Characterization and potential evolutionary impact of transposable elements in the genome of Cochliobolus heterostrophus

Background

Cochliobolus heterostrophus is a dothideomycete that causes Southern Corn Leaf Blight disease. There are two races, race O and race T that differ by the absence (race O) and presence (race T) of ~ 1.2-Mb of DNA encoding genes responsible for the production of T-toxin, which makes race T much more virulent than race O. The presence of repetitive elements in fungal genomes is considered to be an important source of genetic variability between different species.

Results

A detailed analysis of class I and II TEs identified in the near complete genome sequence of race O was performed. In total in race O, 12 new families of transposons were identified. In silico evidence of recent activity was found for many of the transposons and analyses of expressed sequence tags (ESTs) demonstrated that these elements were actively transcribed. Various potentially active TEs were found near coding regions and may modify the expression and structure of these genes by acting as ectopic recombination sites. Transposons were found on scaffolds carrying polyketide synthase encoding genes, responsible for production of T-toxin in race T. Strong evidence of ectopic recombination was found, demonstrating that TEs can play an important role in the modulation of genome architecture of this species. The Repeat Induced Point mutation (RIP) silencing mechanism was shown to have high specificity in C. heterostrophus, acting only on transposons near coding regions.

Conclusions

New families of transposons were identified. In C. heterostrophus, the RIP silencing mechanism is efficient and selective. The co-localization of effector genes and TEs, therefore, exposes those genes to high rates of point mutations. This may accelerate the rate of evolution of these genes, providing a potential advantage for the host. Additionally, it was shown that ectopic recombination promoted by TEs appears to be the major event in the genome reorganization of this species and that a large number of elements are still potentially active. So, this study provides information about the potential impact of TEs on the evolution of C. heterostrophus.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-536) contains supplementary material, which is available to authorized users.     

Array2BIO: from microarray expression data to functional annotation of co-regulated genes

Background  

There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility.     

Ability of thymic lymphocytes to alter CFU kinetics in radiation chimeras.

It is known that the poor colony-forming ability of B6 bone marrow transplanted into B6D2F1 hybrids can be improved if B6 lymphocytes are given in addition. It was recently reported that the augmenting lymphocytes decrease the doubling time of differentiating hemopoietic cells. To determine whether thymus cells alter the self-renewal of CFUs in this parent leads to F1 combination, retransplantation and 3H-thymidine 'suicide' were employed as methods to determine the cell-division rate. We have observed that in the presence of thymocytes, parental bone marrow cells are seeded more efficiently in the spleen, and the lag phase of the CFUs growth curve is shortened. However, thymic lymphocytes do not increase the slope of the exponential growth phase of CFUs.     

Cooperation of nonsyngeneic tolerant lymphocytes: genetic restriction.

We have used a previously devised in vivo experimental model to investigate the ability of mouse thymus-dependent (T) and bone marrow-derived (B) lymphocytes to cooperate in immune (humoral) rejection of rat Yoshida ascites sarcoma (YAS). Because of conflicting reports in the literature concerning the effectiveness of T-B cooperation across major histocompatibility complex (MHC) barriers, we explored the interaction of T and B lymphocytes from mutually tolerant animals. Tolerance was achieved by establishing radiation chimeras of B6 → B6D2F₁ and D2 → B6D2F₁ constitutions. Chimeras' erythrocytes and spleen cells were shown by serological analysis to be the donor type. When the chimera was to serve as the tumor host or B-cell source, it was thymectomized prior to irradiation and reconstitution (TIR). Tolerance was evaluated by noting the inability of chimeric spleen cells to effect graft-versus-host damage upon injection into TIR host-type mice and the markedly reduced anti-host-type reactivity in short-term [³H]thymidine-uptake tests. Successful cooperation, manifested by YAS rejection, was seen whenever donor T and host B lymphocytes were syngeneic. Parental (P) T cells enabled F₁ TIR mice to reject YAS, but the reciprocal was not true: F₁ donor T cells did not cooperate with B cells in parental TIR mice. However, when the host B lymphocytes were tolerant P cells, i.e., in a P → F₁ TIR chimera, injected F₁ T lymphocytes did cooperate successfully. The final test of allogeneic T and B cells gave the clear-cut negative answer that, even when tolerant mice are used as sources of lymphocytes, cooperation does not occur. These results therefore confirm that T and B lymphocytes must at least share one MHC haplotype in order to cooperate.     

Diversity of free-living ‘naked’ amoeboid organisms

Amoeboid organisms are phylogenetically diverse, some being more closely related to plants or metazoans than to each other. Amoeboid organisms are ecologically successful, having been isolated on all continents, including Antarctica, as well as being the main predators controlling bacterial populations in soil. The classification of these organisms has historically relied upon morphological characteristics. The application of electron microscopy, comparison of enzymic profiles after electrophoretic separation, and analysis of nucleic acid fractions have provided reliable bases for classifying amoeboid organisms. The extent of diversity of these organisms has been recognized, as methods to detect, culture, characterize and identify them has increased. It is reasonable to anticipate that the current 40 000 species of protists will increase substantially as amoeboid organisms are cultivated from poorly accessible niches and from extreme environs.