scholarly journals Extreme diversification driven by parallel events of massive loss of heterozygosity in the hybrid lineage of Candida albicans

Genetics ◽  
2020 ◽  
Vol 217 (2) ◽  
Author(s):  
Verónica Mixão ◽  
Ester Saus ◽  
Teun Boekhout ◽  
Toni Gabaldón
Keyword(s):  
Candida Albicans ◽  
Loss Of Heterozygosity ◽  
Type Strain ◽  
Taxonomic Classification ◽  
Hybrid Origin ◽  
Genomic Analyses ◽  
Candida Africana

Abstract Candida albicans is the most commonly reported species causing candidiasis. The taxonomic classification of C. albicans and related lineages is controversial, with Candida africana (syn. C. albicans var. africana) and Candida stellatoidea (syn. C. albicans var. stellatoidea) being considered different species or C. albicans varieties depending on the authors. Moreover, recent genomic analyses have suggested a shared hybrid origin of C. albicans and C. africana, but the potential parental lineages remain unidentified. Although the genomes of C. albicans and C. africana have been extensively studied, the genome of C. stellatoidea has not been sequenced so far. In order to get a better understanding of the evolution of the C. albicans clade, and to assess whether C. stellatoidea could represent one of the unknown C. albicans parental lineages, we sequenced C. stellatoidea type strain (CBS 1905). This genome was compared to that of C. albicans and of the closely related lineage C. africana. Our results show that, similarly to C. africana, C. stellatoidea descends from the same hybrid ancestor as other C. albicans strains and that it has undergone a parallel massive loss of heterozygosity.

scholarly journals Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

2019 ◽  
Vol 10 ◽  
Author(s):  
Marina García-López ◽  
Jan P. Meier-Kolthoff ◽  
Brian J. Tindall ◽  
Sabine Gronow ◽  
Tanja Woyke ◽  
...  
Keyword(s):  
Type Strain ◽  
Taxonomic Classification

scholarly journals Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

2020 ◽  
Vol 11 ◽  
Author(s):  
Anton Hördt ◽  
Marina García López ◽  
Jan P. Meier-Kolthoff ◽  
Marcel Schleuning ◽  
Lisa-Maria Weinhold ◽  
...  
Keyword(s):  
Type Strain ◽  
Taxonomic Classification

233 Contribution of the loss of heterozygosity in the classification of BRCA1 variants

2015 ◽  
Vol 51 ◽  
pp. S38
Author(s):  
E. Santana Dos Santos ◽  
S. Caputo ◽  
A. Briaux ◽  
M. Southey ◽  
A. Spurdle ◽  
...  
Keyword(s):  
Loss Of Heterozygosity

Genetic characteristics and taxonomic classification of Fimic Anthrosols in China

Geoderma ◽  
2003 ◽  
Vol 115 (1-2) ◽  
pp. 31-44 ◽  
Author(s):  
Min Zhang ◽  
Li Ma ◽  
Wenqing Li ◽  
Baocheng Chen ◽  
Jiwen Jia
Keyword(s):  
Taxonomic Classification ◽  
Genetic Characteristics

scholarly journals A singular value decomposition approach for improved taxonomic classification of biological sequences

BMC Genomics ◽  
2011 ◽  
Vol 12 (Suppl 4) ◽  
pp. S11 ◽  
Author(s):  
Anderson R Santos ◽  
Marcos A Santos ◽  
Jan Baumbach ◽  
John A McCulloch ◽  
Guilherme C Oliveira ◽  
...  
Keyword(s):  
Singular Value Decomposition ◽  
Singular Value ◽  
Taxonomic Classification ◽  
Biological Sequences ◽  
Decomposition Approach ◽  
Value Decomposition

scholarly journals CaNdt80 Is Involved in Drug Resistance in Candida albicans by Regulating CDR1

2004 ◽  
Vol 48 (12) ◽  
pp. 4505-4512 ◽  
Author(s):  
Chia-Geun Chen ◽  
Yun-Liang Yang ◽  
Hsin-I Shih ◽  
Chia-Li Su ◽  
Hsiu-Jung Lo
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Drug Resistance ◽  
Candida Albicans ◽  
Type Strain ◽  
Antifungal Agents ◽  
Wild Type Strain ◽  
Efflux Pump ◽  
Antifungal Drugs ◽  
Galactosidase Activity ◽  
Wild Type

ABSTRACT Overexpression of CDR1, an efflux pump, is one of the major mechanisms contributing to drug resistance in Candida albicans. CDR1 p-lacZ was constructed and transformed into a Saccharomyces cerevisiae strain so that the lacZ gene could be used as the reporter to monitor the activity of the CDR1 promoter. Overexpression of CaNDT80, the C. albicans homolog of S. cerevisiae NDT80, increases the β-galactosidase activity of the CDR1 p-lacZ construct in S. cerevisiae. Furthermore, mutations in CaNDT80 abolish the induction of CDR1 expression by antifungal agents in C. albicans. Consistently, the Candt80/Candt80 mutant is also more susceptible to antifungal drugs than the wild-type strain. Thus, the gene for CaNdt80 may be the first gene among the regulatory factors involved in drug resistance in C. albicans whose function has been identified.

VirusTaxo: Taxonomic classification of virus genome using multi-class hierarchical classification by k-mer enrichment

2021 ◽  
Author(s):  
Rajan Saha Raju ◽  
Abdullah Al Nahid ◽  
Preonath Shuvo ◽  
Rashedul Islam
Keyword(s):  
Genome Sequence ◽  
Rna Viruses ◽  
Hierarchical Classification ◽  
Classification Problem ◽  
Virus Genome ◽  
Taxonomic Classification ◽  
Dna Viruses ◽  
Dna And Rna ◽  
Full Length Genome

AbstractTaxonomic classification of viruses is a multi-class hierarchical classification problem, as taxonomic ranks (e.g., order, family and genus) of viruses are hierarchically structured and have multiple classes in each rank. Classification of biological sequences which are hierarchically structured with multiple classes is challenging. Here we developed a machine learning architecture, VirusTaxo, using a multi-class hierarchical classification by k-mer enrichment. VirusTaxo classifies DNA and RNA viruses to their taxonomic ranks using genome sequence. To assign taxonomic ranks, VirusTaxo extracts k-mers from genome sequence and creates bag-of-k-mers for each class in a rank. VirusTaxo uses a top-down hierarchical classification approach and accurately assigns the order, family and genus of a virus from the genome sequence. The average accuracies of VirusTaxo for DNA viruses are 99% (order), 98% (family) and 95% (genus) and for RNA viruses 97% (order), 96% (family) and 82% (genus). VirusTaxo can be used to detect taxonomy of novel viruses using full length genome or contig sequences.AvailabilityOnline version of VirusTaxo is available at https://omics-lab.com/virustaxo/.

scholarly journals Functional and taxonomic classification of a greenhouse water drain metagenome

2018 ◽  
Vol 13 (1) ◽  
Author(s):  
Gamaliel López-Leal ◽  
Fernanda Cornejo-Granados ◽  
Juan Manuel Hurtado-Ramírez ◽  
Alfredo Mendoza-Vargas ◽  
Adrian Ochoa-Leyva
Keyword(s):  
Taxonomic Classification ◽  
Water Drain

scholarly journals Psychroserpens Luteus Sp. Nov., Isolated fFrom Red Algae

2021 ◽  
Author(s):  
Xiu-Ya Ping ◽  
Kai Wang ◽  
Jin-Yu Zhang ◽  
Shu-Xin Wang ◽  
Zong-Jun Du ◽  
...  
Keyword(s):  
Red Algae ◽  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Abstract A Gram-stain-negative, gliding-motile, positive for catalase, facultative anaerobic, designated strain XSD401T, was isolated from the red algae of Xiaoshi Island, Shandong Province, China. Growth occurred at 20–37 °C (optimum, 33 °C), pH 5.5–9.5 (optimum, pH 6.5–7.5), and with 0.5–5% (w/v) NaCl (optimum, 3%). The main fatty acids are iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, iso-C15:0 3-OH, C16:0. Phosphatidylethanolamine (PE), three unidentified aminolipids (AL1, AL2, AL3) and one unidentified lipid (L) were the major polar lipids. The G+C content of the genomic DNA was 33.9 mol%. Strain XSD401T had the highest sequence similarity (96.88%) to the 16S rRNA gene of Psychroserpens damuponensis KCTC 23539T. The similarities with Psychroserpens burtonensis DSM 12212T was 96.31%. The dDDH values between strain XSD401T and P. damuponensis KCTC 23539T, P. burtonensis DSM 12212T, were 20.40% and 20.30%, respectively. The average nucleotide identity (ANI) values between strain XSD401T and P. damuponensis KCTC 23539T, P. burtonensis DSM 12212T were 76.91%, 76.88%, respectively. The differences in morphology, physiology and genotype from the previously described taxa support the classification of strain XSD401T as a representative of a novel species of the genus Psychroserpens, for which the name Psychroserpens luteus sp. nov. is proposed. The type strain is XSD401T (= MCCC 1H00396T = KCTC 72684T = JCM 33931T).

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