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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
...apes, characterized by a diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics, and deep in silico analysis of a southern white-cheeked gibbon , providing the first comprehensive map of 238...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...to the underrepresentation of repetitive elements.View larger version: In this window In a new window Figure 2. Genome conservation and chromosomal rearrangements. (A) Genespace plot depicting chromosomal syntenies (of sequences >1 Mb) and rearrangements (of >5 genes) between turtles and chicken. Chromosomes are scaled...
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Research: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
- Nathan H. Lazar,
- Kimberly A. Nevonen,
- Brendan O'Connell,
- Christine McCann,
- Rachel J. O'Neill,
- Richard E. Green,
- Thomas J. Meyer,
- Mariam Okhovat,
- and Lucia Carbone
Genome Res. July 2018 28: 983-997; Published in Advance June 18, 2018, doi:10.1101/gr.233874.117
...structural variations and recent genomic rearrangementsWhole- maps of chromatin interactions can be used to identify and study nonreference structural variations in a (Dixon et al. 2017; Harewood et al. 2017). To characterize the relationship between gibbon chromosomal rearrangements and TAD organization, we...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...-regulated in human LCLs (SYNRG, DUSP14, TADA2A, ACACA, MYO19, and DDX52) are comprised in the same topologically associating domain in Chr17q12 (Rao et al. 2015) and display human-specific exon usage changes (Fig. 5C). Genomic rearrangements in this locus have been extensively studied given their evolutionary...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
.... 2004; Tuzun et al. 2005; Kidd et al. 2008; Mills et al. 2011; Eichler 2019). SVs can include “balanced” rearrangements, such as inversions and translocations, or genomic imbalances (duplications and deletions), commonly referred to as copy number variants (CNVs). Inversions represent an intriguing...
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Resource: A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons
- Oronzo Capozzi,
- Lucia Carbone,
- Roscoe R. Stanyon,
- Annamaria Marra,
- Fengtang Yang,
- Christopher W. Whelan,
- Pieter J. de Jong,
- Mariano Rocchi,
- and Nicoletta Archidiacono
Genome Res. December 2012 22: 2520-2528; Published in Advance August 14, 2012, doi:10.1101/gr.138651.112
...the homologous human blocks. For details, see Supplemental Table ST2 or the website http://www.biologia.uniba.it/hoolock. This figure also reports the fusion points, the evolutionary new centromeres (ENC), and inactivated centromeres. Genome Research 2521 www..org Chromosome rearrangements in gibbons ancestor...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...in the vicinity of chromosomal breakpoints (Bailey et al. 2004; The Bovine Genome Sequencing and Analysis Consortium 2009; Carbone et al. 2014). It is not clear whether these transposable elements directly cause chromosomal rearrangement by triggering nonallelic homologous recombination (NAHR) (Janoušek et al...
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LETTER: Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites
- Santhosh Girirajan,
- Lin Chen,
- Tina Graves,
- Tomas Marques-Bonet,
- Mario Ventura,
- Catrina Fronick,
- Lucinda Fulton,
- Mariano Rocchi,
- Robert S. Fulton,
- Richard K. Wilson,
- Elaine R. Mardis,
- and Evan E. Eichler
Genome Res. February 2009 19: 178-190; Published in Advance November 24, 2008, doi:10.1101/gr.086041.108
.... Abstract The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of these rearrangement events, we sequenced 24 synteny breakpoint regions in the white-cheeked gibbon...
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Research: Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region
- Kiana Mohajeri,
- Stuart Cantsilieris,
- John Huddleston,
- Bradley J. Nelson,
- Bradley P. Coe,
- Catarina D. Campbell,
- Carl Baker,
- Lana Harshman,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Milinn Kremitzki,
- Archana Raja,
- Claudia Rita Catacchio,
- Tina A. Graves,
- Richard K. Wilson,
- Mario Ventura,
- and Evan E. Eichler
Genome Res. November 2016 26: 1453-1467; Published in Advance October 7, 2016, doi:10.1101/gr.211284.116
...in the last million years of human evolution. The breakpoints associated with these rearrangements map to an ape-specific interchromosomal core duplicon that clusters at sites of evolutionary inversion ( P = 7.8 × 10−5). Refinement of microdeletion breakpoints identifies a subgroup of patients that map...
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RESOURCE: Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping
- Doriana Misceo,
- Oronzo Capozzi,
- Roberta Roberto,
- Maria P. Dell’Oglio,
- Mariano Rocchi,
- Roscoe Stanyon,
- and Nicoletta Archidiacono
Genome Res. September 2008 18: 1530-1537; Published in Advance June 13, 2008, doi:10.1101/gr.078295.108
...with fossil and nuclear DNA evidence . J. Hum. Evol. 48 : 237 – 257 . ↵ Roberto, R. , Capozzi, O. , Wilson, R.K. , Mardis, E.R. , Lomiento, M. , Tuzun, E. , Cheng, Z. , Mootnick, A.R. , Archidiacono, N. , Rocchi, M. , et al. ( 2007 ) Molecular refinement of gibbon rearrangement . Genome Res. 17 : 249 – 257...

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