Role and regulation of ACC deaminase gene in Sinorhizobium meliloti: is it a symbiotic, rhizospheric or endophytic gene?

Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection. However, few reports are present on the actual role in rhizobia, one of the most investigated groups of plant-associated bacteria. In particular, still unclear is the origin and the role of acdS in symbiotic competitiveness and on the selective benefit it may confer to plant symbiotic rhizobia. Here we present a phylogenetic and functional analysis of acdS orthologs in the rhizobium model-species Sinorhizobium meliloti. Results showed that acdS orthologs present in S. meliloti pangenome have polyphyletic origin and likely spread through horizontal gene transfer, mediated by mobile genetic elements. When acdS ortholog from AK83 strain was cloned and assayed in S. meliloti 1021 (lacking acdS), no modulation of plant ethylene levels was detected, as well as no increase in fitness for nodule occupancy was found in the acdS-derivative strain compared to the parental one. Surprisingly, AcdS was shown to confer the ability to utilize formamide and some dipeptides as sole nitrogen source. Finally, acdS was shown to be negatively regulated by a putative leucine-responsive regulator (LrpL) located upstream to acdS sequence (acdR). acdS expression was induced by root exudates of both legumes and non-leguminous plants. We conclude that acdS in S. meliloti is not directly related to symbiotic interaction, but it could likely be involved in the rhizospheric colonization or in the endophytic behavior

Evaluating morphology and geographic range extent of genetically delimited species of mushrooms

Species delimitation directly affects interpretation of evolution and biogeography. Following speciation, independently evolving lineages are expected to fix different characters that eventually distinguish them from their closest relatives. However, rates of fixation vary. I delimited species in the mushroom genus Russula based on the fungal nuclear internal transcribed spacer 2 (ITS2) DNA barcode region. I sampled 713 ITS2 sequences of American Pacific Northwest specimens collected by Seattle architect Benjamin Woo (1923-2008). I compared the morphology within and among DNA-delimited species, according to morphological character state data that Woo had recorded for each of specimen. To Woo's data, I added spore measurements for 23 species. The characters in Russula varied within and overlapped between my delimited species. My multivariate analysis showed that the centroids of morphological characters usually differed significantly between pairs of genetically defined species, indicating evolutionary divergence at the level of morphology. However, because of the variation among and within conspecific collections, morphological characters only correctly predicted the identity of ~50% of the individual specimens. Of the delimited species, nine had been collected ten or more times each and were, based on morphology and sequence analysis, undescribed and restricted to North America. I describe the nine as new species, reporting their character variation. I used data from public databases to ask how frequently geographical ranges are intercontinental as opposed to intracontinental among mushroom-forming species. I calculated the ‘range extent’ (maximum geographical distance) recorded for 2324 species world-wide and 341 species from the Pacific Northwest, representing 12 genera. The ranges of most species extended only to ~2000 km (shorter distances than a continent). By permutation of the data, I showed that this pattern vanished if geographical coordinates were randomized with respect to species suggesting the pattern I found in the data was not due to random sampling. More sampling would be needed to resolve whether the pattern arose from sampling bias or a high frequency of regional endemism. However, because it reflects a common pattern seen in the best sampled fungi and in narrower studies of genera and families, I hypothesize that regional endemism is the general pattern in well-studied genera and more generally fungal biogeography.Science, Faculty ofBotany, Department ofGraduat

Comment on ’single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi’

Chen et al. recently reported evidence for inter-nucleus recombination in arbuscular mycorrhizal fungi (Chen et al., 2018a). Here, we report a reanalysis of their data. After filtering the data by excluding heterozygous sites in haploid nuclei, duplicated regions of the genome, and low-coverage depths base calls, we find the evidence for recombination to be very sparse.</p

raw and output files from geographic range extent study

Input and intermediate files. Scripts can also be found here: https://github.com/abazzical/mushroomRange

Data from: Over the hills, but how far away? estimates of mushroom geographic range extents

Aim: Geographic distributions of mushroom species remain poorly understood despite their importance for advancing our understanding of the habitat requirements, species interactions and ecosystem functions of this key group of organisms. Here, we estimate geographic range extents (maximum within-species geographic distance) of genetically defined operational taxonomic units (OTUs). Location: World-wide, with emphasis on the American Pacific Northwest Taxa: Amanita, Agaricus, Cortinarius, Galerina, Hebeloma, Hydnum, Hygrocybe, Hygrophorus, Inocybe, Lepiota, Pholiota, and Russula+Lactarius; other genera in Agaricomycotina Method: We used publicly available OTUs from ribosomal internal transcribed spacer (ITS) sequences (n=15,373) from 12 mushroom genera with worldwide distributions. For each of 2,324 ~species-level OTUs, we estimated the maximum within-species range extent based on sample locality records. In parallel, we estimated range extents for species in four tree genera. Contrasting estimates from well-studied trees allowed us to test for potential biases in our range estimates of less well inventoried mushrooms. Results: The median range extents across the 2,324 mushroom OTUs varied from ~1,200 km to 4,039 km, depending on assumptions. These extents were significantly lower than estimates from permuted or randomized data. Mushroom ranges were comparable to the median natural range extent of tree species (1,613 km). In contrast, the tree median species range increased to 16,581 km when anthropogenic range extensions were included. At least ten mushroom species were similarly broadly distributed, eight of which have been associated with human activity. Main conclusions: Overall, like tree species, mycorrhizal and saprotrophic fungi show evidence of biogeographic structure rather than global distributions. This reconstruction of geographic range extents drew upon investments into ITS barcoding of extensive herbarium collections. Large scale analyses such as ours can yield estimates of fungal geographic range extents that are a prerequisite to a deeper understanding of the diverse roles of fungi in ecosystems

Population genomic study of an introduced ectomycorrhizal fungus Suillus luteus

Abstracts from the April 12-14, 2019 MASC Conferenc

Little Evidence of Antagonistic Selection in the Evolutionary Strata of Fungal Mating-Type Chromosomes ( Microbotryum lychnidis-dioicae )

International audienceRecombination suppression on sex chromosomes often extends in a stepwise manner, generating evolutionary strata of differentiation between sex chromosomes. Sexual antagonism is a widely accepted explanation for evolutionary strata, postulating that sets of genes beneficial in only one sex are successively linked to the sex-determining locus. The anther-smut fungus Microbotryum lychnidis-dioicae has mating-type chromosomes with evolutionary strata, only some of which link mating-type genes. Male and female roles are non-existent in this fungus, but mating-type antagonistic selection can also generate evolutionary strata, although the life cycle of the fungus suggests it should be restricted to few traits. Here, we tested the hypothesis that mating-type antagonism may have triggered recombination suppression beyond mating-type genes in M. lychnidis-dioicae by searching for footprints of antagonistic selection in evolutionary strata not linking mating-type loci. We found that these evolutionary strata (i) were not enriched in genes upregulated in the haploid phase, where cells are of alternative mating types, (ii) carried no gene differentially expressed between mating types, and (iii) carried no genes displaying footprints of specialization in terms of protein sequences (d N /d S) between mating types after recommended filtering. Without filtering, eleven genes showed signs of positive selection in the strata not linking mating-type genes, which constituted an enrichment compared to autosomes, but their functions were not obviously involved in antagonistic selection. Thus, we found no strong evidence that antagonistic selection has contributed to extending recombination suppression beyond mating-type genes. Alternative hypotheses should therefore be explored to improve our understanding of the sex-related chromosome evolution

Gene Copy Number Variation Does Not Reflect Structure or Environmental Selection in Two Recently Diverged California Populations of Suillus brevipes

Gene copy number variation across individuals has been shown to track population structure and be a source of adaptive genetic variation with significant fitness impacts. In this study, we report opposite results for both predictions based on the analysis of gene copy number variants (CNVs) of Suillus brevipes, a mycorrhizal fungus adapted to coastal and montane habitats in California. In order to assess whether gene copy number variation mirrored population structure and selection in this species, we investigated two previously studied locally adapted populations showing a highly differentiated genomic region encompassing a gene predicted to confer salt tolerance. In addition, we examined whether copy number in the genes related to salt homeostasis was differentiated between the two populations. Although we found many instances of CNV regions across the genomes of S. brevipes individuals, we also found CNVs did not recover population structure and known salt-tolerance-related genes were not under selection across the coastal population. Our results contrast with predictions of CNVs matching single-nucleotide polymorphism divergence and showed CNVs of genes for salt homeostasis are not under selection in S. brevipes