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Sequence divergence

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

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The divergence time of the genus Gynura could not start at hundreds or thousands of years ago [23], and the divergence time es- timated by the BEAST program was in the same time period as that of other genera of land plants [13–16].. 4 Sequence divergence of chloroplast genome sequences in 7 Senecioneae species. a The Pi value (nucleotide diversity) of the 7 chloroplast genome sequences. This study analyses the chloroplast genome of four Gynura species used as herbal medicine in parts of Asia..

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): Insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

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In this study, we elucidated the complete chloroplast genome of S. persica cp genome cp genome annotation. persica cp genome divergence with related eleven species where S. persica phylogenetic analysis and cp genome divergence. Chloroplast genome divergence among S. org/10.1186/s x..

Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae

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Synonymous (dS) and non synonymous (dN) substitu- tion rate as well as dN/dS ration were calculated to evaluate sequence divergence and purifying selection in the protein coding genes. 5 Sequence alignment of eight chloroplast genome in the Acanthaceae family performed with mVISTA using annotation of B. The x-axis represents the coordinates in the cp genome while y- axis represents percentage identity within 50 – 100%. Andrographideae and Barlerieae were placed in the tribe Justiceae as sub.

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

Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii

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Multiple alignment of an internal region of the RtxA toxin in the five poultry strains showing high sequence divergence.. List of candidate genes in the PA17/10312 strain with evidence for horizontal gene transfer from closely-related Mor- ganellaceae species.. Annotation of active prophages in the five sequenced poultry strains.. Annotation of pathogenicity islands in the five sequenced poultry strains.

Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction

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Background: Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non- recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers.

Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

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Coding sequence divergence between syntenic MCTPs in G. Physicochemical properties of the N- terminus and C-terminus of GhMCTP proteins.. Multiple sequence alignment of GhMCTPs.. C2 domains and transmembrane regions are indicated below the alignment.. MCTP: Multiple C2 domains and transmembrane region protein;. Multiple C2 domains and Transmembrane region Proteins (MCTPs) tether membranes at plasmodesmata. Membrane binding and subcellular targeting of C2 domains

De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: Molecular mechanisms underlying scleractinian gametogenesis

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EST Analysis of the Cnidarian Acropora millepora Reveals Extensive Gene Loss and Rapid Sequence Divergence in the Model Invertebrates

Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci

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For example sequence uniformity in reads from a repeat cluster may indicate a recent copy-number expansion, and this is indicated in the tight-knit layout of vertices (Fig. 2a,b) contain more divergent reads and likely represent older populations of repeats, where extensive sequence divergence has accumulated between members of the family.

Species and population specific gene expression in blood transcriptomes of marine turtles

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We tested multiple numbers of samples to use as input for our de novo transcriptomes (n = 34, n = 19, and n = 4) to determine the optimal threshold of individuals for maximizing transcriptome completeness while minimizing computa- tional demands, chimeric sequences, and false-splitting due to sequence divergence between populations [82], and concatenated reads from four Hawai’ian green turtle individuals to generate the green turtle transcriptome..

Trait differentiation and modular toxin expression in palm-pitvipers

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In the case of SVSPs, nucleotide sequence divergence was sufficient to give conflicting phylogenetic signal when compared to. Although we did not find a significant difference in expression of. We tested the hypothesis that dimensions of the neurotoxic-hemorrhagic venom phenotype were associ- ated with specific submodules of toxin expression. In the Bothriechis system, mod- ularity effectively explains many of the toxin expression.

Novel genomic resources for shelled pteropods: A draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance

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The number of SNPs recovered per species using the most conservative filtering settings (80% genotyping rate and 5x depth) was plotted against sequence divergence from L. We thank Erica Goetze, Nina Bednar š ek, Alice Burridge, and Lisette Mekkes as well as the captains and crews of the research cruises for support and assistance with collecting zooplankton samples.. Three individuals per site were included from localities in the Atlantic and Pacific Oceans..

Mining ancient microbiomes using selective enrichment of damaged DNA molecules

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Due to the high level of sequence divergence between the Pseudomonas in our sample and the reference genomes present in the database, it is difficult to assess typical de- amination patterns in the dsDNA library (Fig. vagans, U- selection increases the fraction of molecules carrying a ter- minal C-to-T substitution at the 5′-end 2–3 fold over the li- brary without enrichment, relative to the total number of molecules sequenced.

Campylobacter bacteriophage DA10: An excised temperate bacteriophage targeted by CRISPR-cas

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Pairwise align- ment of DA10 with CJ677CC520 prophage results in an overall ANI of 51%, however mummer alignment of the intact coding regions shows a higher degree of sequence divergence (29% ANI), implying preservation of gene function is not essential.. Of the 59 ORFs annotated in the DA10 genome, CRISPR spacers targeting ~ 75% of these (43 ORFs) were identified (Fig.

Chloroplast phylogenomics and divergence times of Lagerstroemia (Lythraceae)

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The relationship and divergence times of Lagerstroemia were revealed using complete chloroplast genome sequence data. In order to infer the framework of the phylogenetic relationship, we sampled 20 individuals of 17 described species, which represented all the four sec- tions and six of eight subsections. The materials were obtained from the field, botanical gardens and the herb- arium of the Institute of Botany, Chinese Academy of Sciences (PE, Table S1).

Genetic boundaries delineate the potential human pathogen Salmonella bongori into discrete lineages: Divergence and speciation

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Genome Sequence of Salmonella bongori Strain N268 – 08 [corrected]. The XbaI-BlnI-CeuI genomic cleavage map of Salmonella enteritidis shows an inversion relative to Salmonella typhimurium LT2. Genomic cleavage map of Salmonella typhi Ty2. Differential degeneration of the ACTAGT sequence among Salmonella: a reflection of distinct nucleotide amelioration patterns during bacterial divergence. On the serology of the Salmonella group.

New insights into the evolution and functional divergence of the CIPK gene family in Saccharum

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Under salt stress, CIPK21 participates in the regulation of response to osmotic stress in A. the evolution and function of the CIPK gene family, we here analyzed comparative genomics analysis with an emphasis on the functional divergence of the CIPK gene family in Saccharum. In this study, sequence and evolu- tion analysis of the SsCIPK genes were conducted using the available sugarcane genome data [42].

Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old

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To categorize regulatory variations, we referenced the methods applied in the study of regulatory divergence in Drosophila [7] and house mouse [36]. Re-sequencing data from four parents were used to study the sequence conservation of cis- and trans- regulatory divergence genes. The pN/pS ratio of the coding sequence and the number of variants in 1 kb up- stream from the transcription start site were calculated using the results of SNP annotation performed using SnpEff [53].

Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)

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A draft sequence of the rice genome (Oryza sativa L. Registration of the rice diversity panel 1 for genomewide association studies. numerical evaluation of the indica-japonica differentiation

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

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Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria. Full list of author information is available at the end of the article. The haploid genome of the reference isolate IPO323 comprises thirteen core and eight accessory chromosomes [23].