Development and utilisation of conserved-intron scanning marker in sugarcane

Genetic dissection of economic traits in sugarcane requires sufficiently informative molecular markers that are currently lacking in this highly valued crop. Through comparative analysis of publicly available expressed-sequence data of sugarcane, sorghum and barley, and the whole rice genome-sequence survey, novel functional markers based on conserved-intron scanning primers (CISP) were developed and evaluated in different accessions across various taxonomic ranks of sugarcane. Polymorphism was moderate (55.2%), whereas 94.7% of the markers developed amplified fragments in selected genotypes. Mean polymorphism information content value was 0.582 (range 0.320–0.715), which was comparable to that with genic microsatellite markers (0.52) but lower than that with EST-SSR (0.73). Genetic-similarity coefficient ranged from 0.39 to 0.95, indicating variable levels of divergence depending on the taxonomic rank assessed. Cluster analysis revealed that the genotypes grouped in accordance with the taxonomical classification of sugarcane, with a relatively good support from a Mantel’s test (r = 0.847) and a moderate bootstrap value (65–89%). The CISP markers reported in the present study have potential utility for genetic-diversity analysis and application in sugarcane-breeding programs.

Transcriptional Response of Candida parapsilosis following Exposure to Farnesol

ABSTRACT In Candida albicans, the quorum-sensing molecule farnesol inhibits the transition from yeast to hyphae but has no effect on cellular growth. We show that the addition of exogenous farnesol to cultures of Candida parapsilosis causes the cells to arrest, but not at a specific stage in the cell cycle. The cells are not susceptible to additional farnesol. However, the cells do eventually recover from arrest. Unlike in C. albicans, in C. parapsilosis sterols are localized to the tips of budding cells, and this polarization is disrupted by the addition of farnesol. We used the results of a genome sequence survey to design and manufacture partial genomic microarrays that were applied to determining the transcriptional response of C. parapsilosis to the presence of exogenous farnesol. In both C. albicans and C. parapsilosis, exposure to farnesol results in increased expression of the oxidoreductases GRP2 and ADH7 and altered expression of genes involved in sterol metabolism. There is no effect on expression of C. parapsilosis orthologs of genes involved in hyphal growth in C. albicans. Farnesol therefore differs significantly in its effects on C. parapsilosis and C. albicans.

A Genome Sequence Survey Shows that the Pathogenic Yeast Candida parapsilosis Has a Defective MTLa1 Allele at Its Mating Type Locus

ABSTRACT Candida parapsilosis is responsible for ca. 15% of Candida infections and is of particular concern in neonates and surgical intensive care patients. The related species Candida albicans has recently been shown to possess a functional mating pathway. To analyze the analogous pathway in C. parapsilosis, we carried out a genome sequence survey of the type strain. We identified ca. 3,900 genes, with an average amino acid identity of 59% with C. albicans. Of these, 23 are predicted to be predominantly involved in mating. We identified a genomic locus homologous to the MTL a mating type locus of C. albicans, but the C. parapsilosis type strain has at least two internal stop codons in the MTL a 1 open reading frame, and two predicted introns are not spliced. These stop codons were present in MTL a 1 of all eight C. parapsilosis isolates tested. Furthermore, we found that all isolates of C. parapsilosis tested appear to contain only the MTL a idiomorph at the presumptive mating locus, unlike C. albicans and C. dubliniensis. MTLα sequences are present but at a different chromosomal location. It is therefore likely that all (or at least the majority) of C. parapsilosis isolates have a mating pathway that is either defective or substantially different from that of C. albicans.

Genome Sequence Survey Identifies Unique Sequences and Key Virulence Genes with Unusual Rates of Amino Acid Substitution in Bovine Staphylococcus aureus

ABSTRACT Staphylococcus aureus is a major cause of mastitis in bovine and other ruminant species. We here present the results of a comparative genomic analysis between a bovine mastitis-associated clone, RF122, and the recently sequenced human-associated clones, Mu50 and N315, of Staphylococcus aureus. A shotgun sequence survey of ∼10% of the RF122 genome identified numerous unique sequences and those with elevated rates of nonsynonymous substitution. Taken together, these analyses show that there are notable differences in the genomes of bovine mastitis-associated and human clones of S. aureus and provide a framework for the identification of specific factors associated with host specificity in this major human and animal pathogen.