabaga accessions from Nordic countries as revealed by single nucleotide polymorphism markers

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The diversity of the SNP markers expressed as the polymorphic information content (PIC) is presented in Fig. 1 The origin and sample sizes per country of the 124 rutabaga accessions used in this genetic diversity study. 0.1 was of the order ISL gt. also called gene diversity (D), followed similar patterns as the rest of the parameters measured with the exception of the MAF (Fig.

Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis

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Background: Diversity of the CRISPR locus of Mycobacterium tuberculosis complex has been studied since 1997 for molecular epidemiology purposes. In contrast, we found an unexpected diversity in the form of: SNPs in spacers and in Direct Repeats, duplications of various length, and insertions at various locations of the IS 6110 insertion sequence, as well as blocks of DVR deletions. When reconstructing evolutionary steps of the locus, we found no evidence for SNP reversal.

Origin, clonal diversity, and evolution of the parthenogenetic lizard Darevskia unisexualis

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Further, the flanking regions of the alleles had single nucleotide polymor- phisms (SNPs) in fixed positions (Fig. In the paternal parent, Du215(val. raddei nairensis ) in the maternal parent. Six of the 14 alleles in D. The absence of these al- leles in the parental species may have owed to sampling artifacts or genetic recombination in D.