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Microbial Eukaryotes (microbial + eukaryote)

Distribution by Scientific Domains

Life Sciences	100%

Selected Abstracts

A bioinformatic tool for analysis of EST transcript abundance during infection-related development by Magnaporthe grisea

MOLECULAR PLANT PATHOLOGY, Issue 5 2005
DARREN M. SOANES
SUMMARY Information regarding the levels of mRNA transcript abundance under different conditions, or in specific tissue types, can be obtained by analysis of the frequency of EST sequences in randomly sequenced cDNA libraries. Here we report a bioinformatics tool, which provides a means of identifying genes that are differentially expressed during pathogenesis-related development by the rice blast fungus Magnaporthe grisea. A total of 31 534 M. grisea ESTs were obtained from dbEST at NCBI, clustered into 8821 unique sequences (unisequences) and manually annotated. Transcript profiles were then calculated for 958 unigenes identified from eight different cDNA libraries. The data were integrated into the Consortium for Functional Genomics of Microbial Eukaryotes (COGEME) database (http://cogeme.ex.ac.uk/) and a web-based front end was designed to allow users to access and interrogate the generated datasets. [source]

A Hierarchical View of Convergent Evolution in Microbial Eukaryotes,

THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2008
BRIAN S. LEANDER
ABSTRACT. Distinguishing convergent evolution from other causes of similarity in organisms is necessary for reconstructing phylogenetic relationships, inferring patterns of character evolution, and investigating the forces of natural selection. In contrast to animals and land plants, the pervasiveness and adaptive significance of convergent evolution in microbes has yet to be systematically explored or articulated. Convergent evolution in microbial eukaryotes, for instance, often involves very distantly related lineages with relatively limited repertoires of morphological features. These large phylogenetic distances weaken the role of ancestral developmental programs on the subsequent evolution of morphological characters, making convergent evolution between very distantly related lineages fundamentally different from convergent evolution between closely related lineages. This suggests that examples of convergence at different levels in the phylogenetic hierarchy offer different clues about the causes and processes of macroevolutionary diversification. Accordingly (and despite opinions to the contrary), I recognize three broad and overlapping categories of phenotypic convergence,"parallel", "proximate" and "ultimate",that represent either (1) subcellular analogues, (2) subcellular analogues to multicellular systems (and vice versa), or (3) multicellular analogues. Microbial eukaryotes living in planktonic environments, interstitial environments, and the intestinal environments of metazoan hosts provide compelling examples of ultimate convergence. After describing selected examples in microbial eukaryotes, I suggest some future directions needed to more fully understand the hierarchical structure of convergent evolution and the overall history of life. [source]

Complex phylogeographic patterns in the freshwater alga Synura provide new insights into ubiquity vs. endemism in microbial eukaryotes

MOLECULAR ECOLOGY, Issue 19 2010
SUNG MIN BOO
Abstract The global distribution, abundance, and diversity of microscopic freshwater algae demonstrate an ability to overcome significant barriers such as dry land and oceans by exploiting a range of biotic and abiotic colonization vectors. If these vectors are considered unlimited and colonization occurs in proportion to population size, then globally ubiquitous distributions are predicted to arise. This model contrasts with observations that many freshwater microalgal taxa possess true biogeographies. Here, using a concatenated multigene data set, we study the phylogeography of the freshwater heterokont alga Synura petersenii sensu lato. Our results suggest that this Synura morphotaxon contains both cosmopolitan and regionally endemic cryptic species, co-occurring in some cases, and masked by a common ultrastructural morphology. Phylogenies based on both proteins (seven protein-coding plastid and mitochondrial genes) and DNA (nine genes including ITS and 18S rDNA) reveal pronounced biogeographic delineations within phylotypes of this cryptic species complex while retaining one clade that is globally distributed. Relaxed molecular clock calculations, constrained by fossil records, suggest that the genus Synura is considerably older than currently proposed. The availability of tectonically relevant geological time (107,108 years) has enabled the development of the observed, complex biogeographic patterns. Our comprehensive analysis of freshwater algal biogeography suggests that neither ubiquity nor endemism wholly explains global patterns of microbial eukaryote distribution and that processes of dispersal remain poorly understood. [source]

Molecular Evidence that Phylogenetically Diverged Ciliates Are Active in Microbial Mats of Deep-Sea Cold-Seep Sediment

THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 1 2010
KIYOTAKA TAKISHITA
ABSTRACT. Cold seeps are areas of the seafloor where hydrogen sulfide- and methane-rich fluid seepage occurs, often sustaining chemosynthetic ecosystems. It is well known that both archaea and bacteria oxidize sulfides and methane to produce chemical energy and that several endemic animals use this energy to thrive in cold seeps. On the other hand, there is little knowledge regarding diversity and ecology of microbial eukaryotes in this ecosystem. In this study we isolated environmental RNA and DNA from microbial mats of cold-seep sediment in Sagami Bay, Japan, and retrieved eukaryotic small-subunit ribosomal RNA sequences with polymerase chain reaction methods followed by clone library construction. Most RNA-derived clones obtained were from ciliates, although DNA-derived clones were mainly from the fungus Cryptococcus curvatus, suggesting that ciliates are active in the environment. The ciliate sequences were phylogenetically diverse, and represented eight known class lineages as well as undesignated lineages. Because most ciliates are bacterivorous, it is highly likely that the ciliates for which sequences were recovered play a role in the food web of this ecosystem as grazers of microbial mats. In addition, given that the environment studied is under highly reduced (anoxic) conditions, based on the prokaryotic community structure deduced from T-RFLP profiles, the ciliates detected may be obligatory or facultative anaerobes. [source]

A Hierarchical View of Convergent Evolution in Microbial Eukaryotes,

Evolution and implications of genome rearrangements in ciliates

THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2005
LAURA A. KATZ
We are exploring genome evolution in diverse ciliates to assess whether patterns of protein evolution correspond to the presence of genome duality, and to levels of genome rearrangements among ciliates. Ciliate genomes contain an estimated 25,000,35,000 genes, a number higher than that of other characterized microbial eukaryotes and on a similar scale to that of humans and Arabidopsis thaliana. We have previously hypothesized that the divergence among ciliate proteins, and the accumulation of paralogs within ciliate taxa, is due to differential selection on the functional macronucleus and the transcriptionally inactive micronucleus. To assess this hypothesis, we are expanding our analyses of protein-coding gene sequences to compare the fate of proteins in ciliates to that of other eukaryotes, and to test whether the most divergent ciliate proteins are found in ciliates with extensively processed genomes. These analyses, combined with a phylogenetic perspective that reveals multiple origins of extensive fragmentation in ciliates, provide a possible explanation for the large genome size and diversity of proteins in ciliates. [source]

Developmental genome processing and protein evolution in the ciliate Chilodonella uncinata

THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2005
REBECCA A. ZUFALL
Ciliates are microbial eukaryotes with dual genomes, one present in the transcriptionally inactive germline micronucleus (MIC) and the other in the somatic macronucleus (MAC). In the development of the MAC from the MIC, ciliates process their genomes by chromosomal fragmentation, excision of internal excised sequences (IESs), and amplification of chromosomes. Chilodonella uncinata is in a class of ciliates, Phyllopharyngea, that undergo extensive processing to generate MACs containing thousands of gene-sized chromosomes. Previous analyses suggest that sequences involved in this processing are highly variable among ciliate lineages. In this study, we examine cis-acting signals involved in the elimination of IESs in C. uncinata in order to understand the phylogenetic level at which processing signals are conserved. In addition, we are testing the hypothesis that the differential selection on dual genomes in ciliates allows unusually rapid divergence among paralogs of protein coding genes. [source]

Molecular markers for assessing community diversity of coastal ciliates

THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2005
MARY DOHERTY
Biogeography of microbial eukaryotes is widely debated. While some claim that all microbial organisms have a cosmopolitan distribution, other data suggest evidence of endemism. To assess these hypotheses for the distribution of ciliates in the orders Choreotrichia and Oligotrichia, coastal community samples were taken from Long Island Sound. We are obtaining sequences of SSU rRNA, ITS rRNA, and mitochondrial genes to use as molecular markers for assessing gene flow across time and space. These data will serve as a basis for continued study of phylogeographic distribution of Choreotrichia and Oligotrichia. [source]

Rapid diversification of mating systems in ciliates

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009
SUJAL S. PHADKE
Ciliates are a diverse group of microbial eukaryotes that exhibit tremendous variety in several aspects of their mating systems. To understand the evolutionary forces driving mating system diversification in ciliates, we use a comparative approach synthesizing data from many ciliate species in light of recent phylogenetic analyses. Specifically, we investigate the evolution of number of mating types, mode of mating type inheritance, and the molecular determinants of mating types across the taxonomic diversity of ciliates, with an emphasis on three well-studied genera: Tetrahymena, Paramecium, and Euplotes. We find that there have been many transitions in the number of mating types, and that the requirement of nuclear reorganization may be a more important factor than genetic exchange in determining the optimum number of mating types in a species. We also find that the molecular determinants of mating types and mode of inheritance are evolving under different constraints in different lineages of ciliates. Our results emphasize the need for further detailed examination of mating systems in understudied ciliate lineages. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 187,197. [source]