Dataset Information

Incongruence between multi-locus sequence analysis (MLSA) and whole-genome-based phylogenies: Pseudomonas syringae pathovar pisi as a cautionary tale.

ABSTRACT: Previous phylogenies, built using a subset of genomic loci, split Pseudomonas syringae pv. pisi into two well-supported clades and implied convergence in host range for these lineages. The analysis of phenotypic and genotypic data within the context of this phylogenetic relationship implied further convergence at the level of virulence gene loss and acquisition. We generate draft genome assemblies for two additional P.?syringae strains, isolated from diseased pea plants, and demonstrate incongruence between phylogenies created from a subset of the data compared with the whole genomes. Our whole-genome analysis demonstrates that strains classified as pv. pisi actually form a coherent monophyletic clade, so that apparent convergence is actually the product of shared ancestry. We use this example to urge caution when making evolutionary inferences across closely related strains of P.?syringae.

SUBMITTER: Baltrus DA

PROVIDER: S-EPMC6638795 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Incongruence between multi-locus sequence analysis (MLSA) and whole-genome-based phylogenies: Pseudomonas syringae pathovar pisi as a cautionary tale.

Baltrus David A DA Dougherty Kevin K Beckstrom-Sternberg Stephen M SM Beckstrom-Sternberg James S JS Foster Jeffrey T JT

Molecular plant pathology 20140106 5

Previous phylogenies, built using a subset of genomic loci, split Pseudomonas syringae pv. pisi into two well-supported clades and implied convergence in host range for these lineages. The analysis of phenotypic and genotypic data within the context of this phylogenetic relationship implied further convergence at the level of virulence gene loss and acquisition. We generate draft genome assemblies for two additional P. syringae strains, isolated from diseased pea plants, and demonstrate incongru ...[more]

PMID: 24224664

Similar Datasets

Project description:FURIN is a pro-protein convertase previously shown to be important for placental syncytialisation (Zhou et al. [1]), a process of cell fusion whereby placental cytotrophoblast cells fuse to form a multinucleated syncytium. This finding has been broadly accepted however, we have evidence suggesting the contrary. Spontaneously syncytialising term primary human trophoblast cells and BeWo choriocarcinoma cells were treated with either FURIN siRNA or negative control siRNA or the protease inhibitor, DEC-RVKR-CMK, or vehicle. Cells were then left to either spontaneously syncytialise (primary trophoblasts) or were induced to syncytialise with forskolin (BeWo). Effects on syncytialisation were measured by determining human chorionic gonadotrophin secretion and E-cadherin protein levels. We showed that FURIN is not important for syncytialisation in either cell type. However, in primary trophoblasts another protease also inhibited by DEC-RVKR-CMK, may be involved. Our results directly contrast with those published by Zhou et al. Zhou et al. however, used first trimester villous explants to study syncytialisation, and we used term primary trophoblasts. Therefore, we suggest that FURIN may be involved in syncytialisation of first trimester trophoblasts, but not term trophoblasts. What is more concerning is that our results using BeWo cells do not agree with their results, even though for the most part, we used the same experimental design. It is unclear why these experiments yielded different results, however we wanted to draw attention to simple differences in measuring syncytialisation or flaws in method reporting (including omission of cell line source and passage numbers, siRNA concentration and protein molecular weights) and choice of immunoblot loading controls, that could impact on experimental outcomes. Our study shows that careful reporting of methods by authors and thorough scrutiny by referees are vital. Furthermore, a universal benchmark for measuring syncytialisation is required so that various studies of syncytialisation can be validated.

Dataset Information

Incongruence between multi-locus sequence analysis (MLSA) and whole-genome-based phylogenies: Pseudomonas syringae pathovar pisi as a cautionary tale.

Publications

Incongruence between multi-locus sequence analysis (MLSA) and whole-genome-based phylogenies: Pseudomonas syringae pathovar pisi as a cautionary tale.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets