Raghuraman - branch distinguishing the two clades. Analysis...

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Unformatted text preview: branch distinguishing the two clades. Analysis of the entire dataset (474 taxa) by heuristic search using max- imum parsimony criteria yields the same major branch- es depicted in Fig. 2A. For the analysis of consensus sequences shown in Fig. 2B, 382 monomers from the monomeric clade (Fig. 2A) were aligned using ClustalW and a single X monomeric consensus sequence ( Xmon) was derived. Bootstrap analysis was used to determine the relationship of Xmon to the consensus monomers established for the four human suprachromosomal fam- ilies ( 28 ), again using AGM as an outgroup (Fig. 2B). Of 1000 bootstrap replicates, 92% support the major branch separating Xmon and AGM from the remaining consensus monomers. Our analysis indicates that Xmon is more closely related to AGM and to the M1 (suprach- romosomal family 4) sequence than to any of the other human consensus monomers. 28. I. Alexandrov, A. Kazakov, I. Tumereva, V. Shepelev, Y. Yurov, Chromosoma 110 , 253 (2001). 29. S. J. Durfy, H. F. Willard, Genomics 5 , 810 (1989). 30. Specific positions within each DXZ1 monomer at which the sequence varies from a consensus DXZ1 monomer are designated signature sites. The analysis of signature sites was automated using a perl script, modifying the consensus identity index used previ- ously ( 15 ). The script first identifies and then com- pares signature sites of test monomers with the specific signature sites of each DXZ1 monomer. Be- cause any two higher-order repeats of typical DXZ1 (type 1) share 98 to 100% identity ( 31 ), the number of signature sites for each DXZ1 monomer varies slightly. Type 2, 3, and 4 DXZ1 repeats have numbers of signature sites that are outside the range of those detected in type 1 repeats. 31. Approximately 1000 to 2000 copies of the DXZ1 higher-order repeat exist on each X chromosome ( 9, 15 ). Average sequence divergence was estimat- ed from the sequence of seven complete (M. G. Schueler et al. , unpublished data) and over 40 partial repeat units ( 29 ), from at least nine differ- ent X chromosomes. 32. Type 2 and type 3 DXZ1 sequences show approxi- mately the same degree of sequence divergence within each type as they do between types. This indicates that the gradient of divergence from type 1 DXZ1 is very steep and that the diverged types are no longer being homogenized to the same degree as type 1. This is consistent with a model in which the efficiency of homogenization decreases both as a function of physical distance from the type 1 array and as a direct consequence of the increased se- quence dissimilarity itself. ( Type 3 is represented by only a single repeat and thus cannot be evaluated from this perspective.) 33. D. J. Wolff et al. , Am. J. Hum. Genet . 58 , 154 (1996)....
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This note was uploaded on 12/20/2011 for the course BIOLOGICAL 3310 taught by Professor Goldburg during the Spring '10 term at Cornell University (Engineering School).

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Raghuraman - branch distinguishing the two clades. Analysis...

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