Rare Recombination Events Research Articles

Molecular Evolution and Diversity of Conus Peptide Toxins, as Revealed by Gene Structure and Intron Sequence Analyses

Cone snails, which are predatory marine gastropods, produce a cocktail of venoms used for predation, defense and competition. The major venom component, conotoxin, has received significant attention because it is useful in neuroscience research, drug development and molecular diversity studies. In this study, we report the genomic characterization of nine conotoxin gene superfamilies from 18 Conus species and investigate the relationships among conotoxin gene structure, molecular evolution and diversity. The I1, I2, M, O2, O3, P, S, and T superfamily precursors all contain three exons and two introns, while A superfamily members contain two exons and one intron. The introns are conserved within a certain gene superfamily, and also conserved across different Conus species, but divergent among different superfamilies. The intronic sequences contain many simple repeat sequences and regulatory elements that may influence conotoxin gene expression. Furthermore, due to the unique gene structure of conotoxins, the base substitution rates and the number of positively selected sites vary greatly among exons. Many more point mutations and trinucleotide indels were observed in the mature peptide exon than in the other exons. In addition, the first example of alternative splicing in conotoxin genes was found. These results suggest that the diversity of conotoxin genes has been shaped by point mutations and indels, as well as rare gene recombination or alternative splicing events, and that the unique gene structures could have made a contribution to the evolution of conotoxin genes.

PCR assays for the identification of rare recombination types from VP1 to 3D genomic region of vaccine derived poliovirus strains

Poliomyelitis has been effectively controlled by the use of inactivated poliovirus vaccine (IPV) or trivalent live attenuated oral poliovirus vaccine (OPV). Since 1964, the use of OPV in mass vaccinations has resulted in drastic reductions of the number of poliomyelitis cases caused by wild-type polioviruses. However, the characterization of OPV derivatives with increased neurovirulence, constituted a real problem with respect to OPV safety. Mutations at attenuating sites of the genome and recombination events between Sabin strains of the trivalent OPV vaccine have been correlated with the loss of the attenuated phenotype of OPV strains and the acquisition of traits characteristic of wild polioviruses. In consequence, early detection and characterization of recombinant evolved derivatives of vaccine strains is highly important. In this report, ten PCR assays are described which allow for the identification of rare recombination events located in VP1, 2A, 2C, 3A, 3C and 3D genomic regions and predominant recombination events located in 2C and 3D genomic regions of OPV derivatives. These assays could be readily implemented in diagnostics laboratories lacking sequencing facilities as a first approach for the early detection and characterization of recombinant OPV derivatives.

Abstract 19048: Clonal Analysis of Cardiac Tissue Formation Reveals Limited Proliferative Capacity of Mature Cardiomyocytes During Development

Strong evidence supports the ability of the heart to generate new cardiomyocytes during development and in response to injury albeit at a very low rate. However, it still remains unclear whether the newly formed cells originate from cardiac progenitor/stem cells or pre-existing cardiomyocytes capable of proliferation. Identification of the cell populations responsible for new cardiomyocyte formation is imperative towards the development of novel clinical strategies. Herein, we hypothesized that cardiac progenitor cells are the main source of the new cardiomyocytes generated during development while contribution of pre-existing cardiomyocytes is limited. For clonal analysis of cardiomyocyte formation we utilized a stochastic multicolor reporter system called Rainbow that allows random marking of cells with the fluorescent proteins Cerulean (CFP), mOrange or mCherry upon Cre-mediated recombination. Selective labeling of cardiomyocytes was achieved by crossing Rainbow mice αMHC-CreER mice. As control Actin-CreER;Rainbow mice were used where all types of cells can be labeled. Rare recombination events were induced at embryonic day E12.5 and clone formation and expansion were retrospectively analyzed at different time-points from E15.5 to postnatal day P30. To determine at which developmental stage cardiac cells lose their ability to proliferate, recombination was induced at different time-points from early embryonic to postnatal life and analysis was performed at P30. αMHC-CreER;Rainbow hearts exhibited mainly single colored cells randomly distributed within the tissue. A few doublets and some rare four-cell clones were observed. In Actin-CreER;Rainbow mice, we observed clones ranging from two to more than twenty cells. Clone formation and expansion decreased with age. Interestingly we observed clones consisting of more than one cell types indicating the existence of a common progenitor cell. We show that αMHC-positive cardiomyocyte proliferation is limited during development while non-αMHC expressing cells exhibit clonal expansion. Our results suggest a possible contribution of cardiac progenitor cells even during late cardiovascular development.

Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii

Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii

Abstract 173: Clonal Analysis Reveals Limited Proliferative Capacity of Mature Cardiomyocytes during Embryonic Development.

There is growing evidence that supports the ability of the heart to generate new cardiomyocytes during development and in response to injury albeit at a very low rate. It still remains unclear whether the newly generated cells originate from cardiac progenitor/stem cells or from pre-existing cardiomyocytes that re-enter the cell cycle. Understanding the cellular mechanisms regulating new cardiomyocyte formation is imperative towards the development of novel clinical strategies. We assessed the hypothesis that the cardiomyocytes generated during cardiac development are derived from cardiac progenitor cells and to a lesser extent form proliferating cardiomyocytes. We performed clonal analysis of cardiomyocyte formation by utilizing a stochastic multicolor reporter system (Rainbow) that allows random labeling of cells with three fluorescent proteins upon Cre-mediated recombination. Rainbow mice were crossed to αMHC-CreER mice for selective marking of cardiomyocytes or to Actin-CreER mice where all types of cells can be labeled. We induced rare recombination events at embryonic day E12.5 and clonal expansion of labeled cells was retrospectively analyzed at different time-points from E15.5 to postnatal day P30. To determine at which developmental stage cardiac cells lose their ability to proliferate, recombination was induced at different time-points from early embryonic to postnatal life and analysis was performed at P30. For each time-point, data was collected from ten mice. In αMHC-CreER;Rainbow mice, we observed mainly single cell labeling, a few doublets and some rare four-cell clones. At the same time-points, Actin-CreER;Rainbow hearts exhibited a large number of clones ranging from doublets to clones of more than twenty cells. Interestingly, clone formation and expansion was reduced with age. In conclusion, our results indicate that αMHC-positive cardiomyocyte proliferation is limited during development. On the other hand, non-αMHC expressing cells exhibited clonal expansion suggesting the possible contribution of cardiac progenitors even during late cardiovascular development.

Xenotropic MLV envelope proteins induce tumor cells to secrete factors that promote the formation of immature blood vessels

BackgroundXenotropic Murine leukemia virus-Related Virus (XMRV) is a γ-retrovirus initially reported to be present within familial human prostate tumors and the blood of patients with chronic fatigue syndrome. Subsequent studies however were unable to replicate these findings, and there is now compelling evidence that the virus evolved through rare retroviral recombination events in human tumor cell lines established through murine xenograft experiments. There is also no direct evidence that XMRV infection has any functional effects that contribute to tumor pathogenesis.ResultsHerein we describe an additional xenotropic MLV, “B4rv”, found in a cell line derived from xenograft experiments with the human prostate cancer LNCaP cell line. When injected subcutaneously in nude mice, LNCaP cells infected with XMRV or B4rv formed larger tumors that were highly hemorrhagic and displayed poor pericyte/smooth muscle cell (SMC) investment, markers of increased metastatic potential. Conditioned media derived from XMRV- or B4rv-infected LNCaPs, but not an amphotropic MLV control virus infected LNCaPs, profoundly decreased expression of marker genes in cultured SMC, consistent with inhibition of SMC differentiation/maturation. Similar effects were seen with a chimeric virus of the amphotropic MLV control virus containing the XMRV env gene, but not with an XMRV chimeric virus containing the amphotropic MLV env gene. UV-inactivated XMRV and pseudovirions that were pseudotyped with XMRV envelope protein also produce conditioned media that down-regulated SMC marker gene expression in vitro.ConclusionsTogether these results indicate that xenotropic MLV envelope proteins are sufficient to induce the production of factors by tumor cells that suppress vascular SMC differentiation, providing evidence for a novel mechanism by which xenotropic MLVs might alter tumor pathogenesis by disrupting tumor vascular maturation. Although it is highly unlikely that either XMRV or B4Rv themselves infect humans and are pathogenic, the results suggest that xenograft approaches commonly used in the study of human cancer promote the evolution of novel retroviruses with pathogenic properties.

MASTR: A Technique for Mosaic Mutant Analysis with Spatial and Temporal Control of Recombination Using Conditional Floxed Alleles in Mice

Mosaic mutant analysis, the study of cellular defects in scattered mutant cells in a wild-type environment, is a powerful approach for identifying critical functions of genes and has been applied extensively to invertebrate model organisms. A highly versatile technique has been developed in mouse: MASTR (mosaic mutant analysis with spatial and temporal control of recombination), which utilizes the increasing number of floxed alleles and simultaneously combines conditional gene mutagenesis and cell marking for fate analysis. A targeted allele (R26(MASTR)) was engineered; the allele expresses a GFPcre fusion protein following FLP-mediated recombination, which serves the dual function of deleting floxed alleles and marking mutant cells with GFP. Within 24 hr of tamoxifen administration to R26(MASTR) mice carrying an inducible FlpoER transgene and a floxed allele, nearly all GFP-expressing cells have a mutant allele. The fate of single cells lacking FGF8 or SHH signaling in the developing hindbrain was analyzed using MASTR, and it was revealed that there is only a short time window when neural progenitors require FGFR1 for viability and that granule cell precursors differentiate rapidly when SMO is lost. MASTR is a powerful tool that provides cell-type-specific (spatial) and temporal marking of mosaic mutant cells and is broadly applicable to developmental, cancer, and adult stem cell studies.

Dissecting Genotype × Environment Interactions and Trait Correlations Present in the Pee Dee Cotton Germplasm Collection following Seventy Years of Plant Breeding

ABSTRACTGenotype × environment (G × E) interactions and trait correlations significantly impact efforts to develop high‐yield, high‐quality, and environmentally stable Upland cotton (Gossypium hirsutum L.) cultivars. Knowledge of both can and should be used to design optimal breeding programs and effective selection criteria. In this study, we examined the G × E interactions and trait correlations present in the 70‐yr Pee Dee cotton germplasm enhancement program. Since beginning in 1935, the Pee Dee program has employed a variety of unique germplasm and breeding methods to release >80 improved germplasm lines and cultivars. Results suggest that significant G × E interactions exist for several agronomic and fiber quality performance traits that are mostly due to changes in magnitude. Negative genotypic correlations still persist between lint percent/lint yield and fiber length/fiber strength. However, apparently the breeding methods and selection criteria used over 70 yr have lessened the negative relationship between agronomic performance and fiber quality over time to some degree. The results provide cotton breeders a resource to select specific Pee Dee germplasm lines for increased environmental stability. Cotton breeders can also use the information herein to select specific Pee Dee germplasm lines that represent rare recombination events that combine high yield and fiber quality potential.

Determinants of the Drosophila Odorant Receptor Pattern

In most olfactory systems studied to date, neurons that express the same odorant receptor (Or) gene are scattered across sensory epithelia, intermingled with neurons that express different Or genes. In Drosophila, olfactory sensilla that express the same Or gene are dispersed on the antenna and the maxillary palp. Here we show that Or identity is specified in a spatially stereotyped pattern by the cell-autonomous activity of the transcriptional regulators Engrailed and Dachshund. Olfactory sensilla then become highly motile and disperse beneath the epidermis. Thus, positional information and cell motility underlie the dispersed patterns of Drosophila Or gene expression.

Assessment of the genetic diversity of the Tunisian citrus rootstock germplasm

BackgroundCitrus represents a substantial income for farmers in the Mediterranean Basin. However, the Mediterranean citrus industry faces increasing biotic and abiotic constraints. Therefore the breeding and selection of new rootstocks are now of the utmost importance. In Tunisia, in addition to sour orange, the most widespread traditional rootstock of the Mediterranean area, other citrus rootstocks and well adapted to local environmental conditions, are traditionally used and should be important genetic resources for breeding. To characterize the diversity of Tunisian citrus rootstocks, two hundred and one local accessions belonging to four facultative apomictic species (C. aurantium, sour orange; C. sinensis, orange; C. limon, lemon; and C. aurantifolia, lime) were collected and genotyped using 20 nuclear SSR markers and four indel mitochondrial markers. Multi-locus genotypes (MLGs) were compared to references from French and Spanish collections.ResultsThe differentiation of the four varietal groups was well-marked. The groups displayed a relatively high allelic diversity, primarily due to very high heterozygosity. Sixteen distinct MLGs were identified. Ten of these were noted in sour oranges. However, the majority of the analysed sour orange accessions corresponded with only two MLGs, differentiated by a single allele, likely due to a mutation. The most frequent MLG is shared with the reference sour oranges. No polymorphism was found within the sweet orange group. Two MLGs, differentiated by a single locus, were noted in lemon. The predominant MLG was shared with the reference lemons. Limes were represented by three genotypes. Two corresponded to the 'Mexican lime' and 'limonette de Marrakech' references. The MLG of 'Chiiri' lime was unique.ConclusionsThe Tunisian citrus rootstock genetic diversity is predominantly due to high heterozygosity and differentiation between the four varietal groups. The phenotypic diversity within the varietal groups has resulted from multiple introductions, somatic mutations and rare sexual recombination events. Finally, this diversity study enabled the identification of a core sample of accessions for further physiological and agronomical evaluations. These core accessions will be integrated into citrus rootstock breeding programs for the Mediterranean Basin.

Highly Efficient Staphylococcus carnosus Mutant Selection System Based on Suicidal Bacteriocin Activation

Strains from various staphylococcal species produce bacteriocin peptides, which are thought to play important roles in bacterial competition and offer interesting biotechnological avenues. Many bacteriocins are secreted as inactive prepeptides with subsequent activation by specific proteolytic cleavage. By deletion of the protease gene gdmP in Staphylococcus gallinarum Tü3928, which produces the highly active lanthionine-containing bacteriocin gallidermin (lantibiotic), a strain was created producing inactive pregallidermin. On this basis, a new suicidal mutant selection system in the food-grade bacterium Staphylococcus carnosus was developed. Whereas pregallidermin was inactive against S. carnosus, it exerted potent bactericidal activity toward GdmP-secreting S. carnosus strains. To take advantage of this effect, gdmP was cloned in plasmid vectors used for random transposon mutagenesis or targeted allelic replacement of chromosomal genes. Both mutagenesis strategies rely on rare recombination events, and it has remained difficult and laborious to identify mutants among a vast majority of bacterial clones that still contain the delivery vectors. The gdmP-expressing plasmids pGS1 and pGS2 enabled very fast, easy, and reliable identification of transposon and gene replacement mutants, respectively. Mutant selection in the presence of pregallidermin caused suicidal inactivation of all clones that had retained the plasmids and allowed growth of only plasmid-cured mutants. Efficiency of mutant identification was several magnitudes higher than standard screening for the absence of plasmid-encoded antibiotic resistance markers and reached 100% specificity. Thus, the new pregallidermin-based mutant selection system represents a substantial improvement of staphylococcal mutagenesis methodology.

Downregulation of APOBEC3G by xenotropic murine leukemia-virus related virus (XMRV) in prostate cancer cells

BackgroundXenotropic murine leukemia virus (MLV)-related virus (XMRV) is a gammaretrovirus that was discovered in prostate cancer tissues. Recently, it has been proposed that XMRV is a laboratory contaminant and may have originated via a rare recombination event. Host restriction factor APOBEC3G (A3G) has been reported to severely restrict XMRV replication in human peripheral blood mononuclear cells. Interestingly, XMRV infects and replicates efficiently in prostate cancer cells of epithelial origin. It has been proposed that due to lack off or very low levels of A3G protein XMRV is able to productively replicate in these cells.FindingsThis report builds on and challenges the published data on the absence of A3G protein in prostate epithelial cells lines. We demonstrate the presence of A3G in prostate epithelial cell lines (LNCaP and DU145) by western blot and mass spectrometry. We believe the discrepancy in A3G detection is may be due to selection and sensitivity of A3G antibodies employed in the prior studies. Our results also indicate that XMRV produced from A3G expressing LNCaP cells can infect and replicate in target cells. Most importantly our data reveal downregulation of A3G in XMRV infected LNCaP and DU145 cells.ConclusionsWe propose that XMRV replicates efficiently in prostate epithelial cells by downregulating A3G expression. Given that XMRV lacks accessory proteins such as HIV-1 Vif that are known to counteract A3G function in human cells, our data suggest a novel mechanism by which retroviruses can counteract the antiviral effects of A3G proteins.

A Reevaluation of Rice Mitochondrial Evolution Based on the Complete Sequence of Male-Fertile and Male-Sterile Mitochondrial Genomes

Plant mitochondrial genomes have features that distinguish them radically from their animal counterparts: a high rate of rearrangement, of uptake and loss of DNA sequences, and an extremely low point mutation rate. Perhaps the most unique structural feature of plant mitochondrial DNAs is the presence of large repeated sequences involved in intramolecular and intermolecular recombination. In addition, rare recombination events can occur across shorter repeats, creating rearrangements that result in aberrant phenotypes, including pollen abortion, which is known as cytoplasmic male sterility (CMS). Using next-generation sequencing, we pyrosequenced two rice (Oryza sativa) mitochondrial genomes that belong to the indica subspecies. One genome is normal, while the other carries the wild abortive-CMS. We find that numerous rearrangements in the rice mitochondrial genome occur even between close cytotypes during rice evolution. Unlike maize (Zea mays), a closely related species also belonging to the grass family, integration of plastid sequences did not play a role in the sequence divergence between rice cytotypes. This study also uncovered an excellent candidate for the wild abortive-CMS-encoding gene; like most of the CMS-associated open reading frames that are known in other species, this candidate was created via a rearrangement, is chimeric in structure, possesses predicted transmembrane domains, and coopted the promoter of a genuine mitochondrial gene. Our data give new insights into rice mitochondrial evolution, correcting previous reports.

Clonal analysis reveals common lineage relationships between head muscles and second heart field derivatives in the mouse embryo

Head muscle progenitors in pharyngeal mesoderm are present in close proximity to cells of the second heart field and show overlapping patterns of gene expression. However, it is not clear whether a single progenitor cell gives rise to both heart and head muscles. We now show that this is the case, using a retrospective clonal analysis in which an nlaacZ sequence, converted to functional nlacZ after a rare intragenic recombination event, is targeted to the alpha(c)-actin gene, expressed in all developing skeletal and cardiac muscle. We distinguish two branchiomeric head muscle lineages, which segregate early, both of which also contribute to myocardium. The first gives rise to the temporalis and masseter muscles, which derive from the first branchial arch, and also to the extraocular muscles, thus demonstrating a contribution from paraxial as well as prechordal mesoderm to this anterior muscle group. Unexpectedly, this first lineage also contributes to myocardium of the right ventricle. The second lineage gives rise to muscles of facial expression, which derive from mesoderm of the second branchial arch. It also contributes to outflow tract myocardium at the base of the arteries. Further sublineages distinguish myocardium at the base of the aorta or pulmonary trunk, with a clonal relationship to right or left head muscles, respectively. We thus establish a lineage tree, which we correlate with genetic regulation, and demonstrate a clonal relationship linking groups of head muscles to different parts of the heart, reflecting the posterior movement of the arterial pole during pharyngeal morphogenesis.

Rapid generation of markerless recombinant MVA vaccines by en passant recombineering of a self-excising bacterial artificial chromosome

The non-replicating poxviral vector modified vaccinia virus Ankara (MVA) is currently a leading candidate for development of novel recombinant vaccines against globally important diseases. The 1980s technology for making recombinant MVA (and other poxviruses) is powerful and robust, but relies on rare recombination events in poxviral-infected cells. In the 21st century, it has become possible to apply bacterial artificial chromosome (BAC) technology to poxviruses, as first demonstrated by B. Moss’ lab in 2002 for vaccinia virus. A similar BAC clone of MVA was subsequently derived, but while recombination-mediated genetic engineering for rapid production was used of deletion mutants, an alternative method was required for efficient insertion of transgenes. Furthermore “markerless” viruses, which carry no trace of the selectable marker used for their isolation, are increasingly required for clinical trials, and the viruses derived via the new method contained the BAC sequence in their genomic DNA. Two methods are adapted to MVA–BAC to provide more rapid generation of markerless recombinants in weeks rather than months. “ En passant” recombineering is applied to the insertion of a transgene expression cassette and the removal of the selectable marker in bacteria; and a self-excising variant of MVA–BAC is constructed, in which the BAC cassette region is rapidly and efficiently lost from the viral genome following rescue of the BAC into infectious virus. These methods greatly facilitate and accelerate production of recombinant MVA, including markerless constructs.

A trans -Complementing Recombination Trap Demonstrates a Low Propensity of Flaviviruses for Intermolecular Recombination

Intermolecular recombination between the genomes of closely related RNA viruses can result in the emergence of novel strains with altered pathogenic potential and antigenicity. Although recombination between flavivirus genomes has never been demonstrated experimentally, the potential risk of generating undesirable recombinants has nevertheless been a matter of concern and controversy with respect to the development of live flavivirus vaccines. As an experimental system for investigating the ability of flavivirus genomes to recombine, we developed a "recombination trap," which was designed to allow the products of rare recombination events to be selected and amplified. To do this, we established reciprocal packaging systems consisting of pairs of self-replicating subgenomic RNAs (replicons) derived from tick-borne encephalitis virus (TBEV), West Nile virus (WNV), and Japanese encephalitis virus (JEV) that could complement each other in trans and thus be propagated together in cell culture over multiple passages. Any infectious viruses with intact, full-length genomes that were generated by recombination of the two replicons would be selected and enriched by end point dilution passage, as was demonstrated in a spiking experiment in which a small amount of wild-type virus was mixed with the packaged replicons. Using the recombination trap and the JEV system, we detected two aberrant recombination events, both of which yielded unnatural genomes containing duplications. Infectious clones of both of these genomes yielded viruses with impaired growth properties. Despite the fact that the replicon pairs shared approximately 600 nucleotides of identical sequence where a precise homologous crossover event would have yielded a wild-type genome, this was not observed in any of these systems, and the TBEV and WNV systems did not yield any viable recombinant genomes at all. Our results show that intergenomic recombination can occur in the structural region of flaviviruses but that its frequency appears to be very low and that therefore it probably does not represent a major risk in the use of live, attenuated flavivirus vaccines.

The identification of a new HLA‐DPB1 allele (*1302) in one family and the detection of a recombination event between the DR and the DQ regions in another Caucasian T1DGC family

The analysis of families collected by the T1DGC and typed at high resolution for the HLA class I and class II loci provided an opportunity for identifying new alleles and rare recombination events. In one American Caucasian family, a novel allele (HLA-DPB1*1302), detected as an unusual pattern of probe binding, was identified in the mother and in one child. Amplicons from both individuals were sequenced and a new variant of DPB1*1301 with an A->T mutation [TAC to TTC in codon 64, (amino acid 35); Y to F] was confirmed. In another American Caucasian family, one child inherited an unusual haplotype, DRB1*1501-DQA1*0102-DQB1*0609-DPA1*0103-DPB1*0601 resulting from a recombination between the DRB1 loci on the maternal chromosomes DRB1*1501-DQA1*0102-DQB1*0602-DPA1*0103-DPB1*0401 and DRB1*1302-DQA1*0102-DQB1*0609-DPA1*0103-DPB1*0601.

Intra- and inter-molecular recombination of mitochondrial DNA after in vivo induction of multiple double-strand breaks

To investigate mtDNA recombination induced by multiple double strand breaks (DSBs) we used a mitochondria-targeted form of the ScaI restriction endonuclease to introduce DSBs in heteroplasmic mice and cells in which we were able to utilize haplotype differences to trace the origin of recombined molecules. ScaI cleaves multiple sites in each haplotype of the heteroplasmic mice (five in NZB and three in BALB mtDNA) and prolonged expression causes severe mtDNA depletion. After a short pulse of restriction enzyme expression followed by a long period of recovery, mitochondrial genomes with large deletions were detected by PCR. Curiously, we found that some ScaI sites were more commonly involved in recombined molecules than others. In intra-molecular recombination events, deletion breakpoints were close to or upstream of ScaI cleavage sites, confirming the recombinogenic character of DSBs in mtDNA. A region adjacent to the D-loop was preferentially involved in recombination of all molecules. Sequencing through NZB and BALB haplotype markers in recombined molecules enabled us to show that in addition to intra-molecular mtDNA recombination, rare inter-molecular mtDNA recombination events can also occur. This study underscores the role of DSBs in the generation of mtDNA rearrangements and supports the existence of recombination hotspots.

Trypanosoma cruzi: New insights on ecophylogeny and hybridization by multigene sequencing of three nuclear and one maxicircle genes

Natural populations of Trypanosoma cruzi are structured into five genetic lineages, T. cruzi I and T. cruzi II a to e, as the result of clonal evolution with rare genetic recombination events. To explore more in depth these phenomenons, a multigene sequencing approach was used, for the first time in the case of T. cruzi. Three nuclear loci and a maxicircle locus were sequenced on 18 T. cruzi stocks. Sequences were used to build phylogenetic trees from each locus and from concatenated sequences of all loci. The data confirmed the hybrid origin of DTUs IId and IIe, as the result of an ancient genetic recombination between strains pertaining to IIb and IIc. The data confirmed also a hybrid origin of DTUs IIa and IIc. Contrary to previous reports, we failed to detect mosaic genes. The phylogenetic relationship between DTUs and the respective roles of recombination and selection were tested.

Assessing clonality and chemotype monophyly in Thamnolia (Icmadophilaceae)

Here we incorporate molecular sequence data (ITS, IGS, mtLSU, RPB2) to test the hypothesis of strict clonality in the lichen-forming fungus Thamnolia vermicularis. Recombination was rejected by most methods, though, a small number did detect recombination. We intepret these analyses as mostly supporting the hypothesis of strict clonality. We were unable to determine if the recombination detected was the result of rare recombination events in recent time, historic recombination, or false positives by certain methods. In addition, we investigated whether chemotypes in T. vermicularis formed monophyletic groups. Molecular sequence data suggest that the two chemotypes do not form well-supported, monophyletic lineages. Chemotypes were found with identical haplotypes and some populations were composed of more than one haplotype. Our data suggest that there is not a simple dichotomy between chemotypes in T. vermicularis, which may be due to rare or historic recombination, repeated chemotype evolution or incomplete lineage sorting.