The plastid genome of the hornwort Nothoceros aenigmaticus (Dendrocerotaceae): Phylogenetic signal in inverted repeat expansion, pseudogenization, and intron gain

2013 ◽  
Vol 100 (3) ◽  
pp. 467-477 ◽  
Author(s):  
Juan Carlos Villarreal ◽  
Laura Lowe Forrest ◽  
Norman Wickett ◽  
Bernard Goffinet
Keyword(s):  
Inverted Repeat ◽  
Plastid Genome ◽  
Phylogenetic Signal ◽  
Repeat Expansion ◽  
Intron Gain

Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes

2014 ◽  
Vol 12 (6) ◽  
pp. 743-754 ◽  
Author(s):  
Jamal Sabir ◽  
Erika Schwarz ◽  
Nicholas Ellison ◽  
Jin Zhang ◽  
Nabih A Baeshen ◽  
...  
Keyword(s):  
Inverted Repeat ◽  
Plastid Genome ◽  
Genome Variation

scholarly journals Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e60429 ◽  
Author(s):  
Yan-xia Sun ◽  
Michael J. Moore ◽  
Ai-ping Meng ◽  
Pamela S. Soltis ◽  
Douglas E. Soltis ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Inverted Repeat ◽  
Plastid Genome ◽  
Extant Species

Plastome Mutator–Induced Alterations Arise in Oenothera Chloroplast DNA Through Template Slippage

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 347-353 ◽  
Author(s):  
Lara L Stoike ◽  
Barbara B Sears
Keyword(s):  
Secondary Structure ◽  
Homologous Recombination ◽  
Chloroplast Dna ◽  
Inverted Repeat ◽  
Plastid Genome ◽  
Direct Repeats ◽  
Recombination Mechanism ◽  
Plastome Mutator ◽  
Target Sites ◽  
The One

Abstract The plastome mutator of Oenothera hookeri strain Johansen causes deletions and duplications at target sites defined by direct repeats in the plastid genome. Previous studies characterized the mutations long after they had occurred and could not discriminate between the possibilities that the plastome mutator acted through unequal homologous recombination or template slippage. From the known hotspots, the rRNA spacer in the large inverted repeat was chosen for this study because it contains both direct and indirect repeats. Identical deletions were recovered from independently derived plants; the altered regions were always flanked by direct repeats. The regions in which the deletions occurred have the potential to form secondary structures that would stabilize the intervening sequence. Of the two affected regions, the one with the stronger potential secondary structure was altered more frequently. Because no duplication products or inversions were recovered, it is proposed that the plastome mutator acts through template slippage rather than through a recombination mechanism.

scholarly journals PACVr: Plastome Assembly Coverage Visualization in R

2019 ◽  
Author(s):  
Michael Gruenstaeudl ◽  
Nils Jenke
Keyword(s):  
Genome Assembly ◽  
Inverted Repeat ◽  
Plastid Genome ◽  
Genome Structure ◽  
Software Tools ◽  
Coverage Depth ◽  
Assembly Quality ◽  
Gene Synteny ◽  
Plastid Genomes ◽  
A Genome

ABSTRACTBackgroundThe circular, quadripartite structure of plastid genomes which includes two inverted repeat regions renders the automatic assembly of plastid genomes challenging. The correct assembly of plastid genomes is a prerequisite for the validity of subsequent analyses on plastid genome structure and evolution. Plastome-based phylogenetic or population genetic investigations, for example, require the precise identification of DNA sequence and length to determine the location of nucleotide polymorphisms. The average coverage depth of a genome assembly is often used as an indicator for assembly quality. Visualizing coverage depth across a draft genome allows users to inspect the quality of the assembly and, where applicable, identify regions of reduced assembly confidence. Based on such visualizations, users can conduct a local re-assembly or other forms of targeted error correction. Few, if any, contemporary software tools can visualize the coverage depth of a plastid genome assembly while taking its quadripartite structure into account, despite the interplay between genome structure and assembly quality. A software tool is needed that visualizes the coverage depth of a plastid genome assembly on a circular, quadripartite map of the plastid genome.ResultsWe introduce ‘PACVr’, 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 to the individual plastome genes. The tool allows visualizations on different scales using a variable window approach and also visualizes the equality of gene synteny in the inverted repeat regions of the plastid genome, thus providing an additional measure of assembly quality. As a tool for plastid genomics, PACVr provides the functionality to identify regions of coverage depth above or below user-defined threshold values and helps to identify non-identical IR regions. To allow easy integration into bioinformatic workflows, PACVr can be directly invoked from a Unix shell, thus facilitating its use in automated quality control. We illustrate the application of PACVr on two empirical datasets and compare the resulting visualizations with alternative software tools for displaying plastome sequencing coverage.ConclusionsPACVr provides a user-friendly tool to visualize (a) the coverage depth of a plastid genome assembly on a circular, quadripartite plastome map and in relation to individual plastome genes, and (b) the equality of gene synteny in the inverted repeat regions. It, thus, contributes to optimizing plastid genome assemblies and increasing the reliability of publicly available plastome sequences, especially in light of incongruence among the visualization results of alternative software tools. The software, example datasets, technical documentation, and a tutorial are available with the package at https://github.com/michaelgruenstaeudl/PACVr.

scholarly journals Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat

2015 ◽  
Vol 102 (7) ◽  
pp. 1115-1127 ◽  
Author(s):  
M. J. Sanderson ◽  
D. Copetti ◽  
A. Burquez ◽  
E. Bustamante ◽  
J. L. M. Charboneau ◽  
...  
Keyword(s):  
Inverted Repeat ◽  
Plastid Genome ◽  
Carnegiea Gigantea

scholarly journals Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution

2020 ◽  
Vol 88 (7) ◽  
pp. 562-574 ◽  
Author(s):  
Abdullah ◽  
Claudia L. Henriquez ◽  
Furrukh Mehmood ◽  
Monica M. Carlsen ◽  
Madiha Islam ◽  
...  
Keyword(s):  
Inverted Repeat ◽  
Repeat Expansion ◽  
Rate Of Evolution ◽  
Chloroplast Genomes

scholarly journals Conserved gene clusters in the scrambled plastomes of IRLC legumes (Fabaceae: Trifolieae and Fabeae).

2016 ◽  
Author(s):  
Saemundur Sveinsson ◽  
Quentin Cronk
Keyword(s):  
Inverted Repeat ◽  
High Frequency ◽  
Plastid Genome ◽  
Gene Clusters ◽  
Functional Constraint ◽  
Legume Species ◽  
Data Set ◽  
Plastid Genomes ◽  
Conserved Gene ◽  
Internal Rearrangement

The plastid genome retains several features from its cyanobacterial-like ancestor, one being the co-transcriptional organization of genes into operon-like structures. Some plastid operons have been identified but undoubtedly many more remain undiscovered. Here we utilize the highly variable plastome structure that exists within certain legumes of the inverted repeat lost clade (IRLC) to find conserved gene clusters. These plastomes exhibit an unusually high frequency of translocations and inversions. We analysed the plastomes of 23 legume species and identified 32 locally collinear blocks (LCBs), which are regions within the plastid genomes that occur in different orientation and/or order among the plastid genomes but are themselves free from internal rearrangements. Several represent gene clusters that have previously been recognized as plastid operons. It appears that the number of LCBs has reached saturation in our data set, suggesting that these LCBs are not random, but likely represent legume plastid operons protected from internal rearrangement by functional constraint. Some of the LCBs we identify, such as psbD/C/Z, are previously known plastid operons. Others, such as rpl32-ndhF-psbA-matK-rbcL-atpB-atpE, may represent novel polycistronic operons in legumes.

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