The completed genome sequence of the pathogenic ascomycete fungus Penicillium digitatum

P. digitatum, the causative agent of green mold, is one of the most destructive pathogens in the citrus industry. To facilitate basal researches on this important plant pathogen, here we report a finished genome sequence for P. digitatum strain PDW03 using a combination of Illumina, PacBio, and Hi-C sequencing technologies. The assembly comprised 6 chromosomes from telomere to telomere and encodes approximately 9000 proteins. Genomic re-analyses identified 302 Carbohydrate-active enzymes, 420 secreted proteins, and 39 secondary metabolite (SM) gene clusters. Furthermore, we found 10 fragmentary SM clusters in the P. digitatum PDW03 genome. Pangenome analysis based on 5 P. digitatum genomes available showed that conserved orthogroups account for ~68% of the species pangenome. Taken together, this fully completed P. digitatum genome will provide an optimum resource for further researches to investigate the driving forces of fungal host switch and effectors functioning in plant-pathogen interaction.     

The completed human genome: implications for chemical biology

The recently completed human genome sequence represents an enormous opportunity to understand biology and accelerate the development of new therapeutics. However, it also presents equally large logistical, scientific and paradigmatic challenges to efficiently translate the enormous cache of sequence data into functional information that will be the precursor of new drug development. Small-molecule chemical biology applied on a genomic scale promises to speed this translation to novel therapeutics.     

The genome sequence of Podospora anserina, a classic model fungus

The completed genome sequence of the coprophilous fungus Podospora anserina increases the sampling of fungal genomes. In line with its habitat of herbivore dung, this ascomycete has an exceptionally rich gene set devoted to the catabolism of complex carbohydrates.     

Detection and production condition of acetylxylan esterase from a wood-rotting fungus,Coriolus versicolor

Acetyl esterase production was detected in a wood-rotting fungus,Coriolus versicolor, by the formation of a clear zone on a double layer agar plate containing glucose β-d-pentaacetate. Two polysaccharide acetates, carboxymethyl cellulose acetate and xylan acetate, also served as detectable substrates in place of glucose acetate to form clear zone. In an esterase assay, this fungal esterase showed a higher specificity to acetylxylan than did porcine liver esterase, indicating that it is an acetylxylan esterase.     

The fungus Pestalotiopsis guepini as a model for biotransformation of ciprofloxacin and norfloxacin

The metabolism of the fluoroquinolone drugs ciprofloxacin and norfloxacin by Pestalotiopsis guepini strain P-8 was investigated. Cultures were grown at 28 degrees C in sucrose/peptone broth for 18 days after dosing with ciprofloxacin (300 microM) or norfloxacin (313 microM). Four major metabolites were produced from each drug; and these were purified by high-performance liquid chromatography and identified by mass spectrometry and proton nuclear magnetic resonance spectroscopy. Ciprofloxacin metabolites included N-acetylciprofloxacin (52.0%), desethylene-N-acetylciprofloxacin (9.2%), N-formylciprofloxacin (4.2%), and 7-amino-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (2.3%). Norfloxacin metabolites included N-acetylnorfloxacin (55.4%), desethylene-N-acetylnorfloxacin (8.8%), N-formylnorfloxacin (3.6%), and 7-amino-1-ethyl-6-fluoro4-oxo-1,4-dihydroquinoline-3-carboxylic acid (2.1%). N-Formylciprofloxacin and the four transformation products from norfloxacin are all known to be mammalian metabolites.     

Development of simple sequence repeat markers for the plant pathogenic rust fungus,Puccinia graminis

Twenty‐four dinucleotide simple sequence repeat markers were developed for the phytopathogenic fungus, Puccinia graminis. The identified loci were polymorphic, with allelic diversity ranging from two to 11 alleles. Observed and expected levels of heterozygosity ranged from 0.000 to 0.960 and from 0.113 to 0.846, respectively. Fourteen of the loci deviated significantly from Hardy–Weinberg equilibrium. Null alleles were observed for 10 of the 24 loci with a frequency of 4–16%. A preliminary screen of other Puccinia cereal rust fungi (P. coronata, P. striiformis and P. triticina) indicated that these primer pairs are specific to P. graminis.     

Sporothrix globosa,a pathogenic fungus with widespread geographical distribution

Sporothrix globosa, reported from the USA, Europe, and Asia, is a recently described pathogenic species morphologically similar to Sporothrix schenckii. In this study, the phylogenetic affinities of 32 clinical and environmental isolates morphologically identified as S. schenckii, from Mexico, Guatemala, and Colombia, were assessed by cladistic analysis of partial sequences of the calmodulin gene using the maximum parsimony and neighbor-joining methods. The study revealed that one out of 25 isolates from Mexico (4%), one out of three isolates from Guatemala (33.3%), and two out of four isolates from Colombia (50%) belonged to S. globosa, while the other isolates belonged to S. schenckii sensu stricto. This is the first record of S. globosa from Mexico, and Central and South America.     

Influence of vanillin on the production of cellulolytic and xylanolytic enzymes from a wood-rotting fungus,Coriolus versicolor

To examine the influence of a phenolic compound on the production of cellulolytic and xylanolytic enzymes of a woodrotting fungusCoriolus versicolor, a two-dimensional map of enzyme activity was constructed with various concentrations of cellobiose and vanillin. The productions of CMCase, xylanase, β-glucosidase, and β-xylosidase increased with higher cellobiose concentration and were markedly enhanced by addition of vanillin. Higher ratio of vanillin/cellobiose activated the production of these enzymes. Only acetyl esterase, which is not actively produced at the ligninolytic stage ofC. versicolor, was inhibited by the monolignol vanillin. As the presence of vanillin is considered to approximate conditions of wood decay more closely than its absence, the present result demonstrates that addition of vanillin, a phenolic compound, enhanced the production of cellulolytic and xylanolytic enzymes for wood cell wall degradation.     

Evidence for plasmid like DNA in a filamentous fungus, the ascomycete Podospora anserina

Summary The existece of plasmid like DNA was demonstrated in senescent mycelia of Podospora anserina (strain s) by biophysical and electronmicroscopic methods. According to their contour length of about 1.4 and 2.7 m respectively the molecular weight for the monomer is in the range of 3·10⁶.This work was supported by the Deutsche Forschungsgemeinschaft. The sojourn of P.A.L. for six months in Bochum was made possible by a Senior U.S. Scientist Award of the Alexander von Humboldt Stiftung (Bonn).     

Development of simple sequence repeat markers for the plant pathogenic rust fungus Puccinia triticina

Eighteen polymorphic di‐ and trinucleotide simple sequence repeat markers were developed for the phytopathogenic rust fungus Puccinia triticina. The allelic diversity varied from two to nine alleles per locus. Levels of observed heterozygosity ranged from 0.095 to 0.952. Seven of the loci deviated significantly from Hardy–Weinberg equilibrium (P < 0.002) with 70% having levels of observed heterozygosity higher than expected heterozygosity. Null allele(s) were observed for locus PtSSR76 with a frequency of 9%. A preliminary screen of other cereal rust fungi (P. coronata, P. graminis, P. recondita and P. striiformis) indicated that these primer pairs are specific to P. triticina.     

Conservative sorting in the muroplasts of Cyanophora paradoxa: a reevaluation based on the completed genome sequence

After primary endosymbiosis, massive gene transfer occurred from the genome of the cyanobacterial endosymbiont to the nucleus of the protist host cell. In parallel, a specific protein import apparatus arose for reimport of many, but not all products of the genes moved to the nuclear genome. Presequences evolved to allow recognition of plastid proteins at the envelope and their translocation to the stroma. However, plastids (and cyanobacteria) also comprise five other subcompartments. Protein sorting to the cyanobacterial thylakoid membrane, the thylakoid lumen, the inner envelope membrane, the periplasmic space, and the outer envelope membrane is achieved by prokaryotic protein translocases recognizing, e.g., signal sequences. The “conservative sorting” hypothesis postulates that these translocases remained functional in endosymbiotic organelles and obtained their passengers not only from imported proteins but also from proteins synthesized in organello. For proteins synthesized in the cytosol, a collaboration of the general import apparatus and the former prokaryotic translocase is necessary which is often reflected by the use of bipartite presequences, e.g., stroma targeting peptide and signal peptide. For plants, this concept has been experimentally proven and verified. The muroplasts from Cyanophora paradoxa, that have several features more in common with cyanobacteria than with plastids, were analyzed with the availability of the recently completed nuclear genome sequence. Interesting findings include the absence of the post-translational signal recognition particle pathway, dual Sec translocases in thylakoid and inner envelope membranes that are produced from a single set of genes, and a co-translational signal recognition pathway operating without a 4.5S RNA component.     

Complete genome sequence of a highly pathogenic porcine reproductive and respiratory syndrome virus variant

Following the 2006 outbreaks of the highly pathogenic porcine reproductive and respiratory syndrome, the causative agent was identified as the highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV). To investigate whether the HP-PRRSV variant continues circulating and accelerating evolution, we sequenced and analyzed the complete genome of the identified HP-PRRSV field strain SD16. The sequence data indicate that the HP-PRRSV variant continues to prevail and accelerate evolution, especially in the nonstructural protein.     

The complete mitochondrial genome sequence of the pathogenic yeast Candida (Torulopsis) glabrata

We report here the complete sequence of the mitochondrial (mt) genome of the pathogenic yeast Candida glabrata. This 20 kb mt genome is the smallest among sequenced hemiascomycetous yeasts. Despite its compaction, the mt genome contains the genes encoding the apocytochrome b (COB), three subunits of ATP synthetase (ATP6, 8 and 9), three subunits of cytochrome oxidase (COX1, 2 and 3), the ribosomal protein VAR1, 23 tRNAs, small and large ribosomal RNAs and the RNA subunit of RNase P. Three group I introns each with an intronic open reading frame are present in the COX1 gene. This sequence is available under accession number AJ511533.     

The many uses of a genome sequence

A report on the Keystone Symposium on 'Human Genetics and Genomics', Breckenridge, Colorado, USA, 31 March to 6 April, 2001.     

The home stretch,a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1

Rhodobacter sphaeroides 2.4.1 is an α-3 purple nonsulfur eubacterium with an extensive metabolic repertoire. Under anaerobic conditions, it is able to grow by photosynthesis, respiration and fermentation. Photosynthesis may be photoheterotrophic using organic compounds as both a carbon and a reducing source, or photoautotrophic using carbon dioxide as the sole carbon source and hydrogen as the source of reducing power. In addition, R. sphaeroides can grow both chemoheterotrophically and chemoautotrophically. The structural components of this metabolically diverse organism and their modes of integrated regulation are encoded by a genome of ∼4.5 Mb in size. The genome comprises two chromosomes CI and CII (2.9 and 0.9 Mb, respectively) and five other replicons. Sequencing of the genome has been carried out by two groups, the Joint Genome Institute, which carried out shotgun-sequencing of the entire genome and The University of Texas-Houston Medical School, which carried out a targeted sequencing strategy of CII. Here we describe our current understanding of the genome when data from both of these groups are combined. Previous work had suggested that the two chromosomes are equal partners sharing responsibilities for fundamental cellular processes. This view has been reinforced by our preliminary analysis of the virtually completed genome sequence. We also have some evidence to suggest that two of the plasmids, pRS241a and pRS241b encode chromosomal type functions and their role may be more than that of accessory elements, perhaps representing replicons in a transition state. This revised version was published online in June 2006 with corrections to the Cover Date.