Lachancea dasiensis sp. nov., an ascosporogenous yeast isolated from soil and leaves in Taiwan

Lee, Ching-Fu; Yao, Cheng-Hsu; Liu, Yiru; Hsieh, Chin-Wen; Young, Soogil

doi:10.1099/ijs.0.008789-0

Cited by 19 publications

(10 citation statements)

References 17 publications

(17 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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“…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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“…PCR products were analyzed by 1% agarose gel electrophoresis. The nucleotide sequences of the D1/D2 domain of the large subunit (LSU) rRNA gene and internal transcribed spacer (ITS) regions of the strain from Taiwan were done according to procedures described by Lee et al (2009). The D1/D2 variable domains of the LSU rRNA gene and ITS regions of the Brazilian strains were amplified by PCR directly from whole cells as described by Lachance et al (1999).…”

Section: Yeast Isolation and Identificationmentioning

confidence: 99%

Saturnispora serradocipensis sp. nov. and Saturnispora gosingensis sp. nov., two ascomycetous yeasts from ephemeral habitats

Canelhas

Barbosa

Medeiros

et al. 2010

Antonie van Leeuwenhoek

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Two novel ascomycetous yeast species, Saturnispora serradocipensis and Saturnispora gosingensis, were isolated from leaf detritus in a tropical stream of Southeastern Brazil and a mushroom collected in Taiwan, respectively. Analysis of the D1/D2 domains of the large-subunit of the rRNA gene of these strains showed that these species are related to Saturnispora hagleri, their closest relative. Saturnispora serradocipensis and S. gosingensis differed from S. hagleri, respectively, by seven nucleotide substitutions and two indels and three nucleotide substitutions and three indels in D1/D2 rRNA sequences. The two new species differ from each another by four nucleotide substitutions and one indel in D1/D2 rRNA sequences. However, the ITS sequences of S. serradocipensis, S. gosingensis and S. hagleri were quite divergent, showing that they are genetically separate species. The type strain of S. serradocipensis is UFMG-DC-198(T) (=CBS 11756(T) = NRRL Y-48717(T)), and of S. gosingensis GA4M05(T) is (CBS 11755(T) = NRRL Y-48718(T)).

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Lachancea dasiensis sp. nov., an ascosporogenous yeast isolated from soil and leaves in Taiwan

Cited by 19 publications

References 17 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

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

Saturnispora serradocipensis sp. nov. and Saturnispora gosingensis sp. nov., two ascomycetous yeasts from ephemeral habitats

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