Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Ventura, Mario; Catacchio, Claudia Rita; Alkan, Can; Marquès‐Bonet, Tomàs; Sajjadian, Saba; Graves, Tina; Hormozdiari, Fereydoun; Navarro, Arcadi; Malig, Maika; Baker, Carl; Lee, Choli; Turner, Emily H.; Chen, Lin; Kidd, Jeffrey M.; Archidiacono, Nicoletta; Shendure, Jay; Wilson, Richard K.; Eichler, Evan E.

doi:10.1101/gr.124461.111

Cited by 68 publications

(73 citation statements)

References 54 publications

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“…This included a 36-kbp chimpanzee-hyperexpanded segment homologous to human chromosome 2, contained in the chimpanzee clone AC150905, and a 45-kbp gorilla-hyperexpanded segment homologous to human chromosome 10 (19534885-19579478 NCBI35) (Fan et al 2002;Cheng et al 2005;Marques-Bonet et al 2009;Ventura et al 2011). To better define the cap structure organization in both apes and delineate the full extent of these duplications, we performed a series of comparative FISH experiments using a set of overlapping human fosmid clones (Kidd et al 2010) mapping to a 463-kbp region of human chromosome 2 (113840263-114303469) and a 341-kbp region mapping to chromosome 10 (19359773-19700390) (Table 1; Fig.…”

Section: Molecular Cytogenetic Analysis Of Subterminal Regionsmentioning

confidence: 99%

“…Recently, we identified the presence of specific segmental duplications that have hyperexpanded within the subterminal cap of both gorilla and chimpanzee (Cheng et al 2005;MarquesBonet et al 2009;Ventura et al 2011). In this study, we perform a detailed investigation into the organization and evolution of subterminal caps using molecular cytogenetics, targeted clonebased sequencing, and phylogenetic-based analyses.…”

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confidence: 99%

“…These subtelomeric caps are heterochromatic in nature and are completely absent from the karyotype of human and orangutan (Haaf and Schmid 1987;IJdo et al 1991;Ventura et al 2011). Subterminal heterochromatin has been thought to be composed primarily of a tandem array of a 32-bp subterminal satellite (StSat) creating large subterminal blocks of constitutive heterochromatic regions (Royle et al 1994;Koga et al 2011) adjacent to the canonical telomeric TTAGGG sequence (Greider and Blackburn 1989).…”

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confidence: 99%

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The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Ventura¹,

Catacchio²,

Sajjadian³

et al. 2012

Genome Res.

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Chimpanzee and gorilla chromosomes differ from human chromosomes by the presence of large blocks of subterminal heterochromatin thought to be composed primarily of arrays of tandem satellite sequence. We explore their sequence composition and organization and show a complex organization composed of specific sets of segmental duplications that have hyperexpanded in concert with the formation of subterminal satellites. These regions are highly copy number polymorphic between and within species, and copy number differences involving hundreds of copies can be accurately estimated by assaying read-depth of next-generation sequencing data sets. Phylogenetic and comparative genomic analyses suggest that the structures have arisen largely independently in the two lineages with the exception of a few seed sequences present in the common ancestor of humans and African apes. We propose a model where an ancestral humanchimpanzee pericentric inversion and the ancestral chromosome 2 fusion both predisposed and protected the chimpanzee and human genomes, respectively, to the formation of subtelomeric heterochromatin. Our findings highlight the complex interplay between duplicated sequences and chromosomal rearrangements that rapidly alter the cytogenetic landscape in a short period of evolutionary time.

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Section: Molecular Cytogenetic Analysis Of Subterminal Regionsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Ventura¹,

Catacchio²,

Sajjadian³

et al. 2012

Genome Res.

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“…The present results of chromosome C-banding and FISH analysis demonstrate that alpha satellite DNA has expanded to large-scale heterochromatin blocks in the lineage leading to the SSY, regardless of whether they have a common origin. Differences in the sizes of the StSat repeats and other telomere-region repetitive sequences have also been reported in great apes (between chimpanzee and gorilla) (Ventura et al, 2011). The mechanisms leading to these size differences are not known.…”

Section: Origins Of Large-scale Heterochromatin Structures In Differementioning

confidence: 95%

Repetitive sequences originating from the centromere constitute large-scale heterochromatin in the telomere region in the siamang, a small ape

et al. 2012

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Chromosomes of the siamang Symphalangus syndactylus (a small ape) carry large-scale heterochromatic structures at their ends. These structures look similar, by chromosome C-banding, to chromosome-end heterochromatin found in chimpanzee, bonobo and gorilla (African great apes), of which a major component is tandem repeats of 32-bp-long, AT-rich units. In the present study, we identified repetitive sequences that are a major component of the siamang heterochromatin. Their repeat units are 171 bp in length, and exhibit sequence similarity to alpha satellite DNA, a major component of the centromeres in primates. Thus, the large-scale heterochromatic structures have different origins between the great apes and the small ape. The presence of alpha satellite DNA in the telomere region has previously been reported in the white-cheeked gibbon Nomascus leucogenys, another small ape species. There is, however, a difference in the size of the telomere-region alpha satellite DNA, which is far larger in the siamang. It is not known whether the sequences of these two species (of different genera) have a common origin because the phylogenetic relationship of genera within the small ape family is still not clear. Possible evolutionary scenarios are discussed.

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“…Previous studies of CNV have been predominated by array comparative genomic hybridization (CGH) experiments (Fortna et al 2004;Perry et al 2006;Dumas et al 2007;Gazave et al 2011;Locke et al 2011), which provide limited size resolution, are imprecise in absolute copy number differences, and are biased by probes derived from the human reference genome. Comparisons of reference genomes have been complicated by assessments of a single individual and distinguishing CNVs from assembly errors (The Chimpanzee Sequencing and Analysis Consortium 2005; Locke et al 2011;Ventura et al 2011;Prüfer et al 2012). Here, we compare the evolution and diversity of deletions, duplications, and SNVs in 97 great ape individuals sequenced to high coverage (median ;253) (Prado-Martinez et al 2013).…”

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Evolution and diversity of copy number variation in the great ape lineage

et al. 2013

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Copy number variation (CNV) contributes to disease and has restructured the genomes of great apes. The diversity and rate of this process, however, have not been extensively explored among great ape lineages. We analyzed 97 deeply sequenced great ape and human genomes and estimate 16% (469 Mb) of the hominid genome has been affected by recent CNV. We identify a comprehensive set of fixed gene deletions (n = 340) and duplications (n = 405) as well as >13.5 Mb of sequence that has been specifically lost on the human lineage. We compared the diversity and rates of copy number and single nucleotide variation across the hominid phylogeny. We find that CNV diversity partially correlates with single nucleotide diversity (r 2 = 0.5) and recapitulates the phylogeny of apes with few exceptions. Duplications significantly outpace deletions (2.8-fold). The load of segregating duplications remains significantly higher in bonobos, Western chimpanzees, and Sumatran orangutans-populations that have experienced recent genetic bottlenecks (P = 0.0014, 0.02, and 0.0088, respectively). The rate of fixed deletion has been more clocklike with the exception of the chimpanzee lineage, where we observe a twofold increase in the chimpanzee-bonobo ancestor (P = 4.79 3 10 -9 ) and increased deletion load among Western chimpanzees (P = 0.002). The latter includes the first genomic disorder in a chimpanzee with features resembling Smith-Magenis syndrome mediated by a chimpanzee-specific increase in segmental duplication complexity. We hypothesize that demographic effects, such as bottlenecks, have contributed to larger and more gene-rich segments being deleted in the chimpanzee lineage and that this effect, more generally, may account for episodic bursts in CNV during hominid evolution.

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Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Cited by 68 publications

References 54 publications

The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Repetitive sequences originating from the centromere constitute large-scale heterochromatin in the telomere region in the siamang, a small ape

Evolution and diversity of copy number variation in the great ape lineage

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