Book ChapterDOI
The plastid genomes of flowering plants.
TLDR
This chapter presents an overview of some of the seminal and contemporary research that has contributed to the current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and tools ofplastid genetic engineering.Abstract:
The plastid genome (plastome) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations are allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and tools of plastid genetic engineering.read more
Citations
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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
Reconstruction of the Ancestral Plastid Genome in Geraniaceae Reveals a Correlation between Genome Rearrangements, Repeats, and Nucleotide Substitution Rates
TL;DR: The genomic comparison demonstrates that a series of inverted repeat boundary shifts and inversions played a major role in shaping genome organization in the Geraniaceae family and is correlated with the acceleration in nonsynonymous substitution rates but not with synonymous substitution rates.
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
A Comparative Analysis of Whole Plastid Genomes from the Apiales: Expansion and Contraction of the Inverted Repeat, Mitochondrial to Plastid Transfer of DNA, and Identification of Highly Divergent Noncoding Regions
TL;DR: A comparison of pairwise sequence divergence values and numbers of variable and parsimony-informative alignment positions across all introns and intergenic spacers >150 base pairs in the five Apiaceae plastomes revealed that the rpl32-trnL, trnE-trNT, ndhF-rpl32, 5′rps16-trtQ, and trnT-psbD intergenic Spacers are among the most fast-ev
Journal ArticleDOI
The complete chloroplast genome of Onobrychis gaubae (Fabaceae-Papilionoideae): comparative analysis with related IR-lacking clade species
TL;DR: In this paper , the complete plastid genome of Onobrychis gaubae, endemic to Iran, was sequenced using Illumina paired-end sequencing and was compared with previously known genomes of the IRLC species of legumes.
References
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Journal ArticleDOI
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
TL;DR: A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed and it is estimated that 10% of all plant proteins are mitochondrial and 14% chloroplastic, and that the abundance of secretory proteins, in both Arabidopsis and Homo, is around 10%.
Journal ArticleDOI
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.
Journal ArticleDOI
The Mechanism of Double-Strand DNA Break Repair by the Nonhomologous DNA End-Joining Pathway
TL;DR: Patients lacking normal NHEJ are not only sensitive to ionizing radiation (IR), but also severely immunodeficient in the range of DNA end substrate configurations upon which they can act.
Journal ArticleDOI
The relation of recombination to mutational advance.
TL;DR: It is shown that this calculation does not apply for mutant genes that act advantageously only when in some special combinations with one or more other mutant genes, and that as far as these cases of special synergism are concerned recombining lines have no evolutionary advantage over non-recombining ones.
Journal ArticleDOI
Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.
TL;DR: The rate of cpDNA evolution appears to have slowed in some dicot lineages following the monocot/dicot split, and the slowdown is more conspicuous at nonsynonymous sites than at synonymous sites.
Related Papers (5)
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns.
Robert K. Jansen,Zhengqiu Cai,Linda A. Raubeson,Henry Daniell,Claude W. dePamphilis,Jim Leebens-Mack,Kai F. Müller,Mary Guisinger-Bellian,Rosemarie C. Haberle,Anne K. Hansen,Timothy W. Chumley,Seung Bum Lee,Rhiannon M. Peery,Joel R. McNeal,Jennifer V. Kuehl,Jeffrey L. Boore,Jeffrey L. Boore +16 more