Literature DB >> 19664183

The where and wherefore of evolutionary breakpoints.

David Sankoff1.   

Abstract

The 'action' in genome-level evolution lies not in the large gene-containing segments that are conserved among related species, but in the breakpoint regions between these segments. Two recent papers in BMC Genomics detail the pattern of repetitive elements associated with breakpoints and the epigenetic conditions under which breakage occurs.

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Year:  2009        PMID： 19664183      PMCID： PMC2736669          DOI： 10.1186/jbiol162

Source DB:  PubMed          Journal:  J Biol        ISSN： 1475-4924


  13 in total

1.  Genomic features in the breakpoint regions between syntenic blocks.

Authors:  Phil Trinh; Aoife McLysaght; David Sankoff
Journal:  Bioinformatics       Date:  2004-08-04       Impact factor: 6.937

2.  The distribution of genes in the human genome.

Authors:  D Mouchiroud; G D'Onofrio; B Aïssani; G Macaya; C Gautier; G Bernardi
Journal:  Gene       Date:  1991-04       Impact factor: 3.688

3.  Human gene organization driven by the coordination of replication and transcription.

Authors:  Maxime Huvet; Samuel Nicolay; Marie Touchon; Benjamin Audit; Yves d'Aubenton-Carafa; Alain Arneodo; Claude Thermes
Journal:  Genome Res       Date:  2007-08-03       Impact factor: 9.043

4.  Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps.

Authors:  William J Murphy; Denis M Larkin; Annelie Everts-van der Wind; Guillaume Bourque; Glenn Tesler; Loretta Auvil; Jonathan E Beever; Bhanu P Chowdhary; Francis Galibert; Lisa Gatzke; Christophe Hitte; Stacey N Meyers; Denis Milan; Elaine A Ostrander; Greg Pape; Heidi G Parker; Terje Raudsepp; Margarita B Rogatcheva; Lawrence B Schook; Loren C Skow; Michael Welge; James E Womack; Stephen J O'brien; Pavel A Pevzner; Harris A Lewin
Journal:  Science       Date:  2005-07-22       Impact factor: 47.728

5.  Stability of rearrangement measures in the comparison of genome sequences.

Authors:  Matthew Mazowita; Lani Haque; David Sankoff
Journal:  J Comput Biol       Date:  2006-03       Impact factor: 1.479

6.  Sensitivity analysis for reversal distance and breakpoint reuse in genome rearrangements.

Authors:  Amit U Sinha; Jaroslaw Meller
Journal:  Pac Symp Biocomput       Date:  2008

7.  Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution.

Authors:  Pavel Pevzner; Glenn Tesler
Journal:  Proc Natl Acad Sci U S A       Date:  2003-06-16       Impact factor: 11.205

8.  Is mammalian chromosomal evolution driven by regions of genome fragility?

Authors:  Aurora Ruiz-Herrera; Jose Castresana; Terence J Robinson
Journal:  Genome Biol       Date:  2006       Impact factor: 13.583

9.  The signal in the genomes.

Authors:  David Sankoff
Journal:  PLoS Comput Biol       Date:  2006-04       Impact factor: 4.475

10.  Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty.

Authors:  Mark S Longo; Dawn M Carone; Eric D Green; Michael J O'Neill; Rachel J O'Neill
Journal:  BMC Genomics       Date:  2009-07-24       Impact factor: 3.969
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  14 in total

Review 1.  Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery.

Authors:  Martin T Swain; Denis M Larkin; Conor R Caffrey; Stephen J Davies; Alex Loukas; Patrick J Skelly; Karl F Hoffmann
Journal:  Trends Parasitol       Date:  2011-10-23

2.  Segmental duplication, microinversion, and gene loss associated with a complex inversion breakpoint region in Drosophila.

Authors:  Oriol Calvete; Josefa González; Esther Betrán; Alfredo Ruiz
Journal:  Mol Biol Evol       Date:  2012-02-10       Impact factor: 16.240

3.  Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution.

Authors:  Adriana Muñoz; David Sankoff
Journal:  BMC Bioinformatics       Date:  2012-03-21       Impact factor: 3.169

4.  Assessing the role of tandem repeats in shaping the genomic architecture of great apes.

Authors:  Marta Farré; Montserrat Bosch; Francesc López-Giráldez; Montserrat Ponsà; Aurora Ruiz-Herrera
Journal:  PLoS One       Date:  2011-11-04       Impact factor: 3.240

5.  Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process.

Authors:  C D Greenman; S L Cooke; J Marshall; M R Stratton; P J Campbell
Journal:  J Math Biol       Date:  2015-04-02       Impact factor: 2.259

6.  Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats.

Authors:  Dan Wang; Shuaicheng Li; Fei Guo; Kang Ning; Lusheng Wang
Journal:  BMC Genomics       Date:  2017-03-29       Impact factor: 3.969

7.  Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs.

Authors:  Rebecca E O'Connor; Michael N Romanov; Lucas G Kiazim; Paul M Barrett; Marta Farré; Joana Damas; Malcolm Ferguson-Smith; Nicole Valenzuela; Denis M Larkin; Darren K Griffin
Journal:  Nat Commun       Date:  2018-05-21       Impact factor: 14.919

Review 8.  Consequence of Paradigm Shift with Repeat Landscapes in Reptiles: Powerful Facilitators of Chromosomal Rearrangements for Diversity and Evolution.

Authors:  Syed Farhan Ahmad; Worapong Singchat; Maryam Jehangir; Thitipong Panthum; Kornsorn Srikulnath
Journal:  Genes (Basel)       Date:  2020-07-21       Impact factor: 4.096

9.  Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.

Authors:  Halie M Rando; Marta Farré; Michael P Robson; Naomi B Won; Jennifer L Johnson; Ronak Buch; Estelle R Bastounes; Xueyan Xiang; Shaohong Feng; Shiping Liu; Zijun Xiong; Jaebum Kim; Guojie Zhang; Lyudmila N Trut; Denis M Larkin; Anna V Kukekova
Journal:  Genes (Basel)       Date:  2018-06-20       Impact factor: 4.096

10.  GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences.

Authors:  Dan Wang; Lusheng Wang
Journal:  BMC Bioinformatics       Date:  2018-08-13       Impact factor: 3.169
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