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. 2001 Jun;11(6):981–993. doi: 10.1101/gr.165301

Figure 1.

Figure 1

Comparison of the chromosomal organization of the three Pyrococcus genomes. (A) Each genome is represented by three lines. The medium horizontal black line symbolizes the genome. A black vertical line represents the replication origin (Ori). The black vertical ticks indicate the positions of the tRNA genes; orange and red vertical ticks represent the insertion sequences, and the genes encoding the Pyrococcus-specific ATP-binding proteins, respectively. The upper and lower lines of colored arrows illustrate the oppositions of colinear segments between the considered genome and each of the other two genomes as obtained by three pairwise nucleotide comparisons (see Methods). A-H is the comparison between P. abyssi and P. horikoshii (arrows labeled from a1 to a17). A-F is the comparison between P. abyssi and P. furiosus (labeled from b1 to b25). H-F is the comparison between P. horikoshii and P. furiosus (labeled from c1 to c27). The arrows have been labeled arbitrarily, oriented, and colored according to the P. abyssi genome (arrows a1–a17 and arrows b1–b25), and the P. horikoshii genome (arrows c1–c27). For representation convenience, only segments >10 kb are plotted. White boxes inside arrows specify indel areas >2 kb. The P. abyssi genome has been reverse complemented to facilitate the analysis. Only the tRNAs located at the boundaries (2 kb resolution) of colinear segments or indels areas are labeled according to the amino acid one-letter code. The regions of differential conservation (I, II, III, and IV) are delimitated by black boxes. The scale is indicated at the bottom of the figure. (B) Circular representation of the three chromosomes showing the four regions (I, II, III, and IV) according to the colors defined above and the origin of replication Ori. (C) Schematic diagram of the phylogenetic relationships among the three Pyrococcus species. Red circles illustrate the absence of segments (named on the side) in one of the three species. Blue boxes represent major events that occurred within Pyrococcus lineage (see text). The arrow labeled IS symbolizes the putative loss of IS in the common ancestor of P. abyssi and P. horikoshii.