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Safronov, O.

Publications and source records attributed to Safronov, O..

5 recordsLinked to original sources

Convergent evolution of mevalonate pathway in Inonotus obliquus and Betula pendula.

Inonotus obliquus, Chaga mushroom, is a fungal species from Hymenochaetaceae family (Basidiomycota) which has been widely used for traditional medicine in Europe and Asia. Here, chaga genome was sequenced using Pacbio sequencing into a 50.7Mbp assembly consisting of 301 primary contigs with an N50 value of 375 kbp. Genome evolution analyses revealed a lineage-specific whole genome duplication event and an expansion of Cytochrome P450 superfamily. Fungal biosynthetic clusters were enriched for tandemly duplicated genes, suggesting that biosynthetic pathway evolution has proceeded through small-scale duplications. Metabolomic fingerprinting confirmed a highly complex terpene biosynthesis chemistry when compared against related fungal species lacking the genome duplication event.

evolutionary biology↗

The photoreceptor UVR8 mediates the perception of both UV-B and UV-A wavelengths up to 350 nm of sunlight with responsivity moderated by cryptochromes

The photoreceptors UV RESISTANCE LOCUS 8 (UVR8) and CRYPTOCHROMES 1 and 2 (CRYs) play major roles in the perception of UV-B (280-315 nm) and UV-A/blue radiation (315-500 nm), respectively. However, it is poorly understood how they function in sunlight. The roles of UVR8 and CRYs were assessed in a factorial experiment with Arabidopsis thaliana wild-type and photoreceptor mutants exposed to sunlight for 6 h or 12 h under five types of filters with cut-offs in UV and blue-light regions. Transcriptome-wide responses triggered by UV-B and UV-A wavelengths shorter than 350 nm (UV-Asw) required UVR8 whereas those induced by blue and UV-A wavelengths longer than 350 nm (UV-Alw) required CRYs. UVR8 modulated gene expression in response to blue light while lack of CRYs drastically enhanced gene expression in response to UV-B and UV-Asw. These results agree with our estimates of photons absorbed by these photoreceptors in sunlight and with in vitro monomerization of UVR8 by wavelengths up to 335 nm. Motif enrichment analysis predicted complex signaling downstream of UVR8 and CRYs. Our results highlight that it is important to use UV waveband definitions specific to plants photomorphogenesis as is routinely done in the visible region.

plant biology↗

ELIMAKI locus is required for mechanosensing and proprioception in birch trees

The remarkable vertical and radial growth observed in tree species, encompasses a major physical challenge for wood forming tissues. To compensate with increasing size and weight, cambium-derived radial growth increases the stem width, thereby supporting the aerial body of trees. This feedback appears to be part of a so-called \"proprioception\" (1, 2) mechanism that controls plant size and biomass allocation. Yet, how trees experience or respond to mechanical stress derived from their own vertical loading, remains unknown. Here, we combined two strategies to dissect the proprioceptive response in birch. First, we show that in response to physical loading, trees promote radial growth with different magnitudes along the stem. Next, we identified a mutant cultivar (B. pubescens cv. Elimaki) in which the main stem shows normal vertical development, but collapses after three months. By inducing precocious flowering, we generated a backcrossed population (BC1) by producing two generations in 4 years. In his scheme, we uncovered a recessive trait (eki) that segregates and genetically maps with a Mendelian monogenic pattern. Unlike WT, eki is resistant to vertical mechanical stimulation. However, eki responds normally to the gravitropic stimulus by making tension wood. Before the collapse, cell size in eki is compromised resulting in radial growth defects, depending on stem height. Cell walls of developing xylem and phloem tissues have delayed differentiation in eki, and its tissues are softer compared to WT as indicated by atomic force microscopy (AFM). The transcriptomic profile of eki highlighted the overlap with that of the Arabidopsis response to touch. Taken together, our results suggest that the mechanical environment and cell wall properties of developing woody tissues, can significantly affect the growth responses to vertical loading thereby compromising their proprioceptive capacity. Additionally, we introduce a fast forward genetics strategy to dissect complex phenotypes in trees.

plant biology↗

A novel phyllosphere resident Protomyces species that interacts with the Arabidopsis immune system.

We describe the genome contents of six Protomyces spp. that are pathogenic within the typical host range of the genus and a novel Protomyces strain (SC29) that was previously isolated from the phylloplane of wild Arabidopsis thaliana (Arabidopsis), an atypical or possible alternate host. Genome-wide phylogenetic analysis defined SC29 as a distinct Protomyces sp. Analysis of gene family expansions, gene retention, and gene loss patterns among these Protomyces spp. lead us to hypothesize that SC29 may have undergone a host jump. The role of phyllosphere residency in the lifecycle of Protomyces spp. was previously unknown. Genomic changes in SC29 and all other Protomyces spp. were consistent with adaptations to the plant phylloplane. As predicted by our analysis of its mating locus, SC29 did not cause disease on Arabidopsis as a single strain, but could persist in its phylloplane, while the closely related P. inouyei does not. SC29 treated Arabidopsis exhibited enhanced immunity against Botrytis cinerea infection, associated with activation of MAPK3/6, camalexin, and SA-signalling pathways. We conclude that SC29 is a novel Protomyces sp. able to survive in the Arabidopsis phylloplane and that phylloplane residency is an important element in the lifecycle of Protomyces spp.

microbiology↗

Mechanistic insights into the evolution of DUF26-containing proteins in land plants

Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation in plants. Here we infer the evolutionary history of a representative protein family, the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 first appeared in secreted proteins. Domain duplications and rearrangements led to the emergence of CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs) and PLASMODESMATA-LOCALIZED PROTEINS (PDLPs). While the DUF26 itself is specific to land plants, structural analyses of Arabidopsis PDLP5 and PDLP8 ectodomains revealed strong similarity to fungal lectins. Therefore, we propose that DUF26-containing proteins constitute a novel group of plant carbohydrate-binding proteins. Following their appearance, CRKs expanded both through tandem duplications and preferential retention of duplicates in whole genome duplication events, whereas PDLPs evolved according to the dosage balance hypothesis. Based on our findings, we suggest that the main mechanism of expansion in new gene families is small-scale duplication, whereas genome fractionation and genetic drift after whole genome multiplications drive families towards dosage balance.

plant biology↗