Characterization of Non-coding Regions in B Mating Loci of Agrocybe salicacola Groups: Target Sites for B Mating Type Identification

Chen, Weimin; Chai, Hongmei; Yang, Wei; Zhang, Xiaolei; Chen, Yuhui; Zhao, Yongchang

doi:10.1007/s00284-017-1247-5

Cited by 3 publications

(4 citation statements)

References 23 publications

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“…Here, three STEs ( STE3.1 , STE3.2, and STE3.3 ), three PHBs ( PHB1 , PHB2, and PHB3 ), and two STEs ( STE3.s1 and STE3.s2 ) were identified in a ~ 22 kb region on chromosome 8 of H. marmoreus . Similar to Agrocybe salicacola (Chen et al 2017 ) , the pheromone gene in H. marmoreus were closely located to the pheromone receptor genes, indicating that it probably played a mating-type specific role as its orthologous gene. The STEs without neighboring PHB were not considered to participate in the mating-type discrimination (Chen et al 2016a ).…”

Section: Discussionmentioning

confidence: 80%

Genetic structure and evolutionary diversity of mating-type (MAT) loci in Hypsizygus marmoreus

Wang

Chen

et al. 2021

IMA Fungus

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The mating compatibility in fungi is generally governed by genes located within a single or two unlinked mating type (MAT) loci. Hypsizygus marmoreus is an edible mushroom in the order Agaricales with a tetrapolar system, which contains two unlinked MAT loci-homeodomain (HD) transcription factor genes and pheromone/pheromone receptor genes (P/R). In this study, we analyzed the genetic structure and diversity of MAT loci in tetrapolar system of H. marmoreus through sequencing of 54 heterokaryon and 8 homokaryon strains. Although within the HD loci, the gene order was conserved, the gene contents were variable, and the HD loci haplotypes were further classified into four types. By analyzing the structure, phylogeny, and the HD transmissibility based on the progeny of these four HD mating-type loci types, we found that they were heritable and tightly linked at the HD loci. The P/R loci genes were found to comprise three pheromone receptors, three pheromones, and two pheromone receptor-like genes. Intra- and inter-specific phylogenetic analyses of pheromone receptors revealed that the STE3 genes were divided into three groups, and we thus theorize that they diverged before speciation. Comparative analysis of the MAT regions among 73 Basidiomycete species indicated that the diversity of HD and P/R loci in Agaricales and Boletales may contribute to mating compatibility. The number of HD genes were not correlated with the tetrapolar or bipolar systems. In H. marmoreus, the expression levels of these genes at HD and P/R loci of compatible strains were found higher than in those of homonuclear/homokaryotic strains, indicating that these mating genes acted as switches for mating processes. Further collinear analysis of HD loci in interspecific species found that HD loci contains conserved recombination hotspots showing major rearrangements in Coprinopsis cinerea and Schizophyllum commune, suggesting different mechanisms for evolution of physically linked MAT loci in these groups. It seems likely that gene rearrangements are common in Agaricales fungi around HD loci. Together, our study provides insights into the genomic basis of mating compatibility in H. marmoreus.

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Section: Discussionmentioning

confidence: 80%

Genetic structure and evolutionary diversity of mating-type (MAT) loci in Hypsizygus marmoreus

Wang

Chen

et al. 2021

IMA Fungus

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“…The first one almost exclusively comprises strains of European origin, except for C. aegerita (AaM) that was isolated from basidiomes bought in a US supermarket. The Chinese species C. salicaceicola (solely based on C. salicaceicola YAASM0711 from Yunnan, China), a close relative of C. aegerita according to Yang et al ( 1993 ) and Chen et al ( 2012 , 2015 , 2017 ), groups in a well-supported sister clade towards the European lineage of “ C. aegerita s.l.”. The second major branch of “ C. aegerita s.l.” includes all its Asian strains, all assigned to Cyclocybe sp., and one outlier ( C. parasitica PDD 95998) of the Pacific species C. parasitica from New Zealand.…”

Section: Resultsmentioning

confidence: 99%

“…This is an interesting finding as C. salicaceicola was originally described from Yunnan (China) as a species that is morphologically similar to C. aegerita according to Yang et al ( 1993 ) and hardly to distinguish from C. aegerita according to Chen et al ( 2012 ), who based their conclusions on molecular species differentiation. Unfortunately, our official request for strains of C. salicaceicola to the authors of Chen et al ( 2012 , 2015 , 2017 ) was refused with the statement that it is their core resource, which they cannot give abroad. Hence, we could not check whether the fruiting properties of C. salicaceicola may resemble those of C. aegerita .…”

Section: Discussionmentioning

confidence: 99%

“…Despite of requests for strains of the Chinese species C. salicaceicola (Zhu L. Yang, M. Zang & X.X. Liu) Vizzini from the authors Chen et al ( 2012 , 2015 , 2017 ), the handing over of such material was refused. Cryo-stocking of all strains and fruiting induction, with some modifications in single strains (Table 2 ), were carried out as previously described (Herzog et al 2016 ).…”

Section: Methodsmentioning

confidence: 99%

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Multilocus phylogeny- and fruiting feature-assisted delimitation of European Cyclocybe aegerita from a new Asian species complex and related species

et al. 2020

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Cyclocybe aegerita (synonym: Agrocybe aegerita) is a widely cultivated edible and reportedly almost cosmopolitan mushroom species that serves as a model fungus for basidiome formation and as producer of useful natural products and enzymes. Focusing on strains from different continents, here, we present a phylogenetic analysis of this species and some adjacent taxa that employs four phylogenetic markers. In addition, we tested the strains’ capability to fructify on agar media. Our analysis reveals that “C. aegerita sensu lato” splits up into the following two well-supported monophyletic geographic lineages: a European clade and an Asian clade. The European one is closely associated with the Chinese species Cyclocybe salicaceicola. In contrast, the Asian lineage, which we preliminarily designate as Cyclocybe chaxingu agg., may comprise several species (species complex) and clusters with the Pacific species Cyclocybe parasitica (New Zealand). In addition, fruiting properties differ across C. aegerita and its Asian and Pacific relatives; however, strains from the Asian clade and C. parasitica tend to form larger basidiomes with relatively big caps and long stipes and strains from the European clade exhibit a more variable fruiting productivity with the tendency to form more basidiomes, with smaller caps and shorter stipes. Moreover, some strains showed individual fruiting patterns, such as the preference to fruit where they were exposed to injuring stimuli. In conclusion, the delimitation of the newly delimited Asian species complex from our multilocus phylogeny of “C. aegerita sensu lato”, which is supported by phenotypic data, depicts an exemplary case of biogeographic diversity within a previously thought homogeneous species of near worldwide distribution.

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Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights

Chen,

Wei,

Meng

et al. 2024

JoF

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Agrocybe chaxingu is a widely cultivated edible fungus in China, which is rich in nutrients and medicinal compounds. However, the lack of a high-quality genome hinders further research. In this study, we assembled the telomere-to-telomere genomes of two sexually compatible monokaryons (CchA and CchB) derived from a primarily cultivated strain AS-5. The genomes of CchA and CchB were 50.60 Mb and 51.66 Mb with contig N50 values of 3.95 Mb and 3.97 Mb, respectively. Each contained 13 complete chromosomes with telomeres at both ends. The high mapping rate, uniform genome coverage, high LAI score, all BUSCOs with 98.5%, and all base accuracy exceeding 99.999% indicated the high level of integrity and quality of these two assembled genomes. Comparison of the two genomes revealed that approximately 30% of the nucleotide sequences between homologous chromosomes were non-syntenic, including 19 translocations, 36 inversions, and 15 duplications. An additional gene CchA_000467 was identified at the Mat A locus of CchA, which was observed exclusively in the Cyclocybe cylindracea species complex. A total of 613 (4.26%) and 483 (3.4%) unique genes were identified in CchA and CchB, respectively, with over 80% of these being hypothetical proteins. Transcriptomic analysis revealed that the expression levels of unique genes in CchB were significantly higher than those in CchA, and both CchA and CchB had unique genes specifically expressed at stages of mycelium and fruiting body. It was indicated that the growth and development of the A. chaxingu strain AS-5 required the coordinated action of two different nuclei, with CchB potentially playing a more significant role. These findings contributed to a more profound comprehension of the growth and developmental processes of basidiomycetes.

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Characterization of Non-coding Regions in B Mating Loci of Agrocybe salicacola Groups: Target Sites for B Mating Type Identification

Cited by 3 publications

References 23 publications

Genetic structure and evolutionary diversity of mating-type (MAT) loci in Hypsizygus marmoreus

Genetic structure and evolutionary diversity of mating-type (MAT) loci in Hypsizygus marmoreus

Multilocus phylogeny- and fruiting feature-assisted delimitation of European Cyclocybe aegerita from a new Asian species complex and related species

Telomere-to-Telomere Haplotype-Resolved Genomes of Agrocybe chaxingu Reveals Unique Genetic Features and Developmental Insights

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