Biology subjects

Gruenstaeudl, M.

Publications and source records attributed to Gruenstaeudl, M..

6 recordsLinked to original sources

bioRxiv2022

Depth and evenness of sequence coverage are associated with assembly quality, genome structure, and choice of sequencing platform in archived plastid genomes

In plastid genomes, the depth and evenness of sequence coverage are considered important indicators for assembly quality. However, the precise manifestations that sequencing depth and evenness can have in the assembly of these genomes, as well as any differences across individual genome sections, have yet to be evaluated. This investigation aims to identify the impact that sequencing depth and evenness can have on the assembly of plastid genomes and how both metrics are related to plastid genome structure. Specifically, we assess if sequencing evenness and reduced sequencing depth have significant correlations with, or significant differences among, individual genome sections, assembly quality metrics, the sequencing platforms employed, and the software tools used for genome assembly. To that end, we retrieve published plastid genomes as well as their sequence reads and genome metadata from public databases, measure sequencing depth and evenness across their sequences, and test several hypotheses on genome assembly and structure through non-parametric statistical tests. The results of our analyses show significant differences in sequencing depth across the four structural partitions as well as between the coding and non-coding sections of the plastid genomes, a significant correlation between sequencing evenness and the number of ambiguous nucleotides per genome, and significant differences in sequencing evenness between various sequencing platforms. Based on these results, we conclude that the observed differences and correlations are not a product of chance alone but possibly genuine manifestations of sequencing depth and evenness during the assembly of these genomes.

genomics↗

bioRxiv2021

Software choice and depth of sequence coverage can impact plastid genome assembly - A case study in the narrow endemic Calligonum bakuense

Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequence coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense, which forms a distinct lineage in the genus Calligonum. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequence coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and three levels of sequence coverage (original depth, 2,000x, and 500x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic tree inference is also assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produced the most consistent assemblies for C. bakuense. Moreover, we found that a cap in sequence coverage can reduce both the sequence variability across assembly contigs and computation time. While no evidence was found that the sequence variability across assemblies was large enough to affect the phylogenetic position inferred for C. bakuense, differences among the assemblies may influence genotype recognition at the population level.

plant biology↗

bioRxiv2021

Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif-based sequence alignment amid low genetic distances

PREMISEThe genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it. METHODSWe sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif-based adjustments of automatic DNA sequence alignments on phylogenetic tree inference. RESULTSOur results indicate that the inclusion of all plastid genome partitions is needed to infer fully resolved phylogenetic trees of the Gynoxoid group. Whole plastome-based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia. CONCLUSIONSThe concatenation and combined analysis of all plastid genome partitions and the construction of manually curated, motif-based DNA sequence alignments are found to be instrumental in the recovery of strongly supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome-level plastid sequence datasets is crucial for subsequent phylogeny reconstruction and that the manual post-processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa.

plant biology↗

bioRxiv2019

annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA

MotivationThe submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research. The surge of novel DNA sequences awaiting database submission due to the application of next-generation sequencing has increased the need for software tools that facilitate bulk submissions. This need has yet to be met with a concurrent development of tools to automate the preparatory work preceding such submissions.\n\nResultsI introduce annonex2embl, a Python package that automates the preparation of complete sequence flatfiles for large-scale sequence submissions to the European Nucleotide Archive. The tool enables the conversion of DNA sequence alignments that are co-supplied with sequence annotations and metadata to submission-ready flatfiles. Among other features, the software automatically accounts for length differences among the input sequences while maintaining correct annotations, automatically interlaces metadata to each record, and displays a design suitable for easy integration into bioinformatic workflows. As proof of its utility, annonex2embl is employed in preparing a dataset of more than 1,500 fungal DNA sequences for database submission.

bioinformatics↗

bioRxiv2019

PACVr: Plastome Assembly Coverage Visualization in R

BackgroundThe 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.\n\nResultsWe 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.\n\nConclusionsPACVr 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.

bioinformatics↗

bioRxiv2018

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA

BackgroundThe submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant DNA barcoding.\n\nMethodsA Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called \"checklists\") for a subsequent upload to the public sequence database of the European Nucleotide Archive (ENA). The software tool, titled \"EMBL2checklists\", automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates output that can be uploaded via the interactive Webin submission system of ENA.\n\nResultsEMBL2checklists provides a simple, platform-independent tool that automates the conversion of common plant DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in the submission of DNA sequences of two recent plant phylogenetic investigations and one fungal metagenomic study.\n\nDiscussionEMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant biologists without bioinformatics expertise to generate submission-ready checklists from common plant DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.

bioinformatics↗