BackgroundMating-type loci of mushroom fungi contain master regulatory genes that control recognition between compatible nuclei, maintenance of compatible nuclei as heterokaryons, and fruiting body development. Regions near mating-type loci in fungi often show adapted recombination, facilitating the generation of novel mating types and reducing the production of self-compatible mating types. Compared to other fungi, mushroom fungi have complex mating-type systems, showing both loci with redundant function (subloci) and subloci with many alleles. The genomic organization of mating-type loci has been solved in very few mushroom species, which complicates proper interpretation of mating-type evolution and use of those genes in breeding programs.Methodology/Principal FindingsWe report a complete genetic structure of the mating-type loci from the tetrapolar, edible mushroom Flammulina velutipes mating type A3B3. Two matB3 subloci, matB3a that contains a unique pheromone and matB3b, were mapped 177 Kb apart on scaffold 1. The matA locus of F. velutipes contains three homeodomain genes distributed over 73 Kb distant matA3a and matA3b subloci. The conserved matA region in Agaricales approaches 350 Kb and contains conserved recombination hotspots showing major rearrangements in F. velutipes and Schizophyllum commune. Important evolutionary differences were indicated; separation of the matA subloci in F. velutipes was diverged from the Coprinopsis cinerea arrangement via two large inversions whereas separation in S. commune emerged through transposition of gene clusters.Conclusions/SignificanceIn our study we determined that the Agaricales have very large scale synteny at matA (∼350 Kb) and that this synteny is maintained even when parts of this region are separated through chromosomal rearrangements. Four conserved recombination hotspots allow reshuffling of large fragments of this region. Next to this, it was revealed that large distance subloci can exist in matB as well. Finally, the genes that were linked to specific mating types will serve as molecular markers in breeding.
A mesophilic bacterium, strain 15-52 T , was isolated from the rhizosphere of Chinese cabbage (Brassica campestris). On the basis of phenotypic and genotypic characteristics, the bacterium was identified as representing a novel species belonging to the genus Pedobacter. The strain is non-flagellated, non-spore-forming and grows at temperatures in the range 1-37 6C. Physiological tests of the strain showed the presence of oxidase, catalase, protease (gelatin and casein hydrolysis), b-glucosidase and b-galactosidase activities. The highest levels of 16S rRNA gene sequence similarity were found with respect to Pedobacter roseus CL-GP80 T (97.3 %) and Pedobacter sandarakinus DS-27 T (97.2 %). A phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain 15-52 T is a member of the genus Pedobacter. DNA-DNA hybridization analysis revealed low levels of relatedness (<42.3 %) between the isolate and two phylogenetically related type strains, P. roseus KCCM 42272 T and P. sandarakinus KCTC 12559 T . The DNA G+C content is 44.2 mol% and the predominant fatty acids are iso-C 15 : 0 (35.4 %), iso-C 15 : 0 2-OH and/or C 16 : 1 v7c (27.8 %) and iso-C 17 : 0 3-OH (15.8 %). On the basis of these data, strain 15-52 T represents a novel species of the genus Pedobacter, for which the name Pedobacter suwonensis sp. nov. is proposed. The type strain is 15-52 T (=KACC 11317 T =DSM 18130 T ).
BackgroundHypsizygus marmoreus (Beech mushroom) is a popular ingredient in Asian cuisine. The medicinal effects of its bioactive compounds such as hypsin and hypsiziprenol have been reported, but the genetic basis or biosynthesis of these components is unknown.ResultsIn this study, we sequenced a reference strain of H. marmoreus (Haemi 51,987–8). We evaluated various assembly strategies, and as a result the Allpaths and PBJelly produced the best assembly. The resulting genome was 42.7 Mbp in length and annotated with 16,627 gene models. A putative gene (Hypma_04324) encoding the antifungal and antiproliferative hypsin protein with 75% sequence identity with the previously known N-terminal sequence was identified. Carbohydrate active enzyme analysis displayed the typical feature of white-rot fungi where auxiliary activity and carbohydrate-binding modules were enriched. The genome annotation revealed four terpene synthase genes responsible for terpenoid biosynthesis. From the gene tree analysis, we identified that terpene synthase genes can be classified into six clades. Four terpene synthase genes of H. marmoreus belonged to four different groups that implies they may be involved in the synthesis of different structures of terpenes. A terpene synthase gene cluster was well-conserved in Agaricomycetes genomes, which contained known biosynthesis and regulatory genes.ConclusionsGenome sequence analysis of this mushroom led to the discovery of the hypsin gene. Comparative genome analysis revealed the conserved gene cluster for terpenoid biosynthesis in the genome. These discoveries will further our understanding of the biosynthesis of medicinal bioactive molecules in this edible mushroom.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5159-y) contains supplementary material, which is available to authorized users.
Jae-Beom Lee et al. 535With video compression standards such as MPEG-4, a transmission error happens in a video-packet basis, rather than in a macroblock basis. In this context, we propose a semantic error prioritization method that determines the size of a video packet based on the importance of its contents. A video packet length is made to be short for an important area such as a facial area in order to reduce the possibility of error accumulation. To facilitate the semantic error prioritization, an efficient hardware algorithm for face tracking is proposed. The increase of hardware complexity is minimal because a motion estimation engine is efficiently re-used for face tracking. Experimental results demonstrate that the facial area is well protected with the proposed scheme.
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