Identification and sequencing of chimpanzee BACs


We screened high-density filters from the RPCI-43 male chimpanzee BAC library 22 (BACPAC resources) using hybridization probes designed to detect sequences (1) near the inner boundaries of palindromes P1–P6 and P8; (2) near P7; and (3) from a non-ampliconic region of the human MSY. STS content and BAC-end sequences confirmed that, among the candidate BACs identified by hybridization, six contained the central portions of orthologues to human MSY palindromes. The BACs were sequenced as previously described 2. Supplementary Table 4 provides descriptions of the sequenced BACs and their GenBank accession numbers. Sequences were aligned with CLUSTAL W using default parameters 23. In a few cases, the resulting alignments were adjusted manually. All alignments are provided as Supplementary Information. The sites studied were CDY1þ381 (Fig. 2 and Supplementary Fig. 1), CDY1284 (Supplementary Fig. 2), and sY586 (Supplementary Fig. 3). sY586 was genotyped as previously described 24. PCR primers and conditions for amplifying CDY1þ381 (sY1313) and CDY1284 (sY1314) have been deposited in GenBank (accession numbers G73596 and G73597, respectively). When typing CDY1þ381 by sequencing, 'primer A' in GenBank G73596 served as the sequencing primer. CDY1284 was typed by sequencing using 'primer B' in GenBank G73597. For the samples that showed evidence of gene conversion (Fig. 2 and Supplementary Figs 1–3), we excluded the possibility of deletion of one copy of the variant site as discussed in Supplementary Note 1. To show that the combined action of mutation and gene conversion results in a steady-state level of arm-to-arm divergence, we use the following recursion: d nþ1 ¼ ð1 2 c g Þd n þ 2m g where d n is the sequence divergence between repeat copies at generation n, m g is the mutation rate per nucleotide per generation, and c g is the gene conversion rate per duplicated nucleotide per generation. We presume that d 0 ¼ 0, corresponding to no differences between sequence copies immediately after the initial duplication event. However, as 1 2 c g , 1, lim n!1 d n ¼ 2m g /c g , for any value of d 0 small enough to support c g. Because m g and d are very small, mutations almost never occur at sites that already differ between the two palindrome arms, and this possibility can be ignored. As shown in Supplementary Note 2, our analysis is a special case of Ohta's analysis 25. 1. Skaletsky, H. et al. The male-specific …

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