Figure 1.
A circular map representing the genome of Alteromonas sp. SN2.
Forward strand and reverse strand CDSs (blue) are depicted on the outermost two circles of the map, respectively, and RNA genes (tRNA: red; rRNA: violet; others: gray) are also shown on the same circles. The third circle represents the BLASTN comparison of the strain AltDE genome against the strain SN2 genome (dark red indicates highly homologous CDSs). G+C content (black) and GC skews (GC skew+: green, GC skew-: violet) are drawn on the fourth and fifth circles, respectively.
Figure 2.
Comparison of the gene content of strains SN2, AltDE, and ATCC 27126.
(a) A Venn diagram of shared and specific CDS genes in each strain. Percentages of COG categories in the three Alteromonas species. (b) All orthologous genes and (c) specific orthologous genes between strains SN2 and AltDE and (d) between strains SN2 and ATCC 27126. The alphabetic code for the column charts is as follows: C, energy production and conversion; D, cell division and chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme metabolism; I, lipid metabolism; J, translation, ribosomal structure, and biogenesis; K, transcription; L, DNA replication, recombination, and repair; M, cell envelope biogenesis, outer membrane; N, cell motility and secretion; O, posttranslational modification, protein turnover, and chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolite biosynthesis, transport, and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; V, defense mechanisms. Asterisks appear when a difference between treatments was at least 20%.
Table 1.
General features of the whole genomes of three Alteromonas strainsa.
Table 2.
Abundances of gene categories found in the three genomes of Alteromonas strains SN2, AltDE, and ATCC 27126.
Table 3.
Characteristics of genomic islands (GIs) found in Alteromonas sp. SN2.
Table 4.
Correspondence analysis of codon usage among three Alteromonas species genomes.
Figure 3.
Genome-wide analyses of Alteromonas strain SN2.
(a) Dotplot showing chromosomal synteny between strains SN2 and AltDE. The blue and orange-colored circles indicate reciprocal best hits in the forward and reverse strands for amino acid regions with >74% identity. The dotplot shows extensive rearrangement in strain SN2 in the form of reciprocal inversions. Plots of cumulative GC skew for strains SN2 and AltDE are shown next to the axes. The Karlin signature difference and tetranucleotide frequency diagrams are shown above the dotplot. Fifteen genomic islands (shaded regions 1–15) were found in the strain SN2 genome. (b) Recruitment of nucleotide-sequence fragments from Global Ocean Survey (GOS) database sequences against the strain SN2 genome using the Mummer program. Geographic origins of the GOS data sets are shown by color codes as follows: Sargasso Sea (green), North American east coast (pink), Coccus Kelling inside London (light green), Galapagos Island (red), Caribbean Sea (light blue), eastern tropical Pacific (brown), Panama Canal (yellow), Indian Ocean (sky blue), tropical South Pacific (dark green), Polynesian Archipelagos (dark blue).
Figure 4.
Recruitment analysis of the GOS database sequences sorted by source-water temperatures.
(a) Distribution of the normalized BLASTN best hit values recruited against the three marine Alteromonas genomes as a function of habitat temperature. (b) Principal Components Analysis (PCA) plot of data shown in panel A, showing results of factor analysis, and sorting by matched genome.
Figure 5.
Growth (optical density) of three Alteromonas strains (SN2, AltDE and ATCC 27126) in marine broth at eight different temperatures ranging from 5 to 40°C.
Closed circles indicate the growth rate for strain SN2, open circles for strain AltDE and closed triangles for strain ATCC 27126. Data show averages of three replicate tubes.
Figure 6.
Relative synonymous codon usage (RSCU) in three Alteromonas strains (SN2, AltDE, and ATCC 27126).
RSCU values were calculated by summing the values for all of the genes. Correspondence analysis of codon usage as shown was carried out using the web-based codonw 1.4.4 program (Rice et al., 2000). Codons of amino acids on X axis were arranged based on the ascending RSCU values of strain SN2.
Figure 7.
Physical map of a naphthalene degradation gene cluster and transposase coding genes from GI-11 of strain SN2.
(a) and its comparisons with Polaromonas naphthalenivorans CJ2 (b) and Ralstonia sp. U2 (C). The black arrows indicate genes involved in naphthalene metabolism (nagC′ is a partial gene of nagC). R1, R2, and R3 are coding genes of GntR-, LysR-, and MarR-type regulatory proteins, respectively, and orf1 and orf2 are coding genes of putative 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase and 3-hydroxybenzoate 6-hydroxylase, respectively.