Cryptic diversity in Tranzscheliella spp. (Ustilaginales) is driven by host switches.
Ontology highlight
ABSTRACT:
SUBMITTER: Li YM
PROVIDER: S-EPMC5335255 | biostudies-literature | 2017 Mar
REPOSITORIES: biostudies-literature
Publications
Cryptic diversity in Tranzscheliella spp. (Ustilaginales) is driven by host switches.
Li Ying-Ming YM Shivas Roger G RG Cai Lei L
Scientific reports 20170303
Species of Tranzscheliella have been reported as pathogens of more than 30 genera of grasses (Poaceae). In this study, a combined morphological and molecular phylogenetic approach was used to examine 33 specimens provisionally identified as belonging to the T. hypodytes species complex. The phylogenetic analysis resolved several well-supported clades that corresponded to known and novel species of Tranzscheliella. Four new species are described and illustrated. In addition, a new combination in ...[more]
Similar Datasets
Project description:In previous studies, fifteen species of Paratylenchus, commonly known as pin nematodes, have been reported in Spain. These plant-parasitic nematodes are ectoparasites with a wide host range and global distribution. In this research, 27 populations from twelve Paratylenchus species from 18 municipalities in Spain were studied using morphological, morphometrical and molecular data. This integrative taxonomic approach allowed the identification of twelve species, four of them were considered new undescribed species and eight were already known described. The new species described here are P. caravaquenus sp. nov., P. indalus sp. nov., P. pedrami sp. nov. and P. zurgenerus sp. nov. As for the already known described species, five were considered as first reports for the country, specifically P.enigmaticus, P. hamatus, P. holdemani, P. israelensis, and P. veruculatus, while P. baldaccii, P. goodeyi and P. tenuicaudatus had already been recorded in Spain. This study provides detail morphological and molecular data, including the D2-D3 expansion segments of 28S rRNA, ITS rRNA, and partial mitochondrial COI regions for the identification of different Paratylenchus species found in Spain. These results confirm the extraordinary cryptic diversity in Spain and with examples of morphostatic speciation within the genus Paratylenchus.
| S-EPMC8073821 | biostudies-literature
Project description:Background and aimsThe broomrapes, Orobanche sensu lato (Orobanchaceae), are common root parasites found across Eurasia, Africa and the Americas. All species native to the western hemisphere, recognized as Orobanche sections Gymnocaulis and Nothaphyllon, form a clade that has a centre of diversity in western North America, but also includes four disjunct species in central and southern South America. The wide ecological distribution coupled with moderate taxonomic diversity make this clade a valuable model system for studying the role, if any, of host-switching in driving the diversification of plant parasites.MethodsTwo spacer regions of ribosomal nuclear DNA (ITS + ETS), three plastid regions and one low-copy nuclear gene were sampled from 163 exemplars of Orobanche from across the native geographic range in order to infer a detailed phylogeny. Together with comprehensive data on the parasites' native host ranges, associations between phylogenetic lineages and host specificity are tested.Key resultsWithin the two currently recognized species of O. sect. Gymnocaulis, seven strongly supported clades were found. While commonly sympatric, members of these clades each had unique host associations. Strong support for cryptic host-specific diversity was also found in sect. Nothaphyllon, while other taxonomic species were well supported. We also find strong evidence for multiple amphitropical dispersals from central North America into South America.ConclusionsHost-switching is an important driver of diversification in western hemisphere broomrapes, where host specificity has been grossly underestimated. More broadly, host specificity and host-switching probably play fundamental roles in the speciation of parasitic plants.
| S-EPMC5091723 | biostudies-literature
Project description:Different species of bat can be morphologically very similar. In order to estimate the amount of cryptic diversity among European bats we screened the intra- and interspecific genetic variation in 26 European vespertilionid bat species. We sequenced the DNA of subunit 1 of the mitochondrial protein NADH dehydrogenase (ND1) from several individuals of a species, which were sampled in a variety of geographical regions. A phylogeny based on the mitochondrial (mt) DNA data is in good agreement with the current classification in the family. Highly divergent mitochondrial lineages were found in two taxa, which differed in at least 11% of their ND1 sequence. The two mtDNA lineages in Plecotus austriacus correlated with the two subspecies Plecotus austriacus austriacus and Plecotus austriacus kolombatovici. The two mtDNA lineages in Myotis mystacinus were partitioned among two morphotypes. The evidence for two new bat species within Europe is discussed. Convergent adaptive evolution might have contributed to the morphological similarity among distantly related species if they occupy similar ecological niches. Closely related species may differ in their ecology but not necessarily in their morphology. On the other hand, two morphologically clearly different species (Eptesicus serotinus and Eptesicus nilssonii) were found to be genetically very similar. Neither morphological nor mitochondrial DNA sequence analysis alone can be guaranteed to identify species.
| S-EPMC1088815 | biostudies-other
Project description:Although the presence of cryptic host specificity has been documented in Blastocystis, differences in infection rates and high genetic polymorphism within and between populations of some subtypes (ST) have impeded the clarification of the generalist or specialist specificity of this parasite. We assessed the genetic variability and host specificity of Blastocystis spp. in wild howler monkeys from two rainforest areas in the southeastern region of Mexico. Fecal samples of 225 Alouatta palliata (59) and A. pigra (166) monkeys, belonging to 16 sylvatic sites, were analyzed for infection with Blastocystis ST using a region of the small subunit rDNA (SSUrDNA) gene as a marker. Phylogenetic and genetic diversity analyses were performed according to the geographic areas where the monkeys were found. Blastocystis ST2 was the most abundant (91.9%), followed by ST1 and ST8 with 4.6% and 3.5%, respectively; no association between Blastocystis ST and Alouatta species was observed. SSUrDNA sequences in GenBank from human and non-human primates (NHP) were used as ST references and included in population analyses. The haplotype network trees exhibited different distributions: ST1 showed a generalist profile since several haplotypes from different animals were homogeneously distributed with few mutational changes. For ST2, a major dispersion center grouped the Mexican samples, and high mutational differences were observed between NHP. Furthermore, nucleotide and haplotype diversity values, as well as migration and genetic differentiation indexes, showed contrasting values for ST1 and ST2. These data suggest that ST1 populations are only minimally differentiated, while ST2 populations in humans are highly differentiated from those of NHP. The host generalist and specialist specificities exhibited by ST1 and ST2 Blastocystis populations indicate distinct adaptation processes. Because ST1 exhibits a generalist profile, this haplotype can be considered a metapopulation; in contrast, ST2 exists as a set of local populations with preferences for either humans or NHP.
| S-EPMC5215913 | biostudies-literature
Project description:Parasitoids are hyperdiverse and can contain morphologically and functionally cryptic species, making them challenging to study. Parasitoid speciation can arise from specialisation on niches or diverging hosts. However, which process dominates is unclear because cospeciation across multiple parasitoid and host species has rarely been tested. Host specificity and trophic interactions of the parasitoids of psyllids (Hemiptera) remain mostly unknown, but these factors are fundamentally important for understanding of species diversity, and have important applied implications for biological control.We sampled diverse parasitoid communities from eight Eucalyptus-feeding psyllid species in the genera Cardiaspina and Spondyliaspis, and characterised their phylogenetic and trophic relationships using a novel approach that forensically linked emerging parasitoids with the presence of their DNA in post-emergence insect mummies. We also tested whether parasitoids have cospeciated with their psyllid hosts. The parasitoid communities included three Psyllaephagus morphospecies (two primary and, unexpectedly, one heteronomous hyperparasitoid that uses different host species for male and female development), and the hyperparasitoid, Coccidoctonus psyllae. However, the number of genetically delimited Psyllaephagus species was three times higher than the number of recognisable morphospecies, while the hyperparasitoid formed a single generalist species. In spite of this, cophylogenetic analysis revealed unprecedented codivergence of this hyperparasitoid with its primary parasitoid host, suggesting that this single hyperparasitoid species is possibly diverging into host-specific species. Overall, parasitoid and hyperparasitoid diversification was characterised by functional conservation of morphospecies, high host specificity and some host switching between sympatric psyllid hosts.We conclude that host specialisation, host codivergence and host switching are important factors driving the species diversity of endoparasitoid communities of specialist host herbivores. Specialisation in parasitoids can also result in heteronomous life histories that may be more common than appreciated. A host generalist strategy may be rare in endoparasitoids of specialist herbivores despite the high conservation of morphology and trophic roles, and endoparasitoid species richness is likely to be much higher than previously estimated. This also implies that the success of biological control requires detailed investigation to enable accurate identification of parasitoid-host interactions before candidate parasitoid species are selected as biological control agents for target pests.
| S-EPMC5461677 | biostudies-literature
Project description:Proteins are dynamic molecules that undergo conformational changes to a broad spectrum of different excited states. Unfortunately, the small populations of these states make it difficult to determine their structures or functional implications. Computer simulations are an increasingly powerful means to identify and characterize functionally relevant excited states. However, this advance has uncovered a further challenge: it can be extremely difficult to identify the most salient features of large simulation data sets. We reasoned that many functionally relevant conformational changes are likely to involve large, cooperative changes to the surfaces that are available to interact with potential binding partners. To examine this hypothesis, we introduce a method that returns a prioritized list of potentially functional conformational changes by segmenting protein structures into clusters of residues that undergo cooperative changes in their solvent exposure, along with the hierarchy of interactions between these groups. We term these groups exposons to distinguish them from other types of clusters that arise in this analysis and others. We demonstrate, using three different model systems, that this method identifies experimentally validated and functionally relevant conformational changes, including conformational switches, allosteric coupling, and cryptic pockets. Our results suggest that key functional sites are hubs in the network of exposons. As a further test of the predictive power of this approach, we apply it to discover cryptic allosteric sites in two different ?-lactamase enzymes that are widespread sources of antibiotic resistance. Experimental tests confirm our predictions for both systems. Importantly, we provide the first evidence, to our knowledge, for a cryptic allosteric site in CTX-M-9 ?-lactamase. Experimentally testing this prediction did not require any mutations and revealed that this site exerts the most potent allosteric control over activity of any pockets found in ?-lactamases to date. Discovery of a similar pocket that was previously overlooked in the well-studied TEM-1 ?-lactamase demonstrates the utility of exposons.
| S-EPMC6400826 | biostudies-literature
Project description:Sequencing of A. sarmentosa diversity assessment
| PRJEB35174 | ENA
Project description:Modular type I polyketide synthases (PKS) produce a vast array of bacterial metabolites with highly diverse biological functions. Notably, all known polyketides were isolated from aerobic bacteria, and yet no example has been reported for strict anaerobes. In this study we explored the diversity and distribution of PKS genes in the genus Clostridium. In addition to comparative genomic analyses combined with predictions of modular type I polyketide synthase (PKS) gene clusters in sequenced genomes of Clostridium spp., a representative selection of other species inhabiting a variety of ecological niches was investigated by PCR screening for PKS genes. Our data reveal that all studied pathogenic Clostridium spp. are devoid of putative PKS genes. In stark contrast, cryptic PKS genes are widespread in genomes of non-pathogenic Clostridium species. According to phylogenetic analyses, the Clostridium PKS genes have unusual and diverse origins. However, reverse transcription quantitative PCR demonstrates that these genes are silent under standard cultivation conditions, explaining why the related metabolites have been overlooked until now. This study presents clostridia as a putative source for novel bioactive polyketides.
| S-EPMC3250452 | biostudies-literature
Project description:Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystem-level questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective.
| S-EPMC5095379 | biostudies-literature
Project description:Understanding how to control cell fate is crucial in biology, medical science and engineering. In this study, we introduce a method that uses an intracellular protein as a trigger for regulating human cell fate. The ON/OFF translational switches, composed of an intracellular protein L7Ae and its binding RNA motif, regulate the expression of a desired target protein and control two distinct apoptosis pathways in target human cells. Combined use of the switches demonstrates that a specific protein can simultaneously repress and activate the translation of two different mRNAs: one protein achieves both up- and downregulation of two different proteins/pathways. A genome-encoded protein fused to L7Ae controlled apoptosis in both directions (death or survival) depending on its cellular expression. The method has potential for curing cellular defects or improving the intracellular production of useful molecules by bypassing or rewiring intrinsic signal networks.
| S-EPMC3105309 | biostudies-other