Candida species are the most common cause of opportunistic fungal infection worldwide. We report the genome sequences of six Candida species and compare these and related pathogens and nonpathogens. There are significant expansions of cell wall, secreted, and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the Mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/alpha2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine to serine genetic code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the C. albicans gene catalog, identifying many new genes.

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BackgroundThe discovery of genetic code alterations and expansions in both prokaryotes and eukaryotes abolished the hypothesis of a frozen and universal genetic code and exposed unanticipated flexibility in codon and amino acid assignments. It is now clear that codon identity alterations involve sense and non-sense codons and can occur in organisms with complex genomes and proteomes. However, the biological functions, the molecular mechanisms of evolution and the diversity of genetic code alterations remain largely unknown. In various species of the genus Candida, the leucine CUG codon is decoded as serine by a unique serine tRNA that contains a leucine 5′-CAG-3′anticodon (tRNACAG Ser). We are using this codon identity redefinition as a model system to elucidate the evolution of genetic code alterations.Methodology/Principal FindingsWe have reconstructed the early stages of the Candida genetic code alteration by engineering tRNAs that partially reverted the identity of serine CUG codons back to their standard leucine meaning. Such genetic code manipulation had profound cellular consequences as it exposed important morphological variation, altered gene expression, re-arranged the karyotype, increased cell-cell adhesion and secretion of hydrolytic enzymes.Conclusion/SignificanceOur study provides the first experimental evidence for an important role of genetic code alterations as generators of phenotypic diversity of high selective potential and supports the hypothesis that they speed up evolution of new phenotypes.

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The database of the Brazilian Program for Biodiversity Research (PPBio; GIVD ID SA-BR-001) includes data on the environment and biological groups such as plants. It is organized by site, which is usually a grid with 10 to 72 uniformly-distributed plots, and has already surveyed 1,638 relevés across different Brazilian ecosystems. The sampling design is based on the RAPELD system to allow integration of data from diverse taxa and ecosystem processes. RAPELD is a spatially-explicit sampling scheme to monitor biodiversity in long-term ecological research sites and during rapid appraisals of biodiversity that has attracted support from many management agencies, which are using it as their long-term monitoring system. Vegetation surveys include measurements of cover, biomass and number of individuals from woody and herbaceous vascular plants, along with environmental data. We have recently migrated to a metadata catalog and data repository which allows searching for specific groups across all sites. All RAPELD data have been collected since 2001, though the site also allows data from other long-term plots to be archived as associated projects. Database manager(s): Flávia Fonseca Pezzini (flaviapezzini@gmail.com) Owner: [NA] Web address: http://ppbio.inpa.gov.br Availability: after blocking period Online upload: yes Online search: yes Database format(s): CSV file, TXT file Export format(s): CSV file Publication: [NA] Plot type(s): normal plots Plot-size range: 1-10000 m² Non-overlapping plots: 1,843 Estimate of existing plots: [NA] Completeness: [NA] Total plot observations: 1,843 Number of sources: [NA] Valid taxa: [NA] Countries: BR: 100.0% Forest: [NA] -Non-forest: [NA] Guilds: all vascular plants: 100% Environmental data: altitude: 100%; slope inclination: 35%; soil pH: 92%; other soil attributes: 92% Performance measure(s): cover: 100%; number of individuals: 100%; biomass: 100% Geographic localisation: GPS coordinates (precision 25 m or less): 100% Sampling periods:

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In an exploratory sampling of a football field in Porto, Portugal, the root-knot nematode, Meloidogyne naasi, previously unreported from the Iberian Peninsula, was detected. Diagnosis was based on the analysis of perineal patterns and esterase phenotypes of females excised from grass roots, morphometrics and molecular analysis (PCR with specific primers and analysis of partial 28S sequences obtained by amplification using the primers D2A/D3B) of secondstage juveniles (J2) extracted from soil. When collected in water, J2 aggregated into a worm-star. Endospores of Pasteuria penetrans were frequently found attached to the J2. To our knowledge, this is the first report of M. naasi in Portugal and in the Iberian Peninsula, and the first report of worm-star formation in Meloidogyne.

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