Draft Genome Sequence of Naganishia liquefaciens Strain N6, Isolated from the Japan Trench.

The draft genome sequence of the deep-sea yeast Naganishia liquefaciens strain N6, isolated from the Japan Trench, is reported here. This strain was previously classified into a Cryptococcus clade. Phylogenetic analysis using the presented sequence suggests that strain N6 is in the clade of the genus Naganishia.

Next-generation sequencing analysis of lager brewing yeast strains reveals the evolutionary history of interspecies hybridization.

The lager beer yeast Saccharomyces pastorianus is considered an allopolyploid hybrid species between S. cerevisiae and S. eubayanus. Many S. pastorianus strains have been isolated and classified into two groups according to geographical origin, but this classification remains controversial. Hybridization analyses and partial PCR-based sequence data have indicated a separate origin of these two groups, whereas a recent intertranslocation analysis suggested a single origin. To clarify the evolutionary history of this species, we analysed 10 S. pastorianus strains and the S. eubayanus type strain as a likely parent by Illumina next-generation sequencing. In addition to assembling the genomes of five of the strains, we obtained information on interchromosomal translocation, ploidy, and single-nucleotide variants (SNVs). Collectively, these results indicated that the two groups of strains share S. cerevisiae haploid chromosomes. We therefore conclude that both groups of S. pastorianus strains share at least one interspecific hybridization event and originated from a common parental species and that differences in ploidy and SNVs between the groups can be explained by chromosomal deletion or loss of heterozygosity.

The Chloroplast Function Database: a large-scale collection of Arabidopsis Ds/Spm- or T-DNA-tagged homozygous lines for nuclear-encoded chloroplast proteins, and their systematic phenotype analysis.

A majority of the proteins of the chloroplast are encoded by the nuclear genome, and are post-translationally targeted to the chloroplast. From databases of tagged insertion lines at international seed stock centers and our own stock, we selected 3246 Ds/Spm (dissociator/suppressor-mutator) transposon- or T-DNA-tagged Arabidopsis lines for genes encoding 1369 chloroplast proteins (about 66% of the 2090 predicted chloroplast proteins) in which insertions disrupt the protein-coding regions. We systematically observed 3-week-old seedlings grown on agar plates, identified mutants with abnormal phenotypes and collected homozygous lines with wild-type phenotypes. We also identified insertion lines for which no homozygous plants were obtained. To date, we have identified 111 lines with reproducible seedling phenotypes, 122 lines for which we could not obtain homozygotes and 1290 homozygous lines without a visible phenotype. The Chloroplast Function Database presents the molecular and phenotypic information obtained from this resource. The database provides tools for searching for mutant lines using Arabidopsis Genome Initiative (AGI) locus numbers, tagged line numbers and phenotypes, and provides rapid access to detailed information on the tagged line resources. Moreover, our collection of insertion homozygotes provides a powerful tool to accelerate the functional analysis of nuclear-encoded chloroplast proteins in Arabidopsis. The Chloroplast Function Database is freely available at http://rarge.psc.riken.jp/chloroplast/. The homozygous lines generated in this project are also available from the various Arabidopsis stock centers. We have donated the insertion homozygotes to their originating seed stock centers.