Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

Bernhardt, Nadine; Brassac, Jonathan; Kilian, Benjamin; Blattner, Frank R.

doi:10.1186/s12862-017-0989-9

Cited by 97 publications

(140 citation statements)

References 105 publications

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“…tauschii branch, 20.3 major rearrangements per MY, were applicable to the entire tribe, the Ae. tauschii lineage would be expected to accumulate 203 major rearrangements over the 10-MY period, the estimated divergence time of the wheat and barley lineages and the age of Triticeae (Dvorak and Akhunov, 2005;Bernhardt et al, 2017). This number exceeds the total number of 175 major rearrangements that the Ae.…”

Section: Rates Of Genome Evolutionmentioning

confidence: 98%

“…The hexaploid genome of bread wheat is thus a product of convergence of three diploid Triticeae lineages, those of the A, B and D genomes. Their divergence was estimated to have occurred between 1.4 and 4.5 million years ago (MYA) (Huang et al, 2002;Dvorak and Akhunov, 2005;Gornicki et al, 2014;Middleton et al, 2014;Bernhardt et al, 2017), although a time as ancient as 7 MYA has also been suggested (Marcussen et al, 2014). An average divergence time of 3 MY will be used throughout this study.…”

Section: Introductionmentioning

confidence: 99%

“…An array of approaches has been used to reconstruct the phylogeny of the three lineages. Phylogenetic trees placing the A-genome divergence basally (Hsiao et al, 1995;Yamane and Kawahara, 2005;Li et al, 2015;Bernhardt et al, 2017;Jorgensen et al, 2017) dominate these efforts.…”

Section: Introductionmentioning

confidence: 99%

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Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size

et al. 2018

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Homology was searched with genes annotated in the Aegilops tauschii pseudomolecules against genes annotated in the pseudomolecules of tetraploid wild emmer wheat, Brachypodium distachyon, sorghum and rice. Similar searches were performed with genes annotated in the rice pseudomolecules. Matrices of collinear genes and rearrangements in their order were constructed. Optical BioNano genome maps were constructed and used to validate rearrangements unique to the wild emmer and Ae. tauschii genomes. Most common rearrangements were short paracentric inversions and short intrachromosomal translocations. Intrachromosomal translocations outnumbered segmental intrachromosomal duplications. The densities of paracentric inversion lengths were approximated by exponential distributions in all six genomes. Densities of collinear genes along the Ae. tauschii chromosomes were highly correlated with meiotic recombination rates but those of rearrangements were not, suggesting different causes of the erosion of gene collinearity and evolution of major chromosome rearrangements. Frequent rearrangements sharing breakpoints suggested that chromosomes have been rearranged recurrently at some sites. The distal 4 Mb of the short arms of rice chromosomes Os11 and Os12 and corresponding regions in the sorghum, B. distachyon and Triticeae genomes contain clusters of interstitial translocations including from 1 to 7 collinear genes. The rates of acquisition of major rearrangements were greater in the large wild emmer wheat and Ae. tauschii genomes than in the lineage preceding their divergence or in the B. distachyon, rice and sorghum lineages. It is suggested that synergy between large quantities of dynamic transposable elements and annual growth habit have been the primary causes of the fast evolution of the Triticeae genomes.

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Section: Rates Of Genome Evolutionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

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Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size

et al. 2018

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“…Despite prior cytogenetic and phylogenetic studies (e.g. Meimberg et al 2009;Bernhardt et al 2017), diploid progenitors and the recurrent origins of allopolyploid wild wheats were not precisely identified. Accordingly, we first infer the reticulate phylogeny of allopolyploids using plastid and nuclear loci to provide a robust comparative framework.…”

Section: Introductionmentioning

confidence: 99%

Eco‐genetic additivity of diploids in allopolyploid wild wheats

et al. 2020

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Underpinnings of the distribution of allopolyploid species (hybrids with duplicated genome) along spatial and ecological gradients are elusive. As allopolyploid speciation combines the range of genetic and ecological characteristics of divergent diploids, allopolyploids initially show their additivity and are predicted to evolve differentiated ecological niches to establish in face of their competition. Here, we use four diploid wild wheats that differentially combined into four independent allopolyploid species to test for such additivity and assess the impact of ecological constraints on species ranges. Divergent genetic variation from diploids being fixed in heterozygote allopolyploids supports their genetic additivity. Spatial integration of comparative phylogeography and modelling of climatic niches supports ecological additivity of locally adapted diploid progenitors into allopolyploid species which subsequently colonised wide ranges. Allopolyploids fill suitable range to a larger extent than diploids and conservative evolution following the combination of divergent species appears to support their expansion under environmental changes.

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“…Numerous investigations have sequenced and compared complete plastid genome sequences over the past decade (Gao et al, 2010;Gitzendanner et al, 2018b), and the number of publicly available plastid genomes continues to increase dramatically (Tonti-Filippini et al, 2017). Recent studies on plastid genome structure and evolution now evaluate polymorphisms across hundreds of genome sequences (Bernhardt et al, 2017;Teisher et al, 2017;Saarela et al, 2018;Gitzendanner et al, 2018a), rendering the precise assembly process of plastid genomes and its quality assessment ever more important.…”

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confidence: 99%

PACVr: Plastome Assembly Coverage Visualization in R

Gruenstaeudl

Jenke

2019

Preprint

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Background:The 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. Results:We 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. Conclusions:PACVr 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.

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Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

Cited by 97 publications

References 105 publications

Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size

Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size

Eco‐genetic additivity of diploids in allopolyploid wild wheats

PACVr: Plastome Assembly Coverage Visualization in R

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