| 1. |
- Andersson, Karl-Magnus, et al.
(author)
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Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.
- 2013
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In: Applied and Environmental Microbiology. - 0099-2240. ; 79:16, s. 4993-5004
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Journal article (peer-reviewed)abstract
- Many nematophagous fungi use morphological structures called traps to capture nematodes by adhesion or mechanically. To better understand the cellular functions of adhesive traps, the trap cell proteome of the fungus Monacrosporium haptotylum was characterized. The trap of M. haptotylum consists of a unicellular structure called knob that develops at the apex of a hyphae. Proteins extracted from knobs and mycelia were analyzed using SDS-PAGE and LC-MS/MS. The peptide sequences were matched against predicted gene models from the recently sequenced M. haptotylum genome. In total, 336 proteins were identified, with 54 being expressed at significantly higher levels in the knobs than in the mycelia. The upregulated knob proteins included peptidases, small secreted proteins with unknown function and putative cell surface adhesins containing carbohydrate-binding domains including the WSC domain. Phylogenetic analysis showed that all upregulated WSC domain proteins belonged to a large, expanded cluster of paralogs in M. haptotylum. Several peptidases and homologs to experimentally verified proteins in other pathogenic fungi were also upregulated in the knob proteome. Complementary profiling of gene expression at the transcriptome level showed poor correlation between the upregulation of knob proteins and their corresponding transcripts. We propose that the traps of M. haptotylum contain many of the proteins needed in the early stages of infection, and that the trap cells can tightly control the translation and degradation of these proteins to minimize the cost of protein synthesis.
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| 2. |
- Dowling, Damian K., et al.
(author)
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Cytonuclear Interactions and the Economics of Mating in Seed Beetles
- 2010
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In: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 176:2, s. 131-140
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Journal article (peer-reviewed)abstract
- Recent studies have uncovered an abundance of non-neutral cytoplasmic genetic variation within species, which suggests that we should no longer consider the cytoplasm an idle intermediary of evolutionary change. Nonneutrality of cytoplasmic genomes is particularly intriguing, given that these genomes are maternally transmitted. This means that the fate of any given cytoplasmic genetic mutation is directly tied to its performance when expressed in females. For this reason, it has been hypothesized that cytoplasmic genes will coevolve via a sexually antagonistic arms race with the biparentally transmitted nuclear genes with which they interact. We assess this prediction, examining the intergenomic contributions to the costs and benefits of mating in Callosobruchus maculatus females subjected to a mating treatment with three classes (kept virgin, mated once, or forced to cohabit with a male). We find no evidence that the economics of mating are determined by interactions between cytoplasmic genes expressed in females and nuclear genes expressed in males and, therefore, no support for a sexually antagonistic intergenomic arms race. The cost of mating to females was, however, shaped by an interaction between the cytoplasmic and nuclear genes expressed within females. Thus, cytonuclear interactions are embroiled in the economics of mating.
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| 3. |
- Kushwaha, Sandeep, et al.
(author)
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MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics
- 2015
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In: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 16
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Journal article (peer-reviewed)abstract
- Background: Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families. Results: In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 300,000 probes that match more than 400,000 publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/. Conclusion: MetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.
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| 4. |
- Meerupati, Tejashwari
(author)
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Evolutionary Genomics of Nematode-Trapping Fungi
- 2013
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Doctoral thesis (other academic/artistic)abstract
- Nematode-trapping fungi are ubiquitous, soil-living organisms with the ability to infect and kill nematodes. These fungi have developed specialized infection structures for the capture of nematodes. Many nematode species are parasites on plants and animals, which have resulted in an interest to use nematode-trapping fungi as biological control agents. Through bioinformatics approaches, I have used comparative genomics and transcriptomics (RNASeq) to gain insights into the evolution of parasitism in the nematode-trapping fungus, Monacrosporium haptotylum (Ascomycetes; Orbiliales). M. haptotylum is the second nematode-trapping fungus to have its genome sequenced. The genome assembly contains 40.4 million base pairs with 28x coverage and 10,959 predicted protein-encoding genes. Here, I report analyses of the knob forming species M. haptotylum genome in comparison with the net-forming species Arthrobotrys oligospora. The analysis showed that two genomic mechanisms are likely to be involved in the evolution of parasitism in nematode-trapping fungi. First, gene duplications leading to the expansion of gene families resulting in a large number of species-specific genes. Many of these genes were highly expressed and upregulated during infection. Second, the differential gene expression of orthologs between the two fungi during early stages of infection, suggest that differential gene expression has been an important mechanism for the evolution of parasitism in nematode-trapping fungi. Comparative studies of the genomes of the two nematode-trapping fungi with 14 other sequenced fungal genomes show that the lineages of M. haptotylum and A. oligospora diverged about 14-18 million years ago. A total of 7,455 proteins from M. haptotylum were clustered into 3,124 protein domain families and 7,555 proteins from A. oligospora into 3,782 protein domain families. Analysis of the M. haptotylum genome with other ascomycetes genomes revealed a large number of expanded protein families. The expanded gene families contained several peptidases, cell wall degrading enzymes, tyrosinases, and extracellular proteins with WSC and mucin domains. Many of these genes were highly upregulated and highly expressed during infection. In addition the transcripts encoding small-secreted proteins (SSPs) were also highly expressed during infection. In the second part of my thesis, the patterns and mechanisms for expansion and functional divergence of subtilisin-like serine proteases in nematode-trapping fungi were analyzed in more detail. Phylogenetic analyses showed that the genome of M. haptotylum contains many paralogs of these proteases that have arisen through gene duplication. Many of the serine proteases were highly expressed and regulated during infection. The genomic sequence of M. haptotylum and its comparison with A. oligospora has provided a first glimpse into the genomic basis of the evolution of parasitism in nematode-trapping fungi.
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| 5. |
- Meerupati, Tejashwari, et al.
(author)
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Genomic Mechanisms Accounting for the Adaptation to Parasitism in Nematode-Trapping Fungi
- 2013
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In: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 9:11
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Journal article (peer-reviewed)abstract
- Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes. The class contains nematode-trapping fungi that form unique infection structures, called traps, to capture and kill free-living nematodes. The traps have evolved differently along several lineages and include adhesive traps (knobs, nets or branches) and constricting rings. We show, by genome sequencing of the knob-forming species Monacrosporium haptotylum and comparison with the net-forming species Arthrobotrys oligospora, that two genomic mechanisms are likely to have been important for the adaptation to parasitism in these fungi. Firstly, the expansion of protein domain families and the large number of species-specific genes indicated that gene duplication followed by functional diversification had a major role in the evolution of the nematode-trapping fungi. Gene expression indicated that many of these genes are important for pathogenicity. Secondly, gene expression of orthologs between the two fungi during infection indicated that differential regulation was an important mechanism for the evolution of parasitism in nematode-trapping fungi. Many of the highly expressed and highly upregulated M. haptotylum transcripts during the early stages of nematode infection were species-specific and encoded small secreted proteins (SSPs) that were affected by repeat-induced point mutations (RIP). An active RIP mechanism was revealed by lack of repeats, dinucleotide bias in repeats and genes, low proportion of recent gene duplicates, and reduction of recent gene family expansions. The high expression and rapid divergence of SSPs indicate a striking similarity in the infection mechanisms of nematode-trapping fungi and plant and insect pathogens from the crown groups of the filamentous ascomycetes (Pezizomycotina). The patterns of gene family expansions in the nematode-trapping fungi were more similar to plant pathogens than to insect and animal pathogens. The observation of RIP activity in the Orbiliomycetes suggested that this mechanism was present early in the evolution of the filamentous ascomycetes.
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