Metabolites of pathogenic microorganisms database (MPMdb) and its seed metabolite applications.

Seed metabolites are the combination of essential compounds required by an organism across various potential environmental conditions. The seed metabolites screening framework based on the network topology approach can capture important biological information of species. This study aims to identify comprehensively the relationship between seed metabolites and pathogenic bacteria. A large-scale data set was compiled, describing the seed metabolite sets and metabolite sets of 124,192 pathogenic strains from 34 genera, by constructing genome-scale metabolic models. The enrichment analysis method was used to screen the specific seed metabolites of each species/genus of pathogenic bacteria. The metabolites of pathogenic microorganisms database (MPMdb) (http://qyzhanglab.hzau.edu.cn/MPMdb/) was established for browsing, searching, predicting, or downloading metabolites and seed metabolites of pathogenic microorganisms. Based on the MPMdb, taxonomic and phylogenetic analyses of pathogenic bacteria were performed according to the function of seed metabolites and metabolites. The results showed that the seed metabolites could be used as a feature for microorganism chemotaxonomy, and they could mirror the phylogeny of pathogenic bacteria. In addition, our screened specific seed metabolites of pathogenic bacteria can be used not only for further tapping the nutritional resources and identifying auxotrophies of pathogenic bacteria but also for designing targeted bactericidal compounds by combining with existing antimicrobial agents.IMPORTANCEMetabolites serve as key communication links between pathogenic microorganisms and hosts, with seed metabolites being crucial for microbial growth, reproduction, external communication, and host infection. However, the large-scale screening of metabolites and the identification of seed metabolites have always been the main technical bottleneck due to the low throughput and costly analysis. Genome-scale metabolic models have become a recognized research paradigm to investigate the metabolic characteristics of species. The developed metabolites of pathogenic microorganisms database in this study is committed to systematically predicting and identifying the metabolites and seed metabolites of pathogenic microorganisms, which could provide a powerful resource platform for pathogenic bacteria research.

Re-evaluation of the Wehrle's salamander (Plethodon wehrlei Fowler and Dunn) species group (Caudata: Plethodontidae) using genomic data, with the description of a new species.

Woodland salamanders of the genus Plethodon are characterized by strong ecological and morphological conservatism. One assemblage, the Wehrle's salamander (Plethodon wehrlei Fowler Dunn) species group, is distributed from New York to Tennessee, USA, and includes several morphological variants, four of which are sufficiently distinct to have been recognized as species in the past. For many years after two of these species were placed in synonymy, only P. wehrlei and P. punctatus Highton were recognized. A recent phylogeographic study using mitochondrial DNA and nuclear DNA uncovered considerable genetic diversity within the group and conservatively resurrected one of the previously synonymized forms (P. dixi Pope Fowler). However, their analysis could not resolve all relationships among remaining populations of P. wehrlei, leaving the taxon paraphyletic. We re-evaluated the evolutionary history of this group using genomic data, recovered strong support for at least five distinct clades, and corroborated previously reported relationships. We also collected morphological data and demonstrated morphological distinctiveness for four of the five clades that we herein recognize as species. We resurrect the synonymized name P. jacksoni Newman to represent the southern clades of P. wehrlei in southwestern Virginia and North Carolina exclusive of P. dixi. In addition, we describe a yellow-spotted form of P. wehrlei endemic to the Cumberland Plateau as a new species. Although our proposed changes rectify the paraphyly of P. wehrlei, our sampling was not sufficient to resolve potential taxonomic issues remaining within the species herein recognized as P. jacksoni.

Total evidence analysis of the phylogenetic relationships of bandicoots and bilbies (Marsupialia: Peramelemorphia): reassessment of two species and description of a new species.

The phylogenetic relationships of bandicoots and bilbies have been somewhat problematic, with conflicting results between morphological work and molecular data. This conflict makes it difficult to assess the taxonomic status of species and subspecies within this order, and also prevents accurate evolutionary assessments. Here, we present a new total evidence analysis, combining the latest cranio-dental morphological matrix containing both modern and fossil taxa, with molecular data from GenBank. Several subspecies were scored in the morphological dataset to match the molecular data available. Both parsimony and Bayesian analyses were performed, giving similar topologies except for the position of four fossil taxa. Total evidence dating places the peramelemorphian crown origin close to the Oligocene/Miocene boundary, and the radiations of most modern genera beginning in the Late Miocene or Early Pliocene. Our results show that some species and subspecies require taxonomic reassessment, and are revised here. We also describe a new, extinct species from the Nullarbor region. This suggests that the number of recently extinct peramelemorphian species is likely to further increase.