Intraspecific nucleotide divergence in Saccharomycodes ludwigii, and proposal of Saccharomycodes pseudoludwigii sp. nov, a new apiculate yeast isolated from China

2021 ◽  
Vol 114 (5) ◽  
pp. 553-559
Author(s):  
Man-Man Wang ◽  
Marizeth Groenewald ◽  
Feng Wu ◽  
Yun-Tong Guo ◽  
Qi-Ming Wang ◽  
...  
Keyword(s):  
Saccharomycodes Ludwigii ◽  
Nucleotide Divergence

Characteristics of Cornelian cherry sour non-alcoholic beers brewed with the special yeast Saccharomycodes ludwigii

2020 ◽  
Vol 312 ◽  
pp. 125968 ◽  
Author(s):  
Kinga Adamenko ◽  
Joanna Kawa-Rygielska ◽  
Alicja Z. Kucharska
Keyword(s):  
Cornelian Cherry ◽  
Saccharomycodes Ludwigii

scholarly journals Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
J. Robert Macey ◽  
Stephan Pabinger ◽  
Charles G. Barbieri ◽  
Ella S. Buring ◽  
Vanessa L. Gonzalez ◽  
...  
Keyword(s):  
Genomic Organization ◽  
Phylogenetic Analyses ◽  
Genomic Polymorphism ◽  
Sequencing Technologies ◽  
Cold Tolerant ◽  
Long Read ◽  
Sphenodon Punctatus ◽  
Nucleotide Divergence ◽  
Mitochondrial Heteroplasmy ◽  
Transmembrane Regions

AbstractAnimal mitochondrial genomic polymorphism occurs as low-level mitochondrial heteroplasmy and deeply divergent co-existing molecules. The latter is rare, known only in bivalvian mollusks. Here we show two deeply divergent co-existing mt-genomes in a vertebrate through genomic sequencing of the Tuatara (Sphenodon punctatus), the sole-representative of an ancient reptilian Order. The two molecules, revealed using a combination of short-read and long-read sequencing technologies, differ by 10.4% nucleotide divergence. A single long-read covers an entire mt-molecule for both strands. Phylogenetic analyses suggest a 7–8 million-year divergence between genomes. Contrary to earlier reports, all 37 genes typical of animal mitochondria, with drastic gene rearrangements, are confirmed for both mt-genomes. Also unique to vertebrates, concerted evolution drives three near-identical putative Control Region non-coding blocks. Evidence of positive selection at sites linked to metabolically important transmembrane regions of encoded proteins suggests these two mt-genomes may confer an adaptive advantage for an unusually cold-tolerant reptile.

Bulinus species on Madagascar: molecular evolution, genetic markers and compatibility with Schistosoma haematobium

Parasitology ◽  
2001 ◽  
Vol 123 (7) ◽  
pp. 261-275 ◽  
Author(s):  
J. R. STOTHARD ◽  
P. BRÉMOND ◽  
L. ANDRIAMARO ◽  
B. SELLIN ◽  
E. SELLIN ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Subunit ◽  
Population Genetic Analysis ◽  
Basal Node ◽  
Pcr Rflp ◽  
Dna Sequence Variation ◽  
Long Time ◽  
Laboratory Infection ◽  
Species Groups ◽  
Nucleotide Divergence

Of the four species of Bulinus found on Madagascar, three species: B. obtusispira, B. liratus and B. bavayi are endemic while the fourth, B. forskalii, is probably a recent introduction from the African mainland. The evolutionary relationships of these species with Bulinus species from Africa were studied by phylogenetic analysis of DNA sequence variation at two mitochondrial loci: cytochrome oxidase subunit I (COI) and large ribosomal subunit (LSU) or 16S. The observed levels of nucleotide divergence within Bulinus were substantial but may underestimate the true levels as there was evidence of ‘saturation' of transitional substitutions at both loci. A putative secondary structure model for the sequenced segment of the 16S was developed. Subsequent phylogenetic analysis using transversional changes only for both loci, showed that there were contrasting levels of divergence within the four species groups. B. obtusispira was consistently placed within the B. africanus group, appearing ancestral to this group and was closest to the basal node within Bulinus. Together with B. bavayi, the two species appear to have been isolated on Madagascar for a long time, contrasting with both B. liratus and B. forskalii that appear more recent colonisers; however, estimate of exact times of divergence is problematic. A PCR-RFLP assay was developed to enable identification and discrimination of B. obtusispira and B. liratus using discriminatory variation within the COI. To enable population genetic analysis within B. obtusispira, microsatellite markers were developed using an enrichment method and 8 primer pairs are reported. Laboratory infection experiments using Madasgacan S. haematobium from the Mahabo area showed that certain populations of B. obtusispira, B. liratus and B. bavayi were compatible.

scholarly journals Molecular analysis of the hot spot region related to length mutations in wheat chloroplast DNAs. I. Nucleotide divergence of genes and intergenic spacer regions located in the hot spot region.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 873-884 ◽  
Author(s):  
Y Ogihara ◽  
T Terachi ◽  
T Sasakuma
Keyword(s):  
Dna Sequences ◽  
Gene Evolution ◽  
Hot Spot ◽  
Intergenic Spacer ◽  
Open Reading Frames ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Plant Groups ◽  
Nucleotide Divergence ◽  
Chloroplast Dnas

Abstract The nucleotide divergence of chloroplast DNAs around the hot spot region related to length mutation in Triticum (wheat) and Aegilops was analyzed. DNA sequences (ca. 4.5 kbp) of three chloroplast genome types of wheat complex were compared with one another and with the corresponding region of other grasses. The sequences region contained rbcL and psaI, two open reading frames, and a pseudogene, rpl23' (pseudogene for ribosomal protein L23) disrupted by AT-rich intergic spacer regions. The evolution of these genes in the closely related wheat complex is characterized by nonbiased nucleotide substitutions in terms of being synonymous/nonsynonymous, having A-T pressure transitions over transversions, and frequent changes at the third codon position, in contrast with the gene evolution among more distant plant groups where biased nucleotide substitutions have frequently occurred. The sequences of these genes had diverged almost in proportion to taxonomic distance. The sequence of the pseudogene rpl23' changed approximately two times faster than that of the coding region. Sequence comparison between the pseudogene and its protein-coding counterpart revealed different degrees of nucleotide homology in wheat, rice and maize, suggesting that the transposition timing of the pseudogene differed and/or that different rates of gene conversion operated on the pseudogene in the cpDNA of the three plant groups in Gramineae. The intergenic spacer regions diverged approximately ten times faster than the genes. The divergence of wheat from barley, and that from rice are estimated based on the nucleotide similarity to be 1.5, 10 and 40 million years, respectively.

scholarly journals Sequence Diversity and Molecular Evolution of the Leukotoxin (lktA) Gene in Bovine and Ovine Strains ofMannheimia (Pasteurella)haemolytica

2001 ◽  
Vol 183 (4) ◽  
pp. 1394-1404 ◽  
Author(s):  
Robert L. Davies ◽  
Thomas S. Whittam ◽  
Robert K. Selander
Keyword(s):  
Molecular Evolution ◽  
Allelic Diversity ◽  
Pasteurella Haemolytica ◽  
Intragenic Recombination ◽  
Allelic Variants ◽  
Amino Acid Divergence ◽  
History Of ◽  
Nucleotide Divergence ◽  
Pasteurella Trehalosi ◽  
Different Sources

ABSTRACT The molecular evolution of the leukotoxin structural gene (lktA) of Mannheimia (Pasteurella)haemolytica was investigated by nucleotide sequence comparison of lktA in 31 bovine and ovine strains representing the various evolutionary lineages and serotypes of the species. Eight major allelic variants (1.4 to 15.7% nucleotide divergence) were identified; these have mosaic structures of varying degrees of complexity reflecting a history of horizontal gene transfer and extensive intragenic recombination. The presence of identical alleles in strains of different genetic backgrounds suggests that assortative (entire gene) recombination has also contributed to strain diversification in M. haemolytica. Five allelic variants occur only in ovine strains and consist of recombinant segments derived from as many as four different sources. Four of these alleles consist of DNA (52.8 to 96.7%) derived from the lktA gene of the two related species Mannheimia glucosida andPasteurella trehalosi, and four contain recombinant segments derived from an allele that is associated exclusively with bovine or bovine-like serotype A2 strains. The two major lineages of ovine serotype A2 strains possess lktA alleles that have very different evolutionary histories and encode divergent leukotoxins (5.3% amino acid divergence), but both contain segments derived from the bovine allele. Homologous segments of donor and recipient alleles are identical or nearly identical, indicating that the recombination events are relatively recent and probably postdate the domestication of cattle and sheep. Our findings suggest that host switching of bovine strains from cattle to sheep, together with inter- and intraspecies recombinational exchanges, has played an important role in generating leukotoxin diversity in ovine strains. In contrast, there is limited allelic diversity of lktA in bovine strains, suggesting that transmission of strains from sheep to cattle has been less important in leukotoxin evolution.

scholarly journals Remarkable morphological variation in the proboscis of Neorhadinorhynchus nudus (Harada, 1938) (Acanthocephala: Echinorhynchida)

Parasitology ◽  
2018 ◽  
Vol 146 (3) ◽  
pp. 348-355 ◽  
Author(s):  
Liang Li ◽  
Matthew Thomas Wayland ◽  
Hui-Xia Chen ◽  
Yue Yang
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Markers ◽  
South China Sea ◽  
Intraspecific Variation ◽  
Dna Sequences ◽  
Intestinal Wall ◽  
Congeneric Species ◽  
Genetic Lineages ◽  
Nucleotide Divergence ◽  
Auxis Thazard

AbstractThe acanthocephalans are characterized by a retractible proboscis, armed with rows of recurved hooks, which serves as the primary organ for attachment of the adult worm to the intestinal wall of the vertebrate definitive host. Whilst there is a considerable variation in the size, shape and armature of the proboscis across the phylum, intraspecific variation is generally regarded to be minimal. Consequently, subtle differences in proboscis morphology are often used to delimit congeneric species. In this study, striking variability in proboscis morphology was observed among individuals of Neorhadinorhynchus nudus (Harada, 1938) collected from the frigate tuna Auxis thazard Lacépède (Perciformes: Scombridae) in the South China Sea. Based on the length of the proboscis, and number of hooks per longitudinal row, these specimens of N. nudus were readily grouped into three distinct morphotypes, which might be considered separate taxa under the morphospecies concept. However, analysis of nuclear and mitochondrial DNA sequences revealed a level of nucleotide divergence typical of an intraspecific comparison. Moreover, the three morphotypes do not represent three separate genetic lineages. The surprising, and previously undocumented level of intraspecific variation in proboscis morphology found in the present study, underscores the need to use molecular markers for delimiting acanthocephalan species.

Toward a resolution of the cosmopolitan Botryllus schlosseri species complex (Ascidiacea, Styelidae): mitogenomics and morphology of clade E (Botryllus gaiae)

2020 ◽  
Author(s):  
Riccardo Brunetti ◽  
Francesca Griggio ◽  
Francesco Mastrototaro ◽  
Fabio Gasparini ◽  
Carmela Gissi
Keyword(s):  
Species Complex ◽  
Taxonomic Status ◽  
Intestinal Loop ◽  
Botryllus Schlosseri ◽  
Colonial Ascidian ◽  
Coding Regions ◽  
Nucleotide Divergence ◽  
Globally Distributed ◽  
Entire Mitochondrial Genome ◽  
Identical Gene

Abstract Botryllus schlosseri is a model colonial ascidian and a marine invader. It is currently recognized as a species complex comprising five genetically divergent clades, with clade A globally distributed and clade E found only in Europe. This taxon has also been recently redescribed by designation of a clade A specimen as the neotype. To clarify the taxonomic status of clade E and its relationship to clade A, we examine the entire mitochondrial genome and study the morphology of clade E. The mitogenome of clade E has an identical gene order to clade A, but substantially differs in the size of several non-coding regions. Remarkably, the nucleotide divergence of clade A-clade E is incompatible with the intraspecies ascidian divergence, but similar to the congeneric one and almost identical to the divergence between species once considered morphologically indistinguishable (e.g. the pair Ciona intestinalis (Linnaeus, 1767)-Ciona robusta Hoshino & Tokioka, 1967, and the pair Botrylloides niger Herdman, 1886-Botrylloides leachii (Savigny, 1816)). Clade E differs morphologically from the Botryllusschlosseri neotype mainly in the number and appearance of the stomach folds, and the shape of the anal opening, the first intestinal loop and the typhlosole. Our integrative taxonomical approach clearly distinguishes clade E as a species separate from Botryllusschlosseri, with unique morphological and molecular characters. Therefore, we here describe clade E as the new species Botryllus gaiae sp. nov.

scholarly journals Characterizing the Potential of the Non-Conventional Yeast Saccharomycodes ludwigii UTAD17 in Winemaking

2019 ◽  
Vol 7 (11) ◽  
pp. 478 ◽  
Author(s):  
Esteves ◽  
Barbosa ◽  
Vasconcelos ◽  
Tavares ◽  
Mendes-Faia ◽  
...  
Keyword(s):  
Starter Culture ◽  
Grape Juice ◽  
Wine Quality ◽  
Mixed Culture Fermentation ◽  
Saccharomycodes Ludwigii ◽  
Saccharomyces Yeast ◽  
Low Levels ◽  
Wine Region ◽  
Potential Use ◽  
Saccharomyces Yeasts

Non-Saccharomyces yeasts have received increased attention by researchers and winemakers, due to their particular contributions to the characteristics of wine. In this group, Saccharomycodes ludwigii is one of the less studied species. In the present study, a native S. ludwigii strain, UTAD17 isolated from the Douro wine region was characterized for relevant oenological traits. The genome of UTAD17 was recently sequenced. Its potential use in winemaking was further evaluated by conducting grape-juice fermentations, either in single or in mixed-cultures, with Saccharomyces cerevisiae, following two inoculation strategies (simultaneous and sequential). In a pure culture, S. ludwigii UTAD17 was able to ferment all sugars in a reasonable time without impairing the wine quality, producing low levels of acetic acid and ethyl acetate. The overall effects of S. ludwigii UTAD17 in a mixed-culture fermentation were highly dependent on the inoculation strategy which dictated the dominance of each yeast strain. Wines whose fermentation was governed by S. ludwigii UTAD17 presented low levels of secondary aroma compounds and were chemically distinct from those fermented by S. cerevisiae. Based on these results, a future use of this non-Saccharomyces yeast either in monoculture fermentations or as a co-starter culture with S. cerevisiae for the production of wines with greater expression of the grape varietal character and with flavor diversity could be foreseen.

scholarly journals Genome Sequence of the Wine Yeast Saccharomycodes ludwigii UTAD17

2018 ◽  
Vol 7 (18) ◽  
Author(s):  
Maria J. Tavares ◽  
Ulrich Güldener ◽  
Marcos Esteves ◽  
Arlete Mendes-Faia ◽  
Ana Mendes-Ferreira ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Wine Yeast ◽  
Aroma Compounds ◽  
Content Type ◽  
Fermented Beverages ◽  
Spoilage Yeast ◽  
Wine Spoilage ◽  
Saccharomycodes Ludwigii ◽  
First Time

This work describes, for the first time, the genome sequence of a Saccharomycodes ludwigii strain. Although usually seen as a wine spoilage yeast, S. ludwigii has been of interest for the production of fermented beverages because it harbors several interesting properties, including the production of beneficial aroma compounds.

scholarly journals Distribution and Genetic Diversity of the ABC Transporter Lipoproteins PiuA and PiaA within Streptococcus pneumoniae and Related Streptococci

2006 ◽  
Vol 188 (3) ◽  
pp. 1031-1038 ◽  
Author(s):  
Rachael H. Whalan ◽  
Simon G. P. Funnell ◽  
Lucas D. Bowler ◽  
Michael J. Hudson ◽  
Andrew Robinson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Streptococcus Pneumoniae ◽  
Oral Streptococci ◽  
Pneumococcal Infections ◽  
Closely Related Species ◽  
Streptococcus Oralis ◽  
Amino Acid Divergence ◽  
Genes Encoding ◽  
Associated Proteins ◽  
Nucleotide Divergence

ABSTRACT Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide. The existence of approximately 90 antigenically distinct capsular serotypes has greatly complicated the development of an effective pneumococcal vaccine. Virulence-associated proteins common and conserved among all capsular types now represent the best strategy to combat pneumococcal infections. PiuA and PiaA are the lipoprotein components of two pneumococcal iron ABC transporters and are required for full virulence in mouse models of infection. Here we describe a study of the distribution and genetic diversity of PiuA and PiaA within typical and atypical S. pneumoniae, Streptococcus oralis, and Streptococcus mitis strains. The genes encoding both PiuA and PiaA were present in all typical pneumococci tested, (covering 20 and 27 serotypes, respectively). The piuA gene was highly conserved within the typical pneumococci (0.3% nucleotide divergence), but was also present in “atypical” pneumococci and the closely related species S. mitis and S. oralis, showing up to 10.4% nucleotide divergence and 7.5% amino acid divergence from the typical pneumococcal alleles. Conversely, the piaA gene was found to be specific to typical pneumococci, 100% conserved, and absent from the oral streptococci, including isolates of S. mitis known to possess pneumolysin and autolysin. These are desirable qualities for a vaccine candidate and as a diagnostic tool for S. pneumoniae.

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