Whole-genome microsynteny-based phylogeny of angiosperms.

Nature Communications
Tao ZhaoYves Van de Peer

Abstract

Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny-the conservation of local gene content and order-is recognized as a valuable source of phylogenetic information, but its use for the inference of large phylogenies has been limited. Here, by combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference, we provide a way to reconstruct phylogenies based on microsynteny information. Both simulations and use of empirical data sets show our method to be accurate, consistent, and widely applicable. As an example, we focus on the analysis of a large-scale whole-genome data set for angiosperms, including more than 120 available high-quality genomes, representing more than 50 different plant families and 30 orders. Our 'microsynteny-based' tree is largely congruent with phylogenies proposed based on more traditional sequence alignment-based methods and current phylogenetic classifications but differs for some long-contested and controversial relationships. For instance, our synteny-based tree finds Vitales as early diverging eudicots, Saxifragales w...Continue Reading

References

Jul 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·D SankoffR Cedergren
Feb 1, 1984·Proceedings of the National Academy of Sciences of the United States of America·J H Nadeau, B A Taylor
Jun 1, 2000·Molecular Biology and Evolution·A ReyesC Saccone
Jun 22, 2000·Proceedings of the National Academy of Sciences of the United States of America·N Fedoroff
Oct 26, 2000·Trends in Ecology & Evolution·A Rokas, P W Holland
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
May 4, 2002·Science·Ge SunXinfu Wang
Jun 25, 2002·Systematic Biology·Hidetoshi Shimodaira
Jan 17, 2003·Genome Research·Pavel Pevzner, Glenn Tesler
Sep 25, 2003·Proceedings of the National Academy of Sciences of the United States of America·David Sankoff, Joseph H Nadeau
Oct 29, 2004·Nature Reviews. Genetics·Yves Van de Peer
Jun 14, 2005·Bioinformatics·Sophia YancopoulosRichard Friedberg
Oct 21, 2005·The Plant Journal : for Cell and Molecular Biology·Javier SampedroDaniel J Cosgrove
Nov 16, 2005·Annual Review of Genetics·Eugene V Koonin
Jun 10, 2006·Trends in Ecology & Evolution·Jeffrey L Boore
Oct 6, 2006·Bioinformatics·S Blair HedgesSudhir Kumar
Jan 9, 2007·PLoS Computational Biology·Gina CannarozziGaston Gonnet
Nov 13, 2007·Nature·UNKNOWN Drosophila 12 Genomes ConsortiumIain MacCallum
Jan 25, 2008·Proceedings of the National Academy of Sciences of the United States of America·Martin Rosvall, Carl T Bergstrom
Jul 25, 2008·PLoS Genetics·Aaron E DarlingMark A Ragan
Dec 4, 2008·PloS One·Haiwei LuoRobert Friedman
Jan 6, 2009·BMC Evolutionary Biology·Sigisfredo GarnicaFranz Oberwinkler
Feb 17, 2009·Genome Research·Max A Alekseyev, Pavel A Pevzner
Jun 10, 2009·Bioinformatics·Salvador Capella-GutiérrezToni Gabaldón
Feb 24, 2010·Proceedings of the National Academy of Sciences of the United States of America·Michael J MooreDouglas E Soltis
Dec 15, 2010·Current Biology : CB·Cédric FinetFerdinand Marlétaz
Jan 1, 2009·American Journal of Botany·Peter K Endress, James A Doyle
Jun 28, 2011·Briefings in Bioinformatics·Colin N Dewey
Nov 26, 2011·The New Phytologist·UNKNOWN Grass Phylogeny Working Group II
Dec 27, 2011·Plant Physiology·Michiel Van BelKlaas Vandepoele
Jan 6, 2012·Nucleic Acids Research·Yupeng WangAndrew H Paterson
Jan 28, 2012·Algorithms for Molecular Biology : AMB·Nam NguyenTandy Warnow
Jan 28, 2012·Genome Biology·Yuannian JiaoClaude W Depamphilis
Mar 13, 2012·Annual Review of Plant Biology·Rowan F SageFerit Kocacinar
May 24, 2012·Molecular Biology and Evolution·Julien SoubrierAlan Cooper
Jun 23, 2012·Nature·UNKNOWN Heliconius Genome Consortium

❮ Previous
Next ❯

Citations

Sep 4, 2021·Nature Plants·Zhen Li, Yves Van de Peer

❮ Previous
Next ❯

Software Mentioned

Pro
R
YGOB ( Yeast Gene Order Browser )
JTT
TimeTree
TREE
DIAMOND
Julia
trimAl 116
IQ

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.