Pathogenic clones of Vibrio cholerae, which causes cholera, are emerging. Cholera bacteria are serogrouped by O antigens with the 6th and 7th epidemics mainly due to O1. Examining the genome of 23 V. cholerae strains using Sanger, 434, and Solexa/Illumina sequencing, the authors found 12 distinct lineages. The 6th-7th lineage transition was due to a “shift between pathogenic clones” but transition among 7th outbreak clones were “a drift differentiated by varying composition of laterally transferred genomic islands,” leading to variant emergence.

The authors used genome DNA sequencing to investigate the mutability of Acetobacter pasteurianus NBRC 3283 and found over 280 transposons and “five genes with hyper-mutable tandem repeats as common features.” The Genome Analyzer was used for mutation mapping of A. pasteurianus IFO 3283-01-42C. An A pasteurianus strain was bred to survive high temperatures and genome analyses using saturated genome shotgun sequencing showed a 92-kb deletion and three single nucleotide mutations in the genome.

The authors examined spontaneous suppressor mutations that disrupted the sigma(E) encoding rpoE in the cholera bacterium Vibrio cholerae. Single nucleotide polymorphisms and indels were found following sequencing with the Genome Analyzer. The found that many V. cholerae rpoE mutants reduce production of OmpU, the outer membrane porin, which has a vital role in determining the bacteria’s sigma(E) requirement and production. They also found a suppressor mutation that increases sigma(E) activity.

The authors investigated epigenetic DNA methylation in the endosperm and embryo of Arabidopsis during development, with the aid of the Genome Analyzer. They had a number of findings, including that the highest levels of methylation were closer to centromeres, that genes encoding proteins were generally less methylated than those encoding transposable elements, and that methylation was lower in the endosperm compared to the embryo. The also found five previously unknown imprinted genes preferably expressed in the endosperm.

The authors used high-throughput sequencing with the Genome Analyzer to genotype recombinant populations. Using 150 rice recombinant inbred lines (RILs) they collectively assessed single nucleotide polymorphisms (SNPs) using a sliding window approach that encompasses 15 SNPs at once. Genotype calling involved examination of SNP number ratios from the parents. They could determine recombination breakpoints between two SNPs and constructed very accurate recombination maps of the RILs. This method had large time, cost, accuracy, and resolution advantages over PCR.

Paired-end sequencing using the Genome Analyzer, and SNP genotyping using the Human1M-duo DNA analysis BeadChip, helped investigate a Korean male’s genome. Over 420,000 novel SNPs and 21 homozygous alleles were found. More SNPs were shared with a Chinese male (60%), then two Caucasian and one African male (50%, 53% and 56% respectively). Of 343,000 indels, one-third were within genes. Indel similarity was almost 100% between the Asian males, less for the African and Caucasian ones. Deletion structural variants were in 21 coding genes. Nearly 6% of reads were novel.

Genomic structural variations (SVs) include insertions, deletions, and inversions. The authors describe two algorithms—the VariationHunter-Set Cover method and the VariationHunter-Probabilistic method—to analyze SVs of a genome sequence obtained using next generation-based, paired-end, whole genome shotgun-sequencing, using the Genome Analyzer, compared to a reference genome. They find the algorithms to be fast and reliable and report they can also be used for capillary sequencing technology.