Lachancea mirantina sp. nov., an ascomycetous yeast isolated from the cachaça fermentation process

Pereira, Leonardo Costa; Costa, César Raimundo Lima; Brasileiro, Bereneuza Tavares Ramos Valente; Morais, Marcos Antônio de

doi:10.1099/ijs.0.020008-0

Cited by 11 publications

(9 citation statements)

References 18 publications

(29 reference statements)

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“…Previous phylogenetic analysis based on nuclear rDNA sequences (the D1/D2 domains of the 26S rRNA and 5.8S ITS region) already allowed the exploration of the relationship between Lachancea yeasts [4], [6], [7], [8], [9]. Overall, there is a high congruence of the topology found in these studies and the one we previously described.…”

Section: Resultssupporting

confidence: 74%

“…Here, we report the complete mt genome sequence of five Lachancea species: L. dasiensis (CBS 10888), L. nothofagi (CBS 11611), L. mirantina (CBS 11717), L. fantastica (CBS 6924) and L. meyersii (CBS 8951) [6], [7], [8], [9]. These strains were isolated from various geographical locations and ecological niches (seawater, soil, plants, and distillery).…”

Section: Introductionmentioning

confidence: 99%

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Comparative Mitochondrial Genomics within and among Yeast Species of the Lachancea Genus

et al. 2012

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Yeasts are leading model organisms for mitochondrial genome studies. The explosion of complete sequence of yeast mitochondrial (mt) genomes revealed a wide diversity of organization and structure between species. Recently, genome-wide polymorphism survey on the mt genome of isolates of a single species, Lachancea kluyveri, was also performed. To compare the mitochondrial genome evolution at two hierarchical levels: within and among closely related species, we focused on five species of the Lachancea genus, which are close relatives of L. kluyveri. Hence, we sequenced the complete mt genome of L. dasiensis, L. nothofagi, L. mirantina, L. fantastica and L. meyersii. The phylogeny of the Lachancea genus was explored using these data. Analysis of intra- and interspecific variability across the whole Lachancea genus led to the same conclusions regarding the mitochondrial genome evolution. These genomes exhibit a similar architecture and are completely syntenic. Nevertheless, genome sizes vary considerably because of the variations of the intergenic regions and the intron content, contributing to mitochondrial genome plasticity. The high variability of the intergenic regions stands in contrast to the high level of similarity of protein sequences. Quantification of the selective constraints clearly revealed that most of the mitochondrial genes are under purifying selection in the whole genus.

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Section: Resultssupporting

confidence: 74%

Section: Introductionmentioning

confidence: 99%

Comparative Mitochondrial Genomics within and among Yeast Species of the Lachancea Genus

et al. 2012

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“…Based on our survey of the literature, the fungi in Classes 4-6 are capable of sexual reproduction (Wickerham et al, 1970;Sutton, 1982;Goto et al, 1987;Briza et al, 1990;Raju and Perkins, 1994;Gordon and Martyn, 1997;Keller et al, 1997;Britz et al, 1998;Harrington and Wingfield, 1998;Davis and Smith, 2001;Galagan et al, 2003;Dean et al, 2005;Rau et al, 2005;Rouxel and Balesdent, 2005;Paoletti et al, 2007;Rossi and Languasco, 2007;Tavanti et al, 2007;TeBeest et al, 2007;Bentley et al, 2008;Alby et al, 2009;Seidl et al, 2009;Mestre et al, 2010;Pereira et al, 2011;Rubini et al, 2011;Kurtzman and Robnett, 2012;Wada et al, 2012;Böhm et al, 2013;Studt et al, 2013;Short et al, 2014;Terhem and van Kan, 2014;Marin-Felix et al, 2015;Meng et al, 2015;Belfiori et al, 2016;Cowger et al, 2016;Doughan and Rollins, 2016;Gazis et al, 2016;Lee et al, 2016;Pelin et al, 2016;Son et al, 2016;…”

Section: Genome-wide In Silico Rip Analysis Of the Ascomycotamentioning

confidence: 99%

Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota

et al. 2021

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The Repeat-Induced Point (RIP) mutation pathway is a fungus-specific genome defense mechanism that mitigates the deleterious consequences of repeated genomic regions and transposable elements (TEs). RIP mutates targeted sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence and extent of RIP with a sliding-window approach. Using genome-wide RIP data and two sets of control groups, the association between RIP, TEs, and GC content were contrasted in organisms capable and incapable of RIP. Based on these data, we then set out to determine the extent and occurrence of RIP in 58 representatives of the Ascomycota. The findings were summarized by placing each of the fungi investigated in one of six categories based on the extent of genome-wide RIP. In silico RIP analyses, using a sliding-window approach with stringent RIP parameters, implemented simultaneously within the same genetic context, on high quality genome assemblies, yielded superior results in determining the genome-wide RIP among the Ascomycota. Most Ascomycota had RIP and these mutations were particularly widespread among classes of the Pezizomycotina, including the early diverging Orbiliomycetes and the Pezizomycetes. The most extreme cases of RIP were limited to representatives of the Dothideomycetes and Sordariomycetes. By contrast, the genomes of the Taphrinomycotina and Saccharomycotina contained no detectable evidence of RIP. Also, recent losses in RIP combined with controlled TE proliferation in the Pezizomycotina subphyla may promote substantial genome enlargement as well as the formation of sub-genomic compartments. These findings have broadened our understanding of the taxonomic range and extent of RIP in Ascomycota and how this pathway affects the genomes of fungi harboring it.

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“…We selected seven Lachancea species: L. cidri, L. fermentati (both formerly called Zygosaccharomyces species) (Kurtzman 2003), L. meyersii (Fell et al 2004), L. dasiensis (Lee et al 2009), L. mirantina (Pereira et al 2011), L. nothofagi (Mestre et al 2010), and L. fantastica nomen nudum (Fig. 1).…”

Section: Methodsmentioning

confidence: 99%

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

et al. 2016

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Reconstructing genome history is complex but necessary to reveal quantitative principles governing genome evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of genome architecture and gene repertoire. Here, we reconstructed the genome history of the genus Lachancea that appeared to cover a continuous evolutionary range from closely related to more diverged yeast species. Our approach integrated the generation of a high-quality genome data set; the development of AnChro, a new algorithm for reconstructing ancestral genome architecture; and a comprehensive analysis of gene repertoire evolution. We found that the ancestral genome of the genus Lachancea contained eight chromosomes and about 5173 protein-coding genes. Moreover, we characterized 24 horizontal gene transfers and 159 putative gene creation events that punctuated species diversification. We retraced all chromosomal rearrangements, including gene losses, gene duplications, chromosomal inversions and translocations at single gene resolution. Gene duplications outnumbered losses and balanced rearrangements with 1503, 929, and 423 events, respectively. Gene content variations between extant species are mainly driven by differential gene losses, while gene duplications remained globally constant in all lineages. Remarkably, we discovered that balanced chromosomal rearrangements could be responsible for up to 14% of all gene losses by disrupting genes at their breakpoints. Finally, we found that nonsynonymous substitutions reached fixation at a coordinated pace with chromosomal inversions, translocations, and duplications, but not deletions. Overall, we provide a granular view of genome evolution within an entire eukaryotic genus, linking gene content, chromosome rearrangements, and protein divergence into a single evolutionary framework.

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Lachancea mirantina sp. nov., an ascomycetous yeast isolated from the cachaça fermentation process

Cited by 11 publications

References 18 publications

Comparative Mitochondrial Genomics within and among Yeast Species of the Lachancea Genus

Comparative Mitochondrial Genomics within and among Yeast Species of the Lachancea Genus

Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

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