A 460-kb DNA Sequence of the Escherichia coli K-12 Genome Corresponding to the 40.1-50.0 min Region on the Linkage Map

The 465,813 base pair sequence corresponding to the 40.1–50.0min region on the genetic map of Escherichia coli K-12 (W3110)was determined. Analysis of the sequence revealed that thisregion contained at least 466 potential open reading frames,of which 187 (40%) were previously reported, 105 (23%) werehomologous to other known genes, 103 (22%) were identical orsimilar to hypothetical genes registered in databases, and theremaining 71 (15%) did not show a significant similarity toany other gene. At the 45.2–46.0 min region, we founda very large cluster of about 30 genes, whose functions areinvolved in the biosynthesis of polysaccharides as the componentsof outer membranes. In addition, we identified anew asn-tRNAgene, designated asnW, between the asnT and asnU genes and anew lysogenic phage attachment site as the cis-element.     

Complete mitochondrial genomes of the Japanese pink coral (Corallium elatius) and the Mediterranean red coral (Corallium rubrum): a reevaluation of the phylogeny of the family Coralliidae based on molecular data

Precious corals are soft corals belonging to the family Coralliidae (Anthozoa: Octocorallia: Alcyonacea) and class Anthozoa, whose skeletal axes are used for jewelry.The family Coralliidae includes ca. 40 species and was originally thought to comprise of the single genus Corallium. In 2003, Corallium was split into two genera, Corallium and Paracorallium, and seven species were moved to this newly identified genus on the bases of morphological features. Previously, we determined the complete mitochondrial genome sequence of two precious corals Paracorallium japonicum and Corallium konojoi, in order to clarify their systematic positions. The two genomes showed high nucleotide sequence identity, but their gene order arrangements were not identical. Here, we determined three complete mitochondrial genome sequences from the one specimen of Mediterranean Corallium rubrum and two specimens of Corallium elatius coming from Kagoshima (South Japan). The circular mitochondrial genomes of C. rubrum and C. elatius are 18,915 bp and 18,969–18,970 bp in length, respectively, and encode 14 typical octocorallian protein-coding genes (nad1–6, nad4L, cox1–3, cob, atp6, atp8, and mtMutS, which is an octocoral-specific mismatch repair gene homologue), two ribosomal RNA genes (rns and rnl), and one transfer RNA (trnM). The overall nucleotide differences between C. konojoi and each C. elatius haplotype (T2007 and I2011) are only 10 and 11 nucleotides, respectively; this degree of similarity indicates that C. elatius and C. konojoi are very closely related species. Notably, the C. rubrum mitochondrial genome shows more nucleotide sequence identity to P. japonicum (99.5%) than to its congeneric species C. konojoi (95.3%) and C. elatius (95.3%). Moreover, the gene order arrangement of C. rubrum was the same as that of P. japonicum, while that of C. elatius was the same as C. konojoi. Phylogenetic analysis based on three mitochondrial genes from 24 scleraxonian species shows that the family Coralliidae is separated into two distinct groups, recovering Corallium as a paraphyletic genus. Our results indicate that the currently accepted generic classification of Coralliidae should be reconsidered.