Karyotyping Methods for Fungi

Mehrabi, Rahim; Taga, Masatoki; Aghaee, Mostafa; Wit, P.J.G.M. de; Kema, G.H.J.

doi:10.1007/978-1-61779-501-5_37

Cited by 6 publications

(5 citation statements)

References 14 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In order to comprehensively identify genetic components related to sclerotium formation, we sequenced a cultivated strain of W. cocos 2018LT001 (sampled in Luotian, Hubei, China; named WCLT hereafter). We first determined the chromosome number of this strain using the germ burst method ( Mehrabi et al, 2012 ), which clearly showed 14 chromosomes of diploid WCLT under microscopy ( Supplementary Figure 1 ). After sequencing by Illumina and PacBio platforms, we estimated the WCLT genome size to be 62 Mb (in haploid) using 31-nt k-mers ( Marçais and Kingsford, 2011 ).…”

Section: Resultsmentioning

confidence: 99%

“…We performed Illumina and PacBio platform sequencing, together with Hi-C-assisted assembly for a cultivated strain of W. cocos PCmonoA, to draft a chromosomal-level genome. Prior to sequencing, we were able to observe the W. cocos chromosome numbers under light and fluorescent microscopy by a germ bust method ( Mehrabi et al, 2012 ). The 14 chromosomes from microscopy were consistent with the sequence assembly of the diploid W. cocos .…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Genomic and Transcriptomic Insight of Giant Sclerotium Formation of Wood-Decay Fungi

Cao

Yang

Bi³

et al. 2021

Front. Microbiol.

View full text Add to dashboard Cite

Many fungi form persistent and dormant sclerotia with compact hardened mycelia during unfavorable circumstances. While most of these sclerotia are small in size, Wolfiporia cocos, a wood-decay fungus, grows into giant sclerotia, which are mainly composed of polysaccharides of linear (1→3)-β-D-glucans. To explore the underlying mechanism of converting sophisticated wood polysaccharides for biosynthesis of highly homogenized glucans in W. cocos, we sequenced and assembled the genome of a cultivated W. cocos strain (WCLT) in China. The 62-Mb haploid genome contains 44.2% repeat sequences, of which, 48.0% are transposable elements (TEs). Contrary to the genome of W. cocos from North America, WCLT has independently undergone a partial genome duplication (PGD) event. The large-scale TE insertion and PGD occurrence overlapped with an archeological Pleistocene stage of low oxygen and high temperature, and these stresses might have induced the differences in sclerotium due to geographical distribution. The wood decomposition enzymes, as well as sclerotium-regulator kinases, aquaporins, and highly expanded gene families such as NAD-related families, together with actively expressed 1,3-β-glucan synthase for sclerotium polysaccharides, all have contributed to the sclerotium formation and expansion. This study shall inspire further exploration on how fungi convert wood into simple glucans in the sclerotium of W. cocos.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genomic and Transcriptomic Insight of Giant Sclerotium Formation of Wood-Decay Fungi

Cao

Yang

Bi³

et al. 2021

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…dahliae mycelium was prepared for protoplasting following the mycelium-based fungal biomass preparation method (Mehrabi et al 2012). Mycelium was digested in 1 M sorbitol containing 1% (w/v) glucanex and 0.5% driselase (Sigma-Aldrich) at 32°C until protoplast concentration reached 10 8 /mL.…”

Section: Karyotypingmentioning

confidence: 99%

“…Mycelium was digested in 1 M sorbitol containing 1% (w/v) glucanex and 0.5% driselase (Sigma-Aldrich) at 32°C until protoplast concentration reached 10 8 /mL. Protoplast plugs were prepared and stored as described (Mehrabi et al 2012). Karyotyping was carried out using a CHEF Mapper XA pulsed field electrophoresis system (Bio-Rad) using the auto algorithm function with low-and high-molecular weight settings at 2 and 6 Mb, respectively.…”

Section: Karyotypingmentioning

confidence: 99%

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

et al. 2013

View full text Add to dashboard Cite

Sexual recombination drives genetic diversity in eukaryotic genomes and fosters adaptation to novel environmental challenges. Although strictly asexual microorganisms are often considered as evolutionary dead ends, they comprise many devastating plant pathogens. Presently, it remains unknown how such asexual pathogens generate the genetic variation that is required for quick adaptation and evolution in the arms race with their hosts. Here, we show that extensive chromosomal rearrangements in the strictly asexual plant pathogenic fungus Verticillium dahliae establish highly dynamic lineage-specific (LS) genomic regions that act as a source for genetic variation to mediate aggressiveness. We show that such LS regions are greatly enriched for in planta-expressed effector genes encoding secreted proteins that enable host colonization. The LS regions occur at the flanks of chromosomal breakpoints and are enriched for retrotransposons and other repetitive sequence elements. Our results suggest that asexual pathogens may evolve by prompting chromosomal rearrangements, enabling rapid development of novel effector genes. Likely, chromosomal reshuffling can act as a general mechanism for adaptation in asexually propagating organisms.

show abstract

“…Strains were maintained as slant cultures using synthetic low nutrient agar (SNA, Nirenberg 1976 ), vegetable juice agar [10 % (v /v) mix vegetable juice (Kagome, Nagoya, Japan), 0.3 % (w /v) CaCO3, 1.5 % (w/v) agar] or potato dextrose agar (Difco, Detroit, Michigan). The germ tube burst method (GTBM) was used to prepare microscope slides containing mitotic metaphase chromosomes as previously described ( Taga et al , 1998 , Tsuchiya & Taga 2010 , Mehrabi et al 2012 ). To obtain macroconidia for the GTBM, fusaria were cultured on SNA containing small pieces of filter paper ( Aoki & O’Donnell 1999 ), carnation leaf agar (CLA) ( Nelson et al 1983 ) or mung bean broth (MBB, Gale et al 2005 ).…”

Section: Methodsmentioning

confidence: 99%

Karyotype evolution in Fusarium

Waalwijk¹,

Taga

Zheng

et al. 2018

IMA Fungus

Self Cite

View full text Add to dashboard Cite

The germ tube burst method (GTBM) was employed to examine karyotypes of 33 Fusarium species representative of 11 species complexes that span the phylogenetic breadth of the genus. The karyotypes revealed that the nucleolar organizing region (NOR), which includes the ribosomal rDNA region, was telomeric in the species where it was discernible. Variable karyotypes were detected in eight species due to variation in numbers of putative core and/or supernumerary chromosomes. The putative core chromosome number (CN) was most variable in the F. solani (CN = 9‒12) and F. buharicum (CN = 9+1 and 18-20) species complexes. Quantitative real-time PCR and genome sequence analysis rejected the hypothesis that the latter variation in CN was due to diploidization. The core CN in six other species complexes where two or more karyotypes were obtained was less variable or fixed. Karyotypes of 10 species in the sambucinum species complex, which is the most derived lineage of Fusarium, revealed that members of this complex possess the lowest CN in the genus. When viewed in context of the species phylogeny, karyotype evolution in Fusarium appears to have been dominated by a reduction in core CN in five closely related complexes that share a most recent common ancestor (tricinctum and incarnatum-equiseti CN = 8-9, chlamydosporum CN = 8, heterosporum CN = 7, sambucinum CN = 4-5) but not in the sister to these complexes (nisikadoi CN = 11, oxysporum CN = 11 and fujikuroi CN = 10-12). CN stability is best illustrated by the F. sambucinum subclade, where the only changes observed since it diverged from other fusaria appear to have involved two independent putative telomere to telomere fusions that reduced the core CN from five to four, once each in the sambucinum and graminearum subclades. Results of the present study indicate a core CN of 4 may be fixed in the latter subclade, which is further distinguished by the absence of putative supernumerary chromosomes. Karyotyping of fusaria in the not too distant future will be done by whole-genome sequencing such that each scaffold represents a complete chromosome from telomere to telomere. The CN data presented here should be of value to assist such full genome assembling.

show abstract

Karyotyping Methods for Fungi

Cited by 6 publications

References 14 publications

Genomic and Transcriptomic Insight of Giant Sclerotium Formation of Wood-Decay Fungi

Genomic and Transcriptomic Insight of Giant Sclerotium Formation of Wood-Decay Fungi

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

Karyotype evolution in Fusarium

Contact Info

Product

Resources

About