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Lopez, Jose V.
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Model
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Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple
morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic
relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of
cellular functions from a diverse group of sponges.
Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae,
Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21
newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically
defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We
found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but
our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based
on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges
(Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results
as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A wellsupported
clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina
(including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of
Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also
reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of
Hadromerida and Halichondrida.
Conclusions/Significance: These results, using an independent nuclear gene set, confirmed many hypotheses based on
ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted
with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding
questions using more taxon- and gene-rich datasets.
morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic
relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of
cellular functions from a diverse group of sponges.
Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae,
Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21
newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically
defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We
found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but
our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based
on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges
(Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results
as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A wellsupported
clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina
(including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of
Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also
reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of
Hadromerida and Halichondrida.
Conclusions/Significance: These results, using an independent nuclear gene set, confirmed many hypotheses based on
ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted
with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding
questions using more taxon- and gene-rich datasets.
Member of
Model
Digital Document
Description
Consistent biosynthesis of desired secondary metabolites (SMs) from pure microbial cultures is often unreliable. In a proof-ofprinciple
study to induce SM gene expression and production, we describe mixed “co-culturing” conditions and monitoring of
messages via quantitative real-time PCR (qPCR). Gene expression of model bacterial strains (Pseudomonas aeruginosa PAO1 and
Roseobacter denitrificans Och114) was analyzed in pure solo and mixed cocultures to infer the effects of interspecies interactions
on gene expression in vitro, Two P. aeruginosa genes (PhzH coding for portions of the phenazine antibiotic pathway leading
to pyocyanin (PCN) and the RhdA gene for thiosulfate: cyanide sulfurtransferase (Rhodanese)) and two R. denitrificans genes
(BetaLact formetallo-beta-lactamase and the DMSP gene for dimethylpropiothetin dethiomethylase) were assessed for differential
expression. Results showed that R. denitrificans DMSP and BetaLact gene expression became elevated in a mixed culture. In
contrast, P. aeruginosa co-cultures with R. denitrificans or a third species did not increase target gene expression above control
levels. This paper provides insight for better control of target SM gene expression in vitro and bypass complex genetic engineering
manipulations.
study to induce SM gene expression and production, we describe mixed “co-culturing” conditions and monitoring of
messages via quantitative real-time PCR (qPCR). Gene expression of model bacterial strains (Pseudomonas aeruginosa PAO1 and
Roseobacter denitrificans Och114) was analyzed in pure solo and mixed cocultures to infer the effects of interspecies interactions
on gene expression in vitro, Two P. aeruginosa genes (PhzH coding for portions of the phenazine antibiotic pathway leading
to pyocyanin (PCN) and the RhdA gene for thiosulfate: cyanide sulfurtransferase (Rhodanese)) and two R. denitrificans genes
(BetaLact formetallo-beta-lactamase and the DMSP gene for dimethylpropiothetin dethiomethylase) were assessed for differential
expression. Results showed that R. denitrificans DMSP and BetaLact gene expression became elevated in a mixed culture. In
contrast, P. aeruginosa co-cultures with R. denitrificans or a third species did not increase target gene expression above control
levels. This paper provides insight for better control of target SM gene expression in vitro and bypass complex genetic engineering
manipulations.
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