Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions

Kirsch, Stefan; Münch, Claudia; Jiang, Zhaoshi; Cheng, Ze; Chen, Lin; Batz, Christiane; Eichler, Evan E.; Schempp, Werner

doi:10.1101/gr.076711.108

Cited by 32 publications

(35 citation statements)

References 68 publications

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“…We have previously determined the ancestral duplicon architecture of the 4 human Y-chromosome euchromatin/heterochromatin transition regions [Kirsch et al, 2008]. Here, we show that the addition of the recently issued whole-genome shotgun sequence assemblies of Sumatran orangutan, white-tufted-ear marmoset, grey mouse lemur and greater bushbaby refines the process of ancestral duplicon state determination by further minimizing the impact of lineage-specific rearrangements.…”

Section: Discussionmentioning

confidence: 94%

“…wustl.edu/pub/organism/Primates/Callithrix_jacchus/ assembly/Callithrix_jacchus-2.0.2), and the 2 ! genomes [Green, 2007] of grey mouse lemur ( Microcebus murinus ) and greater bushbaby ( Otolemur garnettii ) in our original computational approach [Kirsch et al, 2008]. The updated ancestral duplicon architectures of each region are displayed in figure 1 .…”

Section: Ancestral Origin Of the 4 Human Y-chromosome Euchromatin/hetmentioning

confidence: 99%

“…We increased the resolution of the previously published ancestral duplicon architecture of each region [Kirsch et al, 2008] by including the recently issued whole-genome sequence assemblies of Sumatran orangutan ( P. abelii ; ponAbe2; http://genome.wustl.edu/ genome.cgi?GENOME=Pongo%20abelii) and whitetufted-ear marmoset ( C. jacchus ; calJac1; http://genome. wustl.edu/pub/organism/Primates/Callithrix_jacchus/ assembly/Callithrix_jacchus-2.0.2), and the 2 !…”

Section: Ancestral Origin Of the 4 Human Y-chromosome Euchromatin/hetmentioning

confidence: 99%

“…Duplicon identification was basically conducted for all 4 human Y-chromosome euchromatin/heterochromatin transition regions (Yp11.1/Yp11.2, Yq11.2/Yq11.21, Yq11.23/Yq12, Yq12/ PAR2) as descibed previously [Kirsch et al, 2008], with 2 extensions. First, we included the cross-species chain data between human and Sumatran orangutan and white-tufted-ear marmoset (BLASTZ whole-genome alignments between human and the respective species; http://www.genome.ucsc.edu) and second, we produced human-grey mouse lemur and human-greater bushbaby alignments by BLASTN comparison (http://www.ensembl.…”

Section: Computational Analysismentioning

confidence: 99%

“…Our analysis indicated a continuous process of transposition of duplicated sequences onto the evolving higher primate Y chromosome, providing insights into the development of species-specific Y-chromosomal and autosomal duplicons [Kirsch et al, 2008]. The release of additional whole-genome shotgun sequence assemblies of Sumatran orangutan, white-tuftedear marmoset, grey mouse lemur and greater bushbaby allowed us to refine the original ancestral duplicon architecture.…”

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confidence: 99%

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A Non-Human Primate BAC Resource to Study Interchromosomal Segmental Duplications

Kirsch

Hodler²,

Schempp³

2009

Cytogenet Genome Res

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Segmental duplications (SDs) are involved in the reshaping and evolutionary development of primate genome architecture. Their intrinsic property to promote genomic instability facilitates genome rearrangements, thereby contributing to karyotype diversity in primates. However, comparative analyses of SDs based on whole-genome shotgun assemblies of primate genomes may lead to a distorted view of their evolutionary dynamics as this method will incorrectly assemble or simply not represent these regions. Therefore high-quality sequences of chromosomally assigned SDs are indispensable for unraveling the amplification and dispersal pattern of SDs during primate evolution. Here, we use an updated version of the ancestral duplicon state of the non-palindromic SDs of all 4 human Y-chromosome euchromatin/heterochromatin transition regions to perform a survey of duplicons genome-wide across 7 primate species. By adjusting experimental conditions to the mean nucleotide sequence divergence to human we identified 11,075 BAC clones carrying primate orthologs or paralogs of human Y chromosome-derived duplicons. Preliminary results indicate lineage-specific amplification of duplicons in prosimians and gibbons. This BAC-based framework represents the first complete set of a defined number of duplicons over 60 million years of primate evolution. Comparative sequence analysis of this genetic resource can contribute to our deeper understanding of the impact of segmental duplications on primate genome evolution.

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Section: Discussionmentioning

confidence: 94%

Section: Ancestral Origin Of the 4 Human Y-chromosome Euchromatin/hetmentioning

confidence: 99%

Section: Ancestral Origin Of the 4 Human Y-chromosome Euchromatin/hetmentioning

confidence: 99%

Section: Computational Analysismentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

A Non-Human Primate BAC Resource to Study Interchromosomal Segmental Duplications

Kirsch

Hodler²,

Schempp³

2009

Cytogenet Genome Res

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Evolution of the AZFc Region in Primates

Yen

2009

Encyclopedia of Life Sciences

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The Azoospermia Factor c ( AZFc ) region on the human Y chromosome is one of the most polymorphic regions in the human genome. It encodes several gene families with germ‐cell specific expression and is frequently deleted in infertile men with very low sperm counts or no sperm. AZFc consists mainly of very long repeats (amplicons) that have different evolutionary histories. Some of the ampliconic sequences are remnants of the ancient Y chromosome and share homology with the X chromosome. Other sequences arrived on the Y chromosome through segmental duplication and transposition of autosomal sequences or through messenger ribonucleic acid (mRNA) retroposition. Subsequent rearrangements such as duplication, inversion and intragenic amplification result in the various structures found on the Y chromosomes of today's primates. Key Concepts The AZFc region on the human Y chromosome contains several testis‐specific gene families and is essential for normal spermatogenesis. The AZFc region consists mainly of large amplicons and is prone to rearrangement such as deletion, duplication and inversion. Some ampliconic sequences are remnants of the ancestral Y chromosome and retain sequence similarity with the X chromosome. Other AZFc sequences arrived on the Y chromosome at various time during primate evolution through duplication and transposition of autosomal sequences. The CDY gene within the yellow amplicon arose from retroposition of an ancient autosomal CDYL gene and contains no introns.

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Large Tandem, Higher Order Repeats and Regularly Dispersed Repeat Units Contribute Substantially to Divergence Between Human and Chimpanzee Y Chromosomes

et al. 2010

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Comparison of human and chimpanzee genomes has received much attention, because of paramount role for understanding evolutionary step distinguishing us from our closest living relative. In order to contribute to insight into Y chromosome evolutionary history, we study and compare tandems, higher order repeats (HORs), and regularly dispersed repeats in human and chimpanzee Y chromosome contigs, using robust Global Repeat Map algorithm. We find a new type of long-range acceleration, human-accelerated HOR regions. In peripheral domains of 35mer human alphoid HORs, we find riddled features with ten additional repeat monomers. In chimpanzee, we identify 30mer alphoid HOR. We construct alphoid HOR schemes showing significant human-chimpanzee difference, revealing rapid evolution after human-chimpanzee separation. We identify and analyze over 20 large repeat units, most of them reported here for the first time as: chimpanzee and human ∼1.6 kb 3mer secondary repeat unit (SRU) and ∼23.5 kb tertiary repeat unit (∼0.55 kb primary repeat unit, PRU); human 10848, 15775, 20309, 60910, and 72140 bp PRUs; human 3mer SRU (∼2.4 kb PRU); 715mer and 1123mer SRUs (5mer PRU); chimpanzee 5096, 10762, 10853, 60523 bp PRUs; and chimpanzee 64624 bp SRU (10853 bp PRU). We show that substantial human-chimpanzee differences are concentrated in large repeat structures, at the level of as much as ∼70% divergence, sizably exceeding previous numerical estimates for some selected noncoding sequences. Smeared over the whole sequenced assembly (25 Mb) this gives ∼14% human-chimpanzee divergence. This is significantly higher estimate of divergence between human and chimpanzee than previous estimates.

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Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions

Cited by 32 publications

References 68 publications

A Non-Human Primate BAC Resource to Study Interchromosomal Segmental Duplications

A Non-Human Primate BAC Resource to Study Interchromosomal Segmental Duplications

Evolution of the AZFc Region in Primates

Large Tandem, Higher Order Repeats and Regularly Dispersed Repeat Units Contribute Substantially to Divergence Between Human and Chimpanzee Y Chromosomes

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