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Segmental duplications I

Figure 1

Location of segmental duplications in euchromatin/heterochromatin transitions regions of the human Y chromosome. The region-specific colour-code of the lettering is retained in all consecutive diagrams.

Figure 2

A diagram delineating the evolutionary dynamics of Y-chromosomal segmental duplications. A multi-step process is depicted leading to the current distribution pattern of duplicated sequences on the Y chromosomes of the great- and lesser- apes. Serial intrachromosomal duplicative transpositions and chromosomal rearrangements generated a mosaic pattern on all great-ape Y chromosomes. Continuous interchromosomal transfer of duplicated cassettes provided the basis to develop such a complex structure. The upper row outlines G-banded ideograms for each of the primate Y-chromosome analyzed. Each coloured rectangle on a primate Y chromosome indicates the presence of a discrete SD region: Pink = Yp11.2/Yp11.1, Green = Yq11.1/Yq11.21, Blue = Yq11.23/Yq12 and Yellow = Yq12/PAR2. The phylogenetic tree indicates the divergence time in millions of years for each species: ~6 Mya for the Homo - Pan clade split, ~3 Mya for chimpanzee - bonobo split, ~7 Mya for the gorilla, ~14 Mya for the orangutans; ~17 Mya for the gibbon, ~23 Mya for the macaque (Goodman et al. 2005) and ~2.7-5 Mya for Bornean - Sumatran orangutan split (Steiper 2006). Coloured rectangles intermediate to the evolutionary branching points indicate the period of interchromosomal addition or deletion of the respective duplicated sequences.

Literature: Kirsch S, Münch C, Jiang Z, Cheng Z, Chen L, Batz C, Eichler EE, Schempp W (2008)Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions. Genome Research 18: 1030-1942
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Segmental duplications II

Figure 1

FISH with a CHEK2 duplicon containing Y-chromosomal cosmid probe in anthropoids. (A): Schematic representation of the human Y chromosome with an enlarged view of the CHEK2 duplicon in Yq11.1/Yq11.21. Basepair positions within the Y-chromosomal contig NT-113819 are indicated for the CHEK2 duplicon boundaries, for all probes used to identify a CHEK2 duplicon containing cosmid and for the derivative CAGGG repeat sequences. Localization of FISH probe LLOYNC03’M’22E01 within the Y-chromosomal contig is shown below. (B) Comparative FISH of cosmid LLOYNC03’M’22E01 (labelled in red) covering the human Y-chromosomal derivative CHEK2 duplicon in Yq11.1/Yq11.21 on human (HSA), chimpanzee (PTR), gorilla (GGO), orang-utan (PPY), rhesus macaque (MMU), pig-tailed macaque (MNE), baboon (PHA) and marmoset (CJA) metaphase chromosomes. The great-ape chromosomal designations are given according to [65], for MMU, MNE and PHA according to [47] and for CJA according to [66]. White arrows indicate the ancestral CHEK2 locus.

Literature: Münch C, Kirsch S, Fernandes AMG, Schempp W (2008) Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids. BMC Evolutionary Biology 8: 269 (doi: 10.1186/1471-2148-8-269)
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Segmental duplications III

Figure 1

Overview of the species-specific Y-chromosomal locations of DUXY genes as detected by FISH with human DUXY-containing cosmids LL0YNC03"M"-39H03, -70B12, and -118E07. (A) For each Y chromosome analyzed a G-banded ideogram is outlined. The position of the pseudoautosomal regions (PAR1 in human; PAR in great apes) and the nucleolus organiser region (NOR) is depicted on the respective ideograms. The cytogenetic location of DUXY genes is indicated as a green horizontal bar. Please note that the gorilla Y chromosome presents a distinctive difference in the hybridisation pattern of cosmids 39H03 and 118E07 (standard green bar) when compared with cosmid 70B12 (standard plus striped green bar). (B) FISH of cosmid LL0YNC03"M"-39H03 (green signals) on DAPI-counterstained metaphase Y chromosomes of hominoid species. For the ease of chromosomal orientation, the human pseudoautosomal cosmids LL0YNC03"M"-34F05 (SHOX; Rao et al. 1997) or ICRFc104E0238 (IL3RA; Milatovich et al. 1993) were co-hybridised in great apes and the mouse rDNA-containing plasmid pMR100 (Grummt et al. 1979) in gibbon (red signals). The position of the centromere is indicated as a white horizontal line. (C) Distinctive FISH pattern of cosmid LL0YNC03"M"-70B12 on a metaphase Y chromosome of the gorilla.

Literature: Schmidt J, Kirsch S, Rappold GA, Schempp W (2009) Complex evolution od a Y-chromosomal double homeobox 4 (DUX4)-related gene family in hominoids. PloS ONE 4(4): e5288 (doi: 10.1371/journal.pone.0005288)
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