Lower level relationships in the mushroom genus Cortinarius (Basidiomycota, Agaricales): a comparison of RPB1, RPB2, and ITS phylogenies

We sampled and analyzed approximately 2900bp across the three loci from 54 taxa belonging to a taxonomically difficult group of Cortinarius subgenus Phlegmacium. The combined analyses of ITS and variable regions of RPB1 and RPB2 greatly increase the resolution and nodal support for phylogenies of these closely related species belonging to clades that until now have proven very difficult to resolve with the ribosomal markers, nLSU and ITS. We present the first study of the utility of variable regions of the genes encoding the two largest subunits of RNA polymerase II (RPB1 and RPB2) for inferring the phylogeny of mushroom-forming fungi in combination with and compared to the widely used ribosomal marker ITS. The studied region of RPB1 contains an intron of the size and variability of ITS along with many variable positions in coding regions. Though almost entirely coding, the studied region of RPB2 is more variable than ITS. Both RNA polymerase II genes were alignable across all taxa. Our results indicate that several sections of Cortinarius need redefinition, and that several taxa treated at subspecific and varietal level should be treated at specific level. We suggest a new section for the two species, C. caesiocortinatus and C. prasinocyaneus, which constitute a well-supported separate lineage. We speculate that sequence information from RNA polymerase II genes have the potential for resolving phylogenetic problems at several levels of the diverse and taxonomically very challenging genus Cortinarius.     

Phylogeny and genetic diversity of Bridgeoporus nobilissimus inferred using mitochondrial and nuclear rDNA sequences

The genetic diversity and phylogeny of Bridgeoporus nobilissimus have been analyzed. DNA was extracted from spores collected from individual fruiting bodies representing six geographically distinct populations in Oregon and Washington. Spore samples collected contained low levels of bacteria, yeast and a filamentous fungal species. Using taxon-specific PCR primers, it was possible to discriminate among rDNA from bacteria, yeast, a filamentous associate and B. nobilissimus. Nuclear rDNA internal transcribed spacer (ITS) region sequences of B. nobilissimus were compared among individuals representing six populations and were found to have less than 2% variation. These sequences also were used to design dual and nested PCR primers for B. nobilissimus-specific amplification. Mitochondrial small-subunit rDNA sequences were used in a phylogenetic analysis that placed B. nobilissimus in the hymenochaetoid clade, where it was associated with Oxyporus and Schizopora.     

Genetic variation in TIMP1 but not MMPs predict excess FEV1 decline in two general population-based cohorts

Background

An imbalance in Matrix MetalloProteases (MMPs) and Tissue Inhibitors of MMPs (TIMPs) contributes to Chronic Obstructive Pulmonary Disease (COPD) development. Longitudinal studies investigating Single Nucleotide Polymorphisms (SNPs) in MMPs and TIMPs with respect to COPD development and lung function decline in the general population are lacking.

Methods

We genotyped SNPs in MMP1 (G-1607GG), MMP2 (-1306 C/T), MMP9 (3 tagging SNPs), MMP12 (A-82G and Asn357Ser) and TIMP1 (Phe124Phe and Ile158Ile) in 1390 Caucasians with multiple FEV₁ measurements from a prospective cohort study in the general population. FEV₁ decline was analyzed using linear mixed effect models adjusted for confounders. Analyses of the X-chromosomal TIMP1 gene were stratified according to sex. All significant associations were repeated in an independent general population cohort (n = 1152).

Results

MMP2 -1306 TT genotype carriers had excess FEV₁ decline (-4.0 ml/yr, p = 0.03) compared to wild type carriers. TIMP1 Ile158Ile predicted significant excess FEV₁ decline in both males and females. TIMP1 Phe124Phe predicted significant excess FEV₁ decline in males only, which was replicated (p = 0.10) in the second cohort. The MMP2 and TIMP1 Ile158Ile associations were not replicated. Although power was limited, we did not find associations with COPD development.

Conclusions

We for the first time show that TIMP1 Phe124Phe contributes to excess FEV₁ decline in two independent prospective cohorts, albeit not quite reaching conventional statistical significance in the replication cohort. SNPs in MMPs evidently do not contribute to FEV₁ decline in the general population.     

The secotioid form of Lentinus tigrinus: genetics and development of a fungal morphological innovation

Secotioid fungi resemble gasteromycetes, but are presumably closely related to agaricoid fungi. Lentinus tigrinus is a wood-decaying mushroom that has both a secotioid and an agaricoid form. We examined ontogeny and heritability of the secotioid phenotype in L. tigrinus with a combination of formal genetic crosses, scanning electron microscopy, and macroscopic observation of cultured sporocarps. For F1 analysis, we crossed single-spore isolates (SSIs) representing four mating types derived from a secotioid dikaryon and four mating types from an agaricoid dikaryon. All F1 sporocarps had typical agaricoid morphology. For F2 analysis, 200 SSIs from one F1 sporocarp and 100 SSIs from another F1 sporocarp were backcrossed to tester SSIs from sporocarps produced by the parental secotioid dikaryon. Ratios of secotioid to agaricoid dikaryons thus produced were 47:49 and 84:109, which confirms previous reports that the secotioid phenotype is conferred by a recessive allele at a single locus (χ² = 0.0417, P > 0.05, χ² = 3.2383, P > 0.05, respectively). Early ontogeny of the secotioid form is indistinguishable from that of the agaricoid form. Later, the hymenophore is obscured by a weft of hyphae that proliferates from the margins of the developing lamellae. Longevity of the sporocarps and rate and duration of sporocarp growth are approximately equal in the secotioid and agaricoid forms. Developmental evolution of the secotioid form is interpreted as an example of von Baerian differentiation, rather than paedomorphosis, which has been implicated in evolution of other secotioid taxa.     

After the gold rush,or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century

Mushroom-forming fungi (Agaricomycetes, approx. syn.: Homobasidiomycetes) produce a diverse array of fruiting bodies, ranging from simple crust-like forms to complex, developmentally integrated forms, such as stinkhorns and veiled agarics. The 19th century Friesian system divided the mushroom-forming fungi according to macromorphology. The Friesian taxonomy has long been regarded as artificial, but it continues to influence the language of mycology and perceptions of fungal diversity. Throughout the 20th century, the phylogenetic significance of anatomical features was elucidated, and classifications that departed strongly from the Friesian system were proposed. However, the anatomical studies left many questions and controversies unresolved, due in part to the paucity of characters, as well as the general absence of explicit phylogenetic analyses. Problems in fruiting body evolution were among the first to be addressed when molecular characters became readily accessible in the late 1980s. Today, GenBank contains about 108,000 nucleotide sequences of ‘homobasidiomycetes’, filed under 7300 unique names. Analyses of these data are providing an increasingly detailed and robust view of the phylogeny and the distribution of different fruiting body forms across the 14 major clades that make up the agaricomycetes. However, it would be wrong to suggest that all the important questions about fruiting body evolution have been resolved. Recent studies focusing on resupinate forms suggest that there may still be undetected major clades of agaricomycetes, which could have a significant impact on our estimates of the ancestral forms in this morphologically diverse group. Modern approaches, including comparative phylogenetic analyses and developmental studies, have the potential to yield novel insights into both the macroevolutionary processes and cellular mechanisms of fungal morphological evolution.     

Phylogenetic placement of Diplocystis wrightii in the Sclerodermatineae (Boletales) based on nuclear ribosomal large subunit DNA sequences

Diplocystis wrightii is an enigmatic gasteroid basidiomycete from the Caribbean. It has taxonomic affiliations with Lycoperdaceae, Broomeiaceae, and Sclerodermataceae. This study sampled ITS and 28S ribosomal genes from three D. wrightii specimens to determine the phylogenetic placement and the closest relatives of this species. Results of database searches and phylogenetic analysis indicate this species to be a member of the Sclerodermatineae and most closely related to the genera Astraeus and Tremellogaster.