Dataset Information

Phylogeny of flavobacteria group isolated from freshwater using multilocus sequencing analysis.

ABSTRACT: Sequence analysis of the 16S rRNA gene has been widely used for the classification of microorganisms. However, we have been unable to clearly identify five Flavobacterium species isolated from a freshwater by using the gene as a single marker, because the evolutionary history is incomplete and the pace of DNA substitutions is relatively rapid in the bacteria. In this study, we tried to classify Flavobacterium species through multilocus sequence analysis (MLSA), which is a practical and reliable technique for the identification or classification of bacteria. The five Flavobacterium species isolated from freshwater and 37 other strains were classified based on six housekeeping genes: gyrB, dnaK, tuf, murG, atpA, and glyA. The genes were amplified by PCR and subjected to DNA sequencing. Based on the combined DNA sequence (4,412 bp) of the six housekeeping genes, we analyzed the phylogenetic relationship among the Flavobacterium species. The results indicated that MLSA, based on the six housekeeping genes, is a trustworthy method for the identification of closely related Flavobacterium species.

SUBMITTER: Mun S

PROVIDER: S-EPMC3897856 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Phylogeny of flavobacteria group isolated from freshwater using multilocus sequencing analysis.

Mun Seyoung S Lee Jungnam J Lee Siwon S Han Kyudong K Ahn Tae-Young TY

Genomics & informatics 20131231 4

Sequence analysis of the 16S rRNA gene has been widely used for the classification of microorganisms. However, we have been unable to clearly identify five Flavobacterium species isolated from a freshwater by using the gene as a single marker, because the evolutionary history is incomplete and the pace of DNA substitutions is relatively rapid in the bacteria. In this study, we tried to classify Flavobacterium species through multilocus sequence analysis (MLSA), which is a practical and reliable ...[more]

PMID: 24465240

Similar Datasets

Project description:Aeromonas spp. are the opportunistic pathogens that infect both aquatic and terrestrial homeotherms. They were commonly present in aquatic environments, including effluent, tap water, marine, river, and lake, where they are often isolated from aquatic animals, including fish, molluscs, and crustaceans. The Aeromonas infections can cause sepsis, ulcer, and other symptoms, resulting in the death of massive aquatic animals. Therefore, the prevention and control of Aeromonas is of great significance for the healthy development of aquaculture. In this study, we used modern molecular methods to enhance disease control of Aeromonas isolates from freshwater fish in Hebei Province. A total of 130 Aeromonas spp. isolates were isolated from freshwater fish farms in Hengshui, Handan, and Shijiazhuang and all 130 Aeromonas spp. isolates were sequenced for species identification. Of the 130 Aeromonas spp. isolates, 104 isolates were successfully sequenced, and BLAST analysis showed that Aeromonas veronii was predominant in freshwater fish farms in Hebei Province. In addition, 26 antibiotic resistance profiles were obtained from 102 fully cultured isolates among the 104 Aeromonas spp. isolates whose species was primarily identified, and 44 multidrug-resistant bacteria among the 102 isolates were identified using an antibiotic susceptibility test. Using the Multilocus Sequence Typing (MLST) method, 33 out of 44 multidrug-resistant isolates with 14 non-Aeromonas reference strains were selected for phylogenetic and MLST analysis, and all 33 multidrug-resistant isolates were A. veronii. A total of 30 new Sequence Types (STs) were obtained by comparing concatenated sequences (gyrB-groL-gltA-metG-ppsA-recA) on PubMLST website. Furthermore, recombination event analysis detected using RDP5 and ClonalFrameML software 42 and 49 recombination events, respectively, and 22 recombination events were validated by four or more algorithms. Since mutation and recombination events increase clonal diversity and single housekeeping gene sequence alignments are limited for identifying species, we propose the use of multiple concatenated sequence loci to increase discriminatory power. In addition, we propose that the MLST method is an appropriate technique to study and develop the resistance mechanisms of multidrug-resistant Aeromonas and to identify Aeromonas systematically in complex samples obtained from the environment.

Project description:Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of testing for hybridization versus incomplete lineage sorting, which aids inference of not only species limits but also evolutionary processes influencing genetic diversity.

Project description:Accurate species identification is crucial for developing conservation strategies for freshwater mussels, one of the most imperiled faunas in the world. Traditionally, mussel species description primarily relied on conchological characters. However, shell morphology has great variability, which leads to the complexity of species delimitation. As endemic species to China, Lamprotula caveata was originally described by Heude (1877). Lamprotula quadrangulosus and Lamprotula contritus were considered for synonymization of L. caveata based on shell variants in the early 20th century, which has been long debated due to lack of rigorous molecular analysis. Moreover, great morphological variation caused doubt whether there are cryptic species. In this study, we used a combined phylogenetic and morphometric approach to verify the validity of the synonymization of L. caveata. The results of molecular species delimitation showed that two molecular operational taxonomic units (MOTUs) were identified in Lamprotula spp., including the L. leaii lineage and the complex lineage (L. quadrangulosa, L. cornuumlunae, L. contritus, and L. caveata). Phylogenetic analyses revealed that L. cornuumlunae formed a basal monophyletic clade, whose divergence time was relatively recent (4.26 Ma [95% HPD = 1.91-7.22 Ma]), and L. contritus, L. caveata, and L. quadrangulosa formed a large polytomy group with very shallow branches. In the previous study, we have demonstrated the validity of L. cornuumlunae. The molecular evidences supported that the complex (L. quadrangulosa + L. contritus + L. caveata) was a valid species; L. quadrangulosa and L. contritus were synonyms of L. caveata. In addition, three morphospecies (L. quadrangulosa, L. contritus, and L. caveata) were aggregated without clear differentiation based on shell morphometric analysis. We confirmed multiple phenotypes in L. caveata for species identification and presumed that the phenotypic plasticity was a response to specific habitats. This study clarified the diversity and phylogeny of the Lamprotula group, which is a crucial step for developing new conservation and management strategies for this imperiled group.

Project description:The freshwater Dothideomycetes species are an ecological rather than taxonomic group and comprise approximately 178 meiosporic and mitosporic species. Due to convergent or parallel morphological adaptations to aquatic habitats, it is difficult to determine phylogenetic relationships among freshwater taxa and among freshwater, marine and terrestrial taxa based solely on morphology. We conducted molecular sequence-based phylogenetic analyses using nuclear ribosomal sequences (SSU and/or LSU) for 84 isolates of described and undescribed freshwater Dothideomycetes and 85 additional taxa representative of the major orders and families of Dothideomycetes. Results indicated that this ecological group is not monophyletic and all the freshwater taxa, except three aeroaquatic Tubeufiaceae, occur in Pleosporomycetidae as opposed to Dothideomycetidae. Four clades comprised of only freshwater taxa were recovered. The largest of these is the Jahnulales clade consisting of 13 species, two of which are the anamorphs Brachiosphaera tropicalis and Xylomyces chlamydosporus. The second most speciose clade is the Lindgomycetaceae clade consisting of nine taxa including the anamorph Taeniolella typhoides. The Lindgomycetaceae clade consists of taxa formerly described in Massarina, Lophiostoma, and Massariosphaeriae.g.,Massarina ingoldiana, Lophiostoma breviappendiculatum, and Massariosphaeria typhicola and several newly described and undescribed taxa. The aquatic family Amniculicolaceae, including three species of Amniculicola, Semimassariosphaeria typhicola and the anamorph, Anguillospora longissima, was well supported. A fourth clade of freshwater species consisting of Tingoldiago graminicola,Lentithecium aquaticum,L. arundinaceum and undescribed taxon A-369-2b was not well supported with maximum likelihood bootstrap and Bayesian posterior probability. Eight freshwater taxa occurred along with terrestrial species in the Lophiostoma clades 1 and 2. Two taxa lacking statistical support for their placement with any taxa included in this study are considered singletons within Pleosporomycetidae. These singletons, Ocala scalariformis, and Lepidopterella palustris, are morphologically distinct from other taxa in Pleosporomycetidae. This study suggests that freshwater Dothideomycetes are related to terrestrial taxa and have adapted to freshwater habitats numerous times. In some cases (Jahnulales and Lindgomycetaceae), species radiation appears to have occurred. Additional collections and molecular study are required to further clarify the phylogeny of this interesting ecological group.

Dataset Information

Phylogeny of flavobacteria group isolated from freshwater using multilocus sequencing analysis.

Publications

Phylogeny of flavobacteria group isolated from freshwater using multilocus sequencing analysis.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets