chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data

Ankenbrand, Markus J.; Pfaff, Simon; Terhoeven, Niklas; Qureischi, Musga; Gündel, Maik; Weiß, Clemens L.; Hackl, Thomas; Förster, Frank

doi:10.21105/joss.00464

Cited by 26 publications

(26 citation statements)

References 14 publications

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“…As a graphical user interface is not suitable for automated comparisons, tools only providing a graphical interface have not been included. The following tools were determined to be within the scope of this study: ORG.Asm [29], chloroExtractor [34], Fast-Plast [43], IOGA [44], NOVOPlasty [35], GetOrganelle [45], and Chloroplast assembly protocol [46].…”

Section: Tool Selectionmentioning

confidence: 99%

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A systematic comparison of chloroplast genome assembly tools

Freudenthal

Pfaff

Terhoeven

et al. 2019

Preprint

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Chloroplasts are photosynthetic organelles in plant cells and contain their own genomic information. That genome can be utilized in different scientific fields like phylogenetics or biotechnology. Thus, different assemblers have been developed specialized in chloroplast assemblies. Those assemblers often use the output of whole genome sequencing experiments as input. Such sequencing data usually contain the complete chloroplast genome information, even if the sequencing aims for the core genome. Different assembly tools have never been systematically compared. Here we present a benchmark of seven chloroplast assembly tools, capable to succeed in more than 60 % of real data sets. Our results show significant differences between the tested assemblers in terms of generating whole chloroplast genome sequences and computational requirements. Moreover, we suggest further development to improve user experience and success rate. In terms of reproducibility, we created docker images for each tested tool, which are available for the scientific community. Following the presented guidelines, users are able to analyze and screen data sets for chloroplast genomes using only standard computer infrastructure. Thus large scale screening for chloroplasts as hidden treasures within genomic sequencing data is feasible.

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Section: Tool Selectionmentioning

confidence: 99%

“…Here, a k-mer analysis can be used to extract the most frequent reads. An example for this is implemented in chloroExtractor [34]. A third method combines both approaches by using a reference chloroplast as seed and simultaneously assembling the reads based on k-mers [35].…”

Section: Introductionmentioning

confidence: 99%

A systematic comparison of chloroplast genome assembly tools

Freudenthal

Pfaff

Terhoeven

et al. 2019

Preprint

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“…Despite the development of assembly algorithms customized for plastid genomes, the plastome assembly process remains imperfect and often requires the verification, if not manual correction, of the assembly product. Concurrent with the surge in plastid genome sequencing, many new algorithms and pipelines specifically designed for the assembly of plastid genomes have been developed [16][17][18][19][20][21][22][23]. Most of these tools allow a more accurate and targeted assembly of the plastid genome than generic assembly software, but in many cases some form of manual intervention or post-processing of the assembly results remains necessary [18,21].…”

Section: Introductionmentioning

confidence: 99%

PACVr: plastome assembly coverage visualization in R

2020

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Background: Plastid genomes typically display a circular, quadripartite structure with two inverted repeat regions, which challenges automatic assembly procedures. The correct assembly of plastid genomes is a prerequisite for the validity of subsequent analyses on genome structure and evolution. The average coverage depth of a genome assembly is often used as an indicator of assembly quality. Visualizing coverage depth across a draft genome is a critical step, which allows users to inspect the quality of the assembly and, where applicable, identify regions of reduced assembly confidence. Despite the interplay between genome structure and assembly quality, no contemporary, user-friendly software tool can visualize the coverage depth of a plastid genome assembly while taking its quadripartite genome structure into account. A software tool is needed that fills this void. 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 the individual plastome genes. By using a variable window approach, the tool allows visualizations on different calculation scales. It also confirms sequence equality of, as well as visualizes gene synteny between, the inverted repeat regions of the input genome. 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 invoked from a Unix shell, facilitating its use in automated quality control. We illustrate the application of PACVr on four empirical datasets and compare visualizations generated by PACVr with those of alternative software tools. 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) gene synteny across the inverted repeat regions. It contributes to optimizing plastid genome assemblies and increasing the reliability of publicly available plastome sequences. The software, example datasets, technical

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“…At least, DNA libraries were sequenced on Illumina HiSeq X platform (Illumina, San Diego, CA) for paired-end 150 bp reads. After filtered and trimmed by fastp program (Chen et al 2018), clean reads were obtained and subsequently, the high-quality paired-end reads were used to de novo assemble the complete cp genome with chloroExtractor (Ankenbrand et al 2018). Genome annotation was performed using the online program GeSeq (Tillich et al 2017) with reference to the Malus baccata and Malus doumeri cp genomes previously reported (Zhang et al 2017).…”

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confidence: 99%

The complete chloroplast genome of cultivated apple (Malus domestica Cv. ‘Yantai Fuji 8’)

Yan

Zhao

Jian-qing

et al. 2019

Mitochondrial DNA Part B

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The cultivated apple (Malus domestica Borkh.) is one of the most important crop fruits with high-economic values in the world. In the present study, we characterized the complete chloroplast (cp) genome sequence of apple cultivar 'Yantai Fuji 8'. The complete cp genome is 160,062 bp in length with a typical quadripartite structure. A total of 112 unique genes were found in the newly sequenced genome, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. Of these, 7 protein-coding genes, 7 tRNA genes, and all 4 rRNA genes are duplicated in the inverted regions. A maximum likelihood phylogenetic tree was reconstructed using the full length of cp genome to show the relationships among species in Rosaceae. The complete cp genome will be potential genetic resources for apple breeding programs.

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chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data

Cited by 26 publications

References 14 publications

A systematic comparison of chloroplast genome assembly tools

A systematic comparison of chloroplast genome assembly tools

PACVr: plastome assembly coverage visualization in R

The complete chloroplast genome of cultivated apple (Malus domestica Cv. ‘Yantai Fuji 8’)

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