Variable presence of the inverted repeat and plastome stability in Erodium.
John C. Blazier,Robert K. Jansen,Jeffrey P. Mower,Madhumita Govindu,Jin Zhang,Mao-Lun Weng,Tracey A. Ruhlman +6 more
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TLDR
The presence or absence of the IR does not affect plastome stability in Erodium and the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts.About:
This article is published in Annals of Botany.The article was published on 2016-06-01 and is currently open access. It has received 73 citations till now. The article focuses on the topics: Erodium.read more
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The complete chloroplast genome sequence of Pelargonium xhortorum: Or ganization and evolution of the largest and most highlyrearranged chloroplast genome of land plants
Timothy W. Chumley,Jeffrey D. Palmer,Jeffrey P. Mower,H. Matthew Fourcade,Patrick J. Calie,Jeffrey L. Boore,Robert K. Jansen +6 more
TL;DR: The chloroplast genome of Pelargonium e hortorum has been completely sequenced as mentioned in this paper, and it is shown to contain two copies of a greatly expanded inverted repeat of 75,741 bp each, and consequently diminished single copy regions of 59,710 bp and 6,750 bp.
Journal ArticleDOI
PACVr: plastome assembly coverage visualization in R
Michael Gruenstaeudl,Nils Jenke +1 more
TL;DR: ’PACVr’ is introduced, an R package that visualizes the coverage depth of a plastid genome assembly in relation to the circular, quadripartite structure of the genome as well as the individual plastome genes and confirms sequence equality of and visualizes gene synteny between, the inverted repeat regions of the input genome.
Journal ArticleDOI
Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes
Deise Josely Pereira Gonçalves,Beryl B. Simpson,Edgardo M. Ortiz,Gustavo Hiroaki Shimizu,Robert K. Jansen +4 more
TL;DR: The results show that, in a phylogenetic context, plastid protein-coding genes may not be fully linked and behaving as a single locus, and concatenated matrices may produce highly supported phylogenies that are discordant with individual gene trees.
Book ChapterDOI
Structural Diversity Among Plastid Genomes of Land Plants
TL;DR: This review describes the typical structural features of the land plant plastome, the major variations to this canonical structure that occur in various lineages, and the evolutionary implications of this structural variation.
Journal ArticleDOI
Expansion of Inverted Repeat Does Not Decrease Substitution Rates in Pelargonium Plastid Genomes
TL;DR: The study of Pelargonium plastomes that vary in IR length and gene content demonstrates that the evolutionary consequences of retaining these repeats are more complicated than previously suggested.
References
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A rapid DNA isolation procedure for small quantities of fresh leaf tissue
Edwin Pahlich,Chr. Gerlitz +1 more
TL;DR: From the kinetic data, it becomes evident that the reductive amination reaction is highly adaptive to the ammonium environment.
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
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Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino,Ewan Birney +1 more
TL;DR: Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.
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progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
TL;DR: A new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss is described, demonstrating high accuracy in situations where genomes have undergone biologically feasible amounts of genome rearrangement, segmental loss and loss.