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Transthyretin gene (TTR) intron 1 elucidates crocodylian phylogenetic relationships.

ABSTRACT: Transthyretin (TTR) is an attractive candidate for use in phylogenetic analysis because it is a short, single-copy nuclear gene with regions that are highly conserved across evolutionarily-divergent organisms from Xenopus laevis to Homo sapiens. To explore its utility as a phylogenetic marker, the complete intron one region (789-805 bp) was sequenced in 22 crocodylian species. Detailed analyses of intron 1 resolved the three expected lineages, Alligatorids, Crocodylids, and Gavialids, and offered additional evidence for the utility of synapomorphic indels in elucidating higher-level phylogenetic relationships. When used in conjunction with other genetic and morphological data sets, intron 1 should be a valuable tool in the investigation of other closely related taxa.

SUBMITTER: Willis RE

PROVIDER: S-EPMC2787865 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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Transthyretin gene (TTR) intron 1 elucidates crocodylian phylogenetic relationships.

Willis Ray E RE

Molecular phylogenetics and evolution 20090912 3

Transthyretin (TTR) is an attractive candidate for use in phylogenetic analysis because it is a short, single-copy nuclear gene with regions that are highly conserved across evolutionarily-divergent organisms from Xenopus laevis to Homo sapiens. To explore its utility as a phylogenetic marker, the complete intron one region (789-805 bp) was sequenced in 22 crocodylian species. Detailed analyses of intron 1 resolved the three expected lineages, Alligatorids, Crocodylids, and Gavialids, and offere ...[more]

PMID: 19751836

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Project description:BackgroundTTR (transthyretin) cardiac amyloidosis is caused by dissociation of TTR into monomers, which misassemble into amyloid fibrils. TTR stabilizers act at the dimer-dimer interface to prevent dissociation. We investigated differences in survival among patients with TTR cardiac amyloidosis on stabilizer medications compared with those not on stabilizers.Methods and resultsA retrospective study of patients with TTR cardiac amyloidosis presenting to a single center was conducted. Baseline characteristics were compared between those treated with stabilizers and those not treated with stabilizers. Cox proportional hazards modeling assessed for univariate predictors of the composite outcome of death or orthotopic heart transplant (OHT). Multivariable Cox proportional hazards assessed whether stabilizer treatment was independently associated with improved death or OHT after controlling for significant univariate predictors. One hundred twenty patients (mean age, 75±8, 88% male) were included: 29 patients who received stabilizers and 91 patients who did not. Stabilizer use was associated with a lower risk of the combined end point of death or OHT (hazard ratio, 0.32; 95% confidence interval, 0.18-0.58; P<0.0001). Subjects treated with stabilizers were more likely to be of White race (93% versus 55%; P<0.001), classified as New York Heart Association classes I and II (79% versus 38%; P=0.002), less likely to have a mutation (10% versus 36%; P=0.010), have lower troponin I (median 0.06 versus 0.12 ng/mL; P=0.002), and higher left ventricular ejection fraction (49% versus 40%; P=0.011), suggesting earlier stage of disease. In multivariable Cox analysis, the association between stabilizer and death or OHT persisted when adjusted for all noncollinear univariate predictors with P<0.05 (hazard ratio, 0.37; 95% confidence interval, 0.19-0.75; P=0.003).ConclusionsTTR stabilizers are associated with decreased death and OHT in TTR cardiac amyloidosis. These results need to be confirmed by ongoing randomized clinical trials.

Project description:BackgroundM. morganii is a bacterium frequently associated with urinary infections in humans. While many human strains are sequenced, only the genomes of few poultry strains are available. Here, we performed a detailed characterization of five highly resistant Morganella morganii strains isolated in association with Escherichia coli from diseased domestic Austrian poultry flocks, namely geese, turkeys and chicken layers. Additionally, we sequenced the genomes of these strains by NGS and analyzed phylogenetic clustering, resistance and virulence genes in the context of host-specificity.ResultsTwo strains were identified to be Extended Spectrum Beta Lactamase (ESBL) and one as AmpC beta-lactamases (AMP-C) phenotype, while two were ESBL negative. By integrating the genome sequences of these five poultry strains with all the available M. morganii genomes, we constructed a phylogenetic tree that clearly separates the Morganella genus into two clusters (M1 and M2), which approximately reflect the proposed subspecies classification (morganii and sibonii). Additionally, we found no association between phylogenetic structure and host, suggesting interspecies transmission. All five poultry strains contained genes for resistance to aminocoumarins, beta-lactams, colistin, elfamycins, fluoroquinolones, phenicol, rifampin and tetracycline. A comparative genomics analysis of virulence genes showed acquisition of novel virulence genes involved in secretion system and adherence in cluster M2. We showed that some of these genes were acquired by horizontal gene transfer from closely related Morganellaceae species and propose that novel virulence genes could be responsible for expansion of tissue tropism in M. morganii. Finally, we detected variability in copy number and high sequence divergence in toxin genes and provided evidence for positive selection in insecticidal toxins genes, likely reflecting host-related adaptations.ConclusionsIn summary, this study describes i) the first isolation and characterization of M. morganii from goose and turkey, ii) a large-scale genetic analysis of M. morganii and an attempt to generate a global picture of the M. morganii intraspecific phylogenetic structure.

Dataset Information

Transthyretin gene (TTR) intron 1 elucidates crocodylian phylogenetic relationships.

Publications

Transthyretin gene (TTR) intron 1 elucidates crocodylian phylogenetic relationships.

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