Resistance of rumen bacteria murein to bovine gastric lysozyme

BACKGROUND: Lysozymes, enzymes mostly associated with defence against bacterial infections, are mureinolytic. Ruminants have evolved a gastric c type lysozyme as a digestive enzyme, and profit from digestion of foregut bacteria, after most dietary components, including protein, have been fermented in the rumen. In this work we characterized the biological activities of bovine gastric secretions against membranes, purified murein and bacteria. RESULTS: Bovine gastric extract (BGE) was active against both G+ and G- bacteria, but the effect against Gram- bacteria was not due to the lysozyme, since purified BGL had only activity against Gram+ bacteria. We were unable to find small pore forming peptides in the BGE, and found that the inhibition of Gram negative bacteria by BGE was due to an artefact caused by acetate. We report for first time the activity of bovine gastric lysozyme (BG lysozyme) against pure bacterial cultures, and the specific resistance of some rumen Gram positive strains to BGL. CONCLUSIONS: Some Gram+ rumen bacteria showed resistance to abomasum lysozyme. We discuss the implications of this finding in the light of possible practical applications of such a stable antimicrobial peptide

A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae

Putatively single-copy nuclear (SCN) loci, which are identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment in the distantly related Memecylon and Tibouchina (Melastomataceae)

An updated and extended version of the Melastomataceae probe set for target capture

Abstract Premise A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae. Methods In order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version. Results The final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery. Discussion This updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant‐targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available

Article Navigation revisiting the classification of melastomataceae : implications for habit and fruit evolution

Bertolonieae (Melastomataceae) have traditionally comprised > 100 Neotropical species in Bertolonia, Boyania, Macrocentrum, Monolena, Salpinga and Triolena and another six species in the monospecific genera Diolena, Diplarpea, Maguireanthus, Opisthocentra, Tateanthus and Tryssophyton. The position of the tribe inside or outside Sonerileae has been discussed since the first classifications of Melastomataceae. These tribes were always considered closely related because of overall similar morphology, mainly herbaceous habit and angular fruits. Previous phylogenetic analyses have shown that Bertolonieae as traditionally circumscribed are not monophyletic and require re-evaluation. These previous results also led to questions on why such herbaceous plants from shaded, moist habitats and with angular fruits had evolved so many times in different and geographically/phylogenetically distant groups of Melastomataceae. We conducted molecular phylogenetic analyses in order to evaluate tribal and generic limits, reconstruct morphological patterns and identify clades in the tribe. To infer the monophyly of Bertolonieae and the genera that were traditionally included in the tribe we analysed three plastid (ndhF, rbcL and rpl16) and two ribosomal (nrETS and nrITS) DNA markers, using maximum likelihood and Bayesian inference in individual and variously combined data sets comprising up to 6646 characters and 445 terminals. Bertolonieae as traditionally recognized were recovered in four major lineages across the tree. Bertolonieae are recircumscribed here to include only Bertolonia. A new tribe, Trioleneae, with the genera Monolena and Triolena is described on the basis of molecular, geographical and morphological evidence. Our study also shows that the combination of herbaceous habit and angular capsules has evolved several times in Melastomataceae. Besides the taxonomic changes proposed here, the molecular corroboration that Bertolonieae s.l. are not monophyletic and the geographical and morphological congruence found in these lineages, the convergence of morphological characters historically used to identify Bertolonieae s.l. might be explained by the occupation of similar habitats in different places across the world, i.e. in mostly shaded and moist herbaceous layers under the rainforest canopy. The dependence on water for seed dispersal and the limited dispersability could also explain the restriction of the taxa to a limited area or vegetation type190112

Seed Diversity in the Tribe Miconieae (Melastomataceae): Taxonomic, Systematic, and Evolutionary Implications

<div><p>Miconieae is the largest tribe in the Melastomataceae with over 1,850 species. The members of Miconieae display a wide range of morphological diversity, and seed morphology is no exception. Previous studies have found that seed morphological diversity is not congruent with traditional classifications, and suggest that it may reflect evolutionary relationships within Miconieae. Here we characterize seed morphology of 364 species of Miconieae. The morphological data set and a DNA sequence data matrix were analyzed under a parsimony and Bayesian framework. Seed characters were used to test taxonomic and clade hypotheses, to estimate morphological ancestral character states, and to assess phylogenetic signal. The phylogenetic analyses of morphological data retrieved a poorly-resolved, low-supported phylogeny; in contrast, a relatively strongly supported phylogeny was estimated using the molecular data. Hypothesis testing procedures could only reject the monophyly of <i>Clidemia</i>, <i>Leandra</i>, and <i>Miconia</i>. The results indicated that the seed morphological characters were homoplasious, but contained phylogenetic signal. The morphological seed types that were described in previous studies did not support any of the clades retrieved by the molecular phylogeny. In contrast with previous investigations, our study shows that although seed morphology is very variable, it does not provide information for supporting some genera or clades within Miconieae. However, it is suggested that seed characters in combination with other vegetative and reproductive traits may aid in the characterization of smaller clades. The presence of phylogenetic signal retrieved by homoplasious characters may indicate that diversification of seed characters could have an adaptive component. Further studies that increase taxon sampling, refine seed trait characterization, and evaluate the alleged relationships between environmental variables and seed diversification will contribute to a better understanding of seed morphology and evolution in this species-rich tribe.</p></div

Phylogenetic relationships of species of Miconieae estimated from analyses of seed morphological data.

<p>A) Maximum parsimony (MP) strict consensus tree. B) 50% majority-rule Bayesian consensus tree. Nodal support for relationships among the samples was <75% bootstrap and <0.95 posterior probabilities (p.p.) for the MP and Bayesian analyses, respectively. Red branches  =  outgroup taxa; green branches  =  clade present in both analyses.</p