Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes

BMC Genomics
Yoann AnselmettiSèverine Bérard

Abstract

Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. We present a computational method, ADSEQ, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADSEQ provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADSEQ to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide add...Continue Reading

References

Mar 1, 1965·Journal of Theoretical Biology·E Zuckerkandl, L Pauling
Mar 10, 2001·Insect Molecular Biology·G GentileA Caccone
Oct 5, 2002·Science·Mario ColuzziVincenzo Petrarca
Oct 5, 2002·Science·Igor V SharakhovNora J Besansky
Jul 12, 2003·Bioinformatics·Jijun Tang, Bernard M E Moret
Sep 20, 2006·Genome Research·Jian MaWebb Miller
Nov 29, 2007·PloS One·Rui Wang-SattlerLiangbiao Zheng
Jun 6, 2009·Bioinformatics·Samuel AssefaMatthew Berriman
Jun 12, 2009·Bioinformatics·Anna I RissmanNicole T Perna
Jul 15, 2009·Genome Research·Harris A LewinStephen J O'Brien
Jan 6, 2010·Algorithms for Molecular Biology : AMB·Peter Husemann, Jens Stoye
Nov 30, 2011·Nature Reviews. Genetics·Todd J Treangen, Steven L Salzberg
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
May 16, 2012·BMC Bioinformatics·Zanoni DiasJoão C Setubal
Jul 24, 2012·Bioinformatics·Bradley R JonesCedric Chauve
Sep 11, 2012·Bioinformatics·Sèverine BérardEric Tannier
Jan 11, 2013·BMC Bioinformatics·Ján MaňuchEric Tannier
Jan 12, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jaebum KimJian Ma
Jan 30, 2013·Nature Reviews. Genetics·Niranjan Nagarajan, Mihai Pop
Jun 5, 2013·Bioinformatics·Rayan Chikhi, Paul Medvedev
Sep 18, 2013·Algorithms for Molecular Biology : AMB·Rayan Chikhi, Guillaume Rizk
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jun 7, 2014·Frontiers in Genetics·Diego AyalaJosefa González
Jun 17, 2014·Bioinformatics·Mikhail KolmogorovSon Pham
Aug 17, 2014·BMC Bioinformatics·Kristoffer SahlinLars Arvestad
Nov 28, 2014·Nucleic Acids Research·Evgenia V KriventsevaEvgeny M Zdobnov
Nov 29, 2014·BMC Bioinformatics·Chin Lung LuHsien-Tai Chiu
Dec 5, 2014·PLoS Computational Biology·James F DentonMatthew W Hahn
Jan 3, 2015·Science·Andrew G Clark, Philipp W Messer
Jan 15, 2015·Genome Biology·Haibao TangJianguo Lu
Mar 27, 2015·Bioinformatics·Emanuele BosiMarco Fondi
Apr 19, 2015·Bioinformatics·Igor Mandric, Alex Zelikovsky
May 26, 2015·Nature Biotechnology·Konstantin BerlinAdam M Phillippy
Aug 5, 2015·Molecular Phylogenetics and Evolution·Mark S Springer, John Gatesy
Oct 10, 2015·BMC Genomics·Yoann AnselmettiSèverine Bérard
Dec 24, 2015·BMC Bioinformatics·Cedric ChauveJoão Zanetti
Feb 6, 2016·Genome Research·Nicholas H PutnamRichard E Green
Feb 18, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Pavel AvdeyevMax A Alekseyev

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Citations

May 12, 2020·Algorithms for Molecular Biology : AMB·Aniket C ManeCedric Chauve
Nov 23, 2021·Journal of Bioinformatics and Computational Biology·Daniel Doerr, Cedric Chauve

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Software Mentioned

MINIA
KMERGENIE
DESCHRAMBLER
ADSEQ
RaxML
TRIMMOMATIC
BOWTIE2
OrthoDB
BESST
PROFILENJ

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