Genome rearrangements near the ends of chromosomes. (A) Full-length Chr6 sequences aligned with the Artemis Comparative Tool software (Carver et al. 2005). Red lines connect regions of sequence similarity higher than 85%; gaps in white lower or absent similarity; green indicates S288c Chr6 sequences; thick areas indicate regions conserved in JAY291; thin areas indicate nonconserved regions. The small segment in blue is a translocated fragment from S288c Chr10. Black indicates S. cerevisiae sequences not found in the S288c genome. The thick gray line corresponds to S. paradoxus Chr6 assembled from contigs 346, 345, 344, 434, and 433, from left to right, in this order (Kellis et al. 2003). SEC53 and RPN12 indicate the positions of the most distal essential genes in Chr6. The black circles indicate the position of the centromere (CEN6); the arrow denotes the YFLWTy2-1 element. Y′ and X subtelomeric sequences are not represented in this alignment. (B) Multistrain chromosome alignment around the left end of Chr6. The horizontal lines represent the left ends of the designated chromosomes, with the exception of S288c Chr1 (top line), for which the inverted right end is shown. The source strain for each sequence is indicated to the left in bold; other strains with similar chromosome structures are also indicated. Rectangles represent ORFs and their positions above and below the central line designate the Watson and Crick orientations, respectively. Chromosomal regions are color coded according to their correspondence to S288c (orange) Chr1, (green) Chr6, and (blue) Chr10. Regions in black correspond to sequences not found in the S288c genome. The dotted line in S288c Chr6 represents a discontinuity in the alignment at the site of a 19.3-kb insertion in JAY291. Rectangles hatched in red between chromosomes indicate a high level of sequence similarity (>85%; analogous to the red lines in A). All sequence similarities are indicated in red except for the left end of YJM789 Chr10, which contains the SNO3 and SNZ3 genes and is nearly identical to the collinear region in S288c Chr6. Boxed letters (A–F) indicate the specific chromosomal rearrangements discussed in the text, and SNO3, SNZ3, AGP3, and YAR064W indicate the positions of Southern blot probes used in Figure 4. The source sequences for this figure were the complete Chr6 sequences from S288c and JAY291, contigs 1.67 (Chr10) and 1.109 (Chr6) from RM11-1a, contigs 100 (Chr10) and 7 (Chr6) from YJM789, and contig 386 (Chr10) from JAY291. The 10-kb scale bar indicates the size scale for B.
