Plastid genome structure and phylogenomics of Nymphaeales: conserved gene order and new insights into relationships

Gruenstaeudl, Michael; Nauheimer, Lars; Borsch, Thomas

doi:10.1007/s00606-017-1436-5

Cited by 35 publications

(66 citation statements)

References 72 publications

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“…The plastid genomes represent the species Dasyphyllum excelsum (Asteraceae; GenBank accession MH899017) and Nuphar japonica (Nymphaeaceae; MH161174). The assemblies of both genomes were generated via Illumina MiSeq sequencing following the sequencing protocol of Gruenstaeudl et al (2017) and the assembly protocol of Gruenstaeudl et al (2018). To keep the size of the BAM input files at a maximum of 2.5 megabytes for each test genome and, thus, ensure a lightweight distribution of the R package, the coverage depth of both assemblies was capped at 20 by applying script 'bbnorm.sh' of the software BBTools v.33.89 (Bushnell, 2015)…”

Section: Testing Of Softwarementioning

confidence: 99%

“…The post-processing of automated assembly results often pertains to the correction of the IR length (Tonti-Filippini et al, 2017;Twyford and Ness, 2017), differences in junction boundaries (Wu et al, 2015), and genome circularization (Hunt et al, 2015). Common uncertainties and outright errors in plastid genome assemblies include the inequality of the IR regions in length or sequence (Williams et al, 2015;Gruenstaeudl et al, 2017;Amiryousefi et al, 2018), long homopolymer runs (Kim et al, 2015;Tonti-Filippini et al, 2017), and the imperfect duplication of repeats at the junction of the SC regions (Wu et al, 2015). The differential orientation of the SSC, by contrast, does not constitute an assembly error but reflects the natural presence of heteroplasmy in organellar genomes (Walker et al, 2015).…”

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confidence: 99%

“…To ensure correctness and reproducibility in plastid genome sequencing and analysis, it is paramount to confirm the validity of plastid genome assemblies (Wu et al, 2015;Tonti-Filippini et al, 2017;Gruenstaeudl et al, 2018). Many of the ambiguities and putative errors recognized in published plastid genome sequences, including those of genome annotations (Tonti-Filippini et al, 2017;Gruenstaeudl et al, 2017;Amiryousefi et al, 2018), could potentially be averted by the application of simple quality assessment strategies (Kim et al, 2015;Gruenstaeudl et al, 2018).…”

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confidence: 99%

“…The IRs of a plastid genome, for example, represent recombinogenic isomers and, thus, share the same DNA sequence and gene synteny (Palmer, 1983;Blazier et al, 2016); exceptions to this rule are very rare (Turmel et al, 2017). Equality in length, sequence and gene synteny of the IR regions can, thus, be used as an indicator for the quality of the plastid genome assembly as a whole (Gruenstaeudl et al, 2017). The depth of sequencing coverage ('coverage depth' hereafter) represents yet another indicator for the quality of a genome assembly .…”

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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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PACVr: Plastome Assembly Coverage Visualization in R

Gruenstaeudl

Jenke

2019

Preprint

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“…), full chloroplast sequences support a polyphyletic Nymphaea , with Victoria related to the tropical Nymphaea (Grünstäudl et al . ).…”

Section: Introductionmentioning

confidence: 97%

Disentangling historical signal and pollinator selection on the micromorphology of flowers: an example from the floral epidermis of the Nymphaeaceae

Coiro

Lumaga

2018

Plant Biol J

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The family Nymphaeaceae includes most of the diversity among the ANA-grade angiosperms. Among the species of this family, floral structures and pollination strategies vary. The genus Victoria, as well as subgenera Lotos and Hydrocallis in Nymphaea, present night-blooming, scented flowers pollinated by scarab beetles. Such similar pollination strategies have led to macromorphological similarities among the flowers of these species, which could be interpreted as homologies or convergences based on different phylogenetic hypotheses about the relationships of these groups. We employed scanning electron microscopy of floral epidermis for seven species of the Nymphaeaceae with contrasting pollination biology to identify the main characters of the floral organs and the potential homologous nature of the structures involved in pollinator attraction. Moreover, we used transmission electron microscopy to observe ultrastructure of papillate-conical epidermis in the stamen of Victoria cruziana. We then tested the phylogenetic or ecological distribution of these traits using both consensus network approaches and ancestral state reconstruction on fixed phylogenies. Our results show that the night-blooming flowers present different specialisations in their epidermis, with V. cruziana presenting the most elaborate floral anatomy. We also identify for the first time the presence of conical-papillate cells in the order Nymphaeales. The epidermal characters tend to reflect phylogenetic relationships more than convergence due to pollinator selection. These results point to an independent and parallel evolution of scarab pollination in Nymphaeaceae and demonstrate the promise of floral anatomy as a phylogenetic marker. Moreover, they indicate a degree of sophistication in the anatomical basis of cantharophilous flowers in the Nymphaeales that diverges from the most simplistic views of floral evolution in the angiosperms.

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Cryptic species in an ancient flowering‐plant lineage (Hydatellaceae, Nymphaeales) revealed by molecular and micromorphological data

Sokoloff

Marques

Macfarlane

et al. 2019

TAXON

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The flora of the southwestern Australian biodiversity hotspot is rich in endemic species, many of which remain to be discovered or properly described; estimates of species diversity and levels of endemism should take into account the possible occurrence of cryptic species. Here we explore taxonomic diversity in a Western Australian lineage belonging to the primarily Australian genus Trithuria, the sole genus of Hydatellaceae (Nymphaeales). Recent molecular evidence supports the existence of cryptic species in self-pollinating members of section Trithuria. We investigate Western Australian plants currently classified as T. australis s.l., a selfpollinating member of the section Hydatella. Using evidence from microsatellite data (SSRs), an expanded molecular phylogenetic analysis based on four plastid markers, and fruit micromorphology, we suggest that material traditionally classified as T. australis s.l. belongs to at least four species. Two species occur in the northern part of the distribution range of the group (31°S to 33°27′ S), and two in the southern part (33°27′ S to 35°S). Each northern species has distinctive fruit micromorphology not recorded in other members of the genus. The two southern species are well characterized by molecular characters and seem to be allopatric, but lack obvious morphological differences from each other. We describe one of the northern species as T. fitzgeraldii sp. nov. However, clarifying the names of the other three species is currently problematic as T. australis and another available name are based on collections made 117 years ago, from localities distant from any subsequent records of Hydatellaceae. Based on genome size estimations, we also demonstrate two ploidy levels in the T. australis complex. Our study supports the view that species diversity in Hydatellaceae is strongly underestimated.

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Plastid genome structure and phylogenomics of Nymphaeales: conserved gene order and new insights into relationships

Cited by 35 publications

References 72 publications

PACVr: Plastome Assembly Coverage Visualization in R

PACVr: Plastome Assembly Coverage Visualization in R

Disentangling historical signal and pollinator selection on the micromorphology of flowers: an example from the floral epidermis of the Nymphaeaceae

Cryptic species in an ancient flowering‐plant lineage (Hydatellaceae, Nymphaeales) revealed by molecular and micromorphological data

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