Draft Genome Sequence of Naganishia liquefaciens Strain N6, Isolated from the Japan Trench

Han, Yong-Woon; Kajitani, Rei; Morimoto, Hiroya; Palihati, Maierdan; Kurokawa, Yumiko; Ryusui, Rie; Argunhan, Bilge; Tsubouchi, Hideo; Abe, Fumiyoshi; Kajiwara, Susumu; Iwasaki, Hiroshi; Itoh, Takehiko

doi:10.1128/mra.00827-20

Cited by 7 publications

(13 citation statements)

References 11 publications

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“…Close relatives of Vishniacozyma carnescens, i.e., V. alagoana and V. victoriae, were recently reported as endophytes of bromeliads (Félix et al, 2020) and maple tree (Wemheuer et al, 2019), respectively. In addition, some of the yeasts isolated in this study (Tausonia pullulans and Naganishia liquefaciens) were not reported earlier as endophytic colonizers in plants; however, their existence in soils and extreme habitats has been reported (Han et al, 2020;Li A. H. et al, 2020).…”

Section: Microbial Communities In a Euchromacontrasting

confidence: 48%

Arnebia euchroma, a Plant Species of Cold Desert in the Himalayas, Harbors Beneficial Cultivable Endophytes in Roots and Leaves

et al. 2021

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The endophytic mutualism of plants with microorganisms often leads to several benefits to its host including plant health and survival under extreme environments. Arnebia euchroma is an endangered medicinal plant that grows naturally in extreme cold and arid environments in the Himalayas. The present study was conducted to decipher the cultivable endophytic diversity associated with the leaf and root tissues of A. euchroma. A total of 60 bacteria and 33 fungi including nine yeasts were isolated and characterized at the molecular level. Among these, Proteobacteria was the most abundant bacterial phylum with the abundance of Gammaproteobacteria (76.67%) and genus Pseudomonas. Ascomycota was the most abundant phylum (72.73%) dominated by class Eurotiales (42.42%) and genus Penicillium among isolated fungal endophytes. Leaf tissues showed a higher richness (Schao1) of both bacterial and fungal communities as compared to root tissues. The abilities of endophytes to display plant growth promotion (PGP) through phosphorus (P) and potassium (K) solubilization and production of ACC deaminase (ACCD), indole acetic acid (IAA), and siderophores were also investigated under in vitro conditions. Of all the endophytes, 21.51% produced ACCD, 89.25% solubilized P, 43.01% solubilized K, 68.82% produced IAA, and 76.34% produced siderophores. Six bacteria and one fungal endophyte displayed all the five PGP traits. The study demonstrated that A. euchroma is a promising source of beneficial endophytes with multiple growth-promoting traits. These endophytes can be used for improving stress tolerance in plants under nutrient-deficient and cold/arid conditions.

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Section: Microbial Communities In a Euchromacontrasting

confidence: 48%

Arnebia euchroma, a Plant Species of Cold Desert in the Himalayas, Harbors Beneficial Cultivable Endophytes in Roots and Leaves

et al. 2021

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“…S6b), and the ability to thrive under conditions that are practically the same as those for S. cerevisiae, are highly advantageous traits as a model organism. Furthermore, we recently determined the draft genome sequence of this organism (Han et al 2020). Together, this has enabled the application of molecular genetics approaches to N. liquefaciens, which provide further means to promote in-depth study of Basidiomycota biology.…”

Section: Discussionmentioning

confidence: 99%

“…We recently drafted the whole genome sequence and gene structure of the strain N6 and used the obtained genomic data to construct a maximum-likelihood phylogenetic tree in the class Tremellomycetes (Han et al 2020). While the genome annotation is ongoing, this result further supported the classification of strain N6 within the clade of the genus Naganishia, leading us to propose that this strain be named Naganishia liquefaciens N6 (Han et al 2020). We do not currently have information about the ploidy or sexual cycle of this strain.…”

Section: Introductionmentioning

confidence: 90%

“…Genomic DNA sequence of the genes used in this study are available in the DDBJ/EMBL/GenBank databases under the following accession numbers: MT185598 for HIS3, MT185599 for ADE2, MT185600 for LEU2, MT185601 for TRP2, MT185602 for RAD51, MT185603 for RAD52, MT185604 for KU70, MT210101 for ACT1 and MT210102 for TEF1. The draft genome sequence of N. liquefaciens is available in the DDBJ/EMBL/GenBank databases (accession number BLZA00000000.1) (Han et al 2020).…”

Section: Genomic Dna Sequences Of the Genes Used In This Studymentioning

confidence: 99%

“…However, recent studies have proposed that C. liquefaciens actually belongs to the genus Naganishia in the order Filobasidiales, while C. neoformans belongs to the order Tremellales (Liu et al 2015). We recently drafted the whole genome sequence and gene structure of the strain N6 and used the obtained genomic data to construct a maximum-likelihood phylogenetic tree in the class Tremellomycetes (Han et al 2020). While the genome annotation is ongoing, this result further supported the classification of strain N6 within the clade of the genus Naganishia, leading us to propose that this strain be named Naganishia liquefaciens N6 (Han et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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Homology length dictates the requirement for Rad51 and Rad52 in gene targeting in the Basidiomycota yeast Naganishia liquefaciens

et al. 2021

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Here, we report the development of methodologies that enable genetic modification of a Basidiomycota yeast, Naganishia liquifaciens. The gene targeting method employs electroporation with PCR products flanked by an 80 bp sequence homologous to the target. The method, combined with a newly devised CRISPR-Cas9 system, routinely achieves 80% gene targeting efficiency. We further explored the genetic requirement for this homologous recombination (HR)-mediated gene targeting. The absence of Ku70, a major component of the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair, almost completely eliminated inaccurate integration of the marker. Gene targeting with short homology (80 bp) was almost exclusively dependent on Rad52, an essential component of HR in the Ascomycota yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. By contrast, the RecA homolog Rad51, which performs homology search and strand exchange in HR, plays a relatively minor role in gene targeting, regardless of the homology length (80 bp or 1 kb). The absence of both Rad51 and Rad52, however, completely eliminated gene targeting. Unlike Ascomycota yeasts, the absence of Rad52 in N. liquefaciens conferred only mild sensitivity to ionizing radiation. These traits associated with the absence of Rad52 are reminiscent of findings in mice.

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Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeastFilobasidium floriforme

Guerreiro

Ahrendt

Pangilinan

et al. 2021

G3 Genes|Genomes|Genetics

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The Tremellomycetes are a species-rich group within the basidiomycete fungi; however, most analyses of this group to date have focused on pathogenic Cryptococcus species within the order Tremellales. Recent genome-assisted studies of other Tremellomycetes have identified interesting features with respect to biotechnological applications as well as the evolution of genes involved in mating and sexual development. Here, we report genome sequences of two strains of Filobasidium floriforme, a species from the order Filobasidiales, which branches basally to the Tremellales, Trichosporonales, and Holtermanniales. The assembled genomes of strains CBS6241 and CBS6242 are 27.4 Mb and 26.4 Mb in size, respectively, with 8314 and 7695 predicted protein-coding genes. Overall sequence identity at nucleic acid level between the strains is 97%. Among the predicted genes are pheromone precursor and pheromone receptor genes as well as two genes encoding homedomain (HD) transcription factors, which are predicted to be part of the mating type (MAT) locus. Sequence analysis indicates that CBS6241 and CBS6242 carry different alleles for both the pheromone/receptor genes as well as the HD transcription factors. Orthology inference identified 1482 orthogroups exclusively found in F. floriforme, some of which were involved in carbohydrate transport and metabolism. Subsequent CAZyme repertoire characterization identified 267 and 247 enzymes for CBS6241 and CBS6242, respectively, the second highest number of CAZymes among the analyzed Tremellomycete species. In addition, F. floriforme contains five CAZymes absent in other species and several plant-cell-wall degrading CAZymes with the highest copy number in Tremellomycota, indicating the biotechnological potential of this species.

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Draft Genome Sequence of Naganishia liquefaciens Strain N6, Isolated from the Japan Trench

Cited by 7 publications

References 11 publications

Arnebia euchroma, a Plant Species of Cold Desert in the Himalayas, Harbors Beneficial Cultivable Endophytes in Roots and Leaves

Arnebia euchroma, a Plant Species of Cold Desert in the Himalayas, Harbors Beneficial Cultivable Endophytes in Roots and Leaves

Homology length dictates the requirement for Rad51 and Rad52 in gene targeting in the Basidiomycota yeast Naganishia liquefaciens

Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeastFilobasidium floriforme

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