Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes.

BMC Plant Biology
Xu ZhangH. Wang

Abstract

Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored. Moreover, structural and functional characteristics of plastomes indicate that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces, yet the genetic characteristics of plastid genes within a lineage remain poorly studied. We sequenced and annotated 10 plastome sequences of Gentianeae. Phylogenomic analyses yielded robust relationships among genera within Gentianeae. We detected great variation of gene tree topologies and revealed that more than half of the genes, including one (atpB) of the three widely used plastid markers (rbcL, atpB and matK) in phylogenetic inference of Gentianeae, are likely contributing to phylogenetic ambiguity of Gentianeae. Estimation of nucleotide substitution rates showed extensive rate heterogeneity among different plastid genes and among different functional groups of genes. Comparative analysis suggested that the ribosomal prot...Continue Reading

References

Oct 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·M Nei, W H Li
Dec 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·K H WolfeP M Sharp
Aug 1, 1993·Genetics·B CharlesworthD Charlesworth
Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Oct 29, 2004·Bioinformatics·Sergei L Kosakovsky PondSpencer V Muse
Aug 29, 2006·BMC Plant Biology·Michael J MooreDouglas E Soltis
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Dec 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·Robert K JansenJeffrey L Boore
Dec 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·Michael J MooreDouglas E Soltis
Nov 18, 2008·Proceedings of the National Academy of Sciences of the United States of America·Mary M GuisingerRobert K Jansen
Mar 25, 2009·Trends in Ecology & Evolution·James H Degnan, Noah A Rosenberg
Feb 24, 2010·Proceedings of the National Academy of Sciences of the United States of America·Michael J MooreDouglas E Soltis
May 25, 2010·Plant Physiology and Biochemistry : PPB·Mercedes Martín, Bartolomé Sabater
Mar 23, 2011·PLoS Biology·Hervé PhilippeDenis Baurain
Mar 23, 2011·Plant Molecular Biology·Susann WickeDietmar Quandt
Mar 30, 2011·The Plant Journal : for Cell and Molecular Biology·Beverley R Green
Jun 2, 2011·BMC Evolutionary Biology·Francesc López-Giráldez, Jeffrey P Townsend
Feb 10, 2012·Molecular Biology and Evolution·Robert LanfearStephane Guindon
Mar 7, 2014·Methods in Molecular Biology·Tracey A Ruhlman, Robert K Jansen
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jul 16, 2014·Proceedings of the National Academy of Sciences of the United States of America·Eric B Knox
Feb 1, 2013·Applications in Plant Sciences·Gregory W StullMatthew A Gitzendanner
Feb 13, 2015·Scientific Reports·Wenpan DongShiliang Zhou
May 24, 2015·Molecular Phylogenetics and Evolution·Mark P Simmons, John Gatesy
Nov 1, 2015·Molecular Phylogenetics and Evolution·Scott V EdwardsCharles C Davis
May 18, 2016·Genome Biology and Evolution·Mao-Lun WengRobert K Jansen
Dec 3, 2016·Nucleic Acids Research·UNKNOWN BIG Data Center Members
Apr 5, 2017·Molecular Ecology Resources·Thibaut JombartCaroline Colijn
Oct 14, 2017·Molecular Biology and Evolution·Julio RozasAlejandro Sánchez-Gracia

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Software Mentioned

Plastid Genome Annotator ( PGA )
Principal Coordinate Analysis ( PCoA )
DnaSP
TREESPACE
III
R package stats
PAML
NOVOPlasty
Geneious
MrBayes

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