The diversity of fungal genome

Mohanta, Tapan Kumar; Bae, Hanhong

doi:10.1186/s12575-015-0020-z

Cited by 181 publications

(123 citation statements)

References 56 publications

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“…The powdery mildew genomes are some of the largest among fungi with an estimated size of 150-180 Mb, 90% of which corresponds to transposable element (TE) sequences (Spanu et al, 2010;Wicker et al, 2013). Contrasting with genome size, the gene content of powdery mildews is one of the lowest in fungi with c. 6500 genes, compared to an average of 11 000 in ascomycetes and 15 000 in basidiomycetes Mohanta & Bae, 2015). The mildew genomes encode a very large complement of candidate secreted effector proteins (CSEPs) that account for almost 10% of all predicted coding genes (Spanu et al, 2010;Pedersen et al, 2012;Wicker et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

AvrPm2 encodes an RNase‐like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus

et al. 2016

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Summary There is a large diversity of genetically defined resistance genes in bread wheat against the powdery mildew pathogen Blumeria graminis (B. g.) f. sp. tritici. Many confer race‐specific resistance to this pathogen, but until now only the mildew avirulence gene AvrPm3 a2/f2 that is recognized by Pm3a/f was known molecularly.We performed map‐based cloning and genome‐wide association studies to isolate a candidate for the mildew avirulence gene AvrPm2. We then used transient expression assays in Nicotiana benthamiana to demonstrate specific and strong recognition of AvrPm2 by Pm2.The virulent AvrPm2 allele arose from a conserved 12 kb deletion, while there is no protein sequence diversity in the gene pool of avirulent B. g. tritici isolates. We found one polymorphic AvrPm2 allele in B. g. triticale and one orthologue in B. g. secalis and both are recognized by Pm2. AvrPm2 belongs to a small gene family encoding structurally conserved RNase‐like effectors, including Avr a13 from B. g. hordei, the cognate Avr of the barley resistance gene Mla13.These results demonstrate the conservation of functional avirulence genes in two cereal powdery mildews specialized on different hosts, thus providing a possible explanation for successful introgression of resistance genes from rye or other grass relatives to wheat.

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Section: Introductionmentioning

confidence: 99%

AvrPm2 encodes an RNase‐like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus

et al. 2016

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“…Multalin server was used to conduct the multiple sequence alignment (http://multalin.toulouse.inra.fr/multalin/). The statistical parameters used to run the multiple sequence alignments were described previously (Mohanta et al, 2014, 2015b; Mohanta and Bae, 2015), with minor modification. In short they are as follows: sequence input format, fasta; nucleotide weight matrix.…”

Section: Methodsmentioning

confidence: 99%

Analyses of Genomic tRNA Reveal Presence of Novel tRNAs in Oryza sativa

Mohanta

Bae

2017

Front. Genet.

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Transfer rRNAs are important molecules responsible for the translation event during protein synthesis. tRNAs are widespread found in unicellular to multi-cellular organisms. Analysis of tRNA gene family members in Oryza sativa revealed the presence of 750 tRNA genes distributed unevenly in different chromosomes. The length of O. sativa tRNAs genes were ranged from 66 to 91 nucleotides encoding 52 isoacceptor in total. tRNASer found in chromosome 8 of O. sativa encoded only 66 nucleotides which is the smallest tRNA of O. sativa and to our knowledge, this is the smallest gene of eukaryotic lineage reported so far. Analyses revealed the presence of several novel/pseudo tRNA genes in O. sativa which are reported for the first time. Multiple sequence alignment of tRNAs revealed the presence of family specific conserved consensus sequences. Functional study of these novel tRNA and family specific conserved consensus sequences will be crucial to decipher their importance in biological events. The rate of transition of O. sativa tRNA was found to be higher than the rate of transversion. Evolutionary study revealed, O. sativa tRNAs were evolved from the lineages of multiple common ancestors. Duplication and loss study of tRNAs genes revealed, majority of the O. sativa tRNA were duplicated and 17 of them were found to be undergone loss during the evolution. Orthology and paralogy study showed, the majority of O. sativa tRNA were paralogous and only a few of tRNASer were found to contain orthologous tRNAs.

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“…The output read 68 , and 37 Mb for oomycetes 69 . Note that the assigned values for fungi and oomycete are the lower bounds for genome sizes for these taxa, hence this assignment is likely to inflate the estimate of abundance of genomes with less complete assemblies (i.e.…”

Section: Metagenomic Library Analysismentioning

confidence: 99%

The relationship between microbial population size and disease in the Arabidopsis thaliana phyllosphere

Karasov

Neumann

Duque‐Jaramillo

et al. 2019

Preprint

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A central goal in microbiome research is to learn what distinguishes a healthy from a dysbiotic microbial community. Shifts in diversity and taxonomic composition are important indicators of dysbiosis, but a full understanding also requires knowledge of absolute microbial biomass. Simultaneous information on both microbiome composition and the quantity of its components can provide insight into microbiome function and disease state. Here we use shotgun metagenomics to simultaneously assess microbiome composition and microbial load in the phyllosphere of wild populations of the plant Arabidopsis thaliana. We find that wild plants vary substantially in the load of colonizing microbes, and that high loads are typically associated with the proliferation of single taxa, with only a few putatively pathogenic taxa achieving high abundances in the field. Our results suggest (i) that the inside of a plant leaf is on average sparsely colonized with an estimated two bacterial genomes per plant genome and an order of magnitude fewer eukaryotic microbial genomes, and (ii) that higher levels of microbial biomass often indicate successful colonization by pathogens. Lastly, our results show that load is a significant explanatory variable for loss of estimated Shannon diversity in phyllosphere microbiomes, implying that reduced diversity may be a significant predictor of microbial dysbiosis in a plant leaf.

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The diversity of fungal genome

Cited by 181 publications

References 56 publications

AvrPm2 encodes an RNase‐like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus

AvrPm2 encodes an RNase‐like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus

Analyses of Genomic tRNA Reveal Presence of Novel tRNAs in Oryza sativa

The relationship between microbial population size and disease in the Arabidopsis thaliana phyllosphere

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