GetOrganelle: a fast and versatile toolkit for accurate <i>de novo</i> assembly of organelle genomes

Jin, Jianjun; Yu, Wenbin; Yang, Jun‐Bo; Song, Yu; dePamphilis, Claude W.; Yi, Ting‐Shuang; D, Li

doi:10.1101/256479

Cited by 322 publications

(313 citation statements)

References 56 publications

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“…The circular cp genome of S. setschwanensis was filtered from sequenced plastid‐like reads and then assembled into contigs using the GetOrganelle pipeline with the suitable parameter setting for Sorbus (wordsize = 95, k‐mer = 99) (Jin et al ). The mean base coverage was 82×.…”

Section: Methodsmentioning

confidence: 99%

The complete chloroplast genome sequence of the Chinese endemic species Sorbus setschwanensis (Rosaceae) and its phylogenetic analysis

Wang

Niu

et al. 2020

Nordic Journal of Botany

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Sorbus setschwanensis Koehne is a pinnate‐leaved Sorbus s.str. species endemic to China with narrow distribution and intriguing phylogeny that needs wider attention. In this paper, the complete chloroplast (cp) genome of S. setschwanensis is reported, and its phylogenetic position is analyzed. The complete cp genome of S. setschwanensis is 160 064 bp in size with 36.50% GC content. It has a typical quadripartite structure including a pair of inverted repeat regions (IRs) of 26 378 bp that separates a large single copy (LSC) region of 86 013 bp and a small single copy (SSC) region of 19 295 bp. The cp genome encodes 108 genes, comprising 76 protein‐coding genes, 28 tRNA genes and 4 rRNA genes. Additionally, 52 simple sequence repeats (SSRs) and 43 dispersed repeats were identified. Comparison of the whole cp genome with those of other Sorbus species showed an overall high degree of sequence similarity, but there are six highly variable regions (trnR‐atpA, petN‐psbM, ndhC‐trnV, trnE‐trnT, trnT‐trnL and rpl32‐trnL) located in intergenic spacers that may be useful as molecular markers in future population genetic and phylogenetic studies in the genus. Phylogenetic analyses based on 108 coding genes from 25 species in Rosaceae revealed that S. setschwanensis is nested within Sorbus sect. Sorbus together with other pinnately leaved species, but does not form a sister lineage to S. rufopilosa belonging to the same series Multijugae. Thus, the systematic position of S. setschwanensis and relationships with other species in the genus needs to be further studied.

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Section: Methodsmentioning

confidence: 99%

The complete chloroplast genome sequence of the Chinese endemic species Sorbus setschwanensis (Rosaceae) and its phylogenetic analysis

Wang

Niu

et al. 2020

Nordic Journal of Botany

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“…Raw paired‐end reads were assessed using FastQC (Andrews, ), and the high quality paired‐end reads were assembled using the GetOrganelle toolkit (Jin et al, ). To filter the plastid‐like reads, we set the published plastome of Lonicera japonica Thunb.…”

Section: Methodsmentioning

confidence: 99%

Revisiting the phylogeny of Dipsacales: New insights from phylogenomic analyses of complete plastomic sequences

Xiang

Dong

Landrein

et al. 2019

J of Sytematics Evolution

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Phylogenetic relationships in Dipsacales have long been a major challenge. Although considerable progress has been made during the past two decades, questions remain; the uncertain systematic positions of Heptacodium, Triplostegia, and Zabelia, in particular, impede our understanding of Dipsacales evolution. Here we use 75 complete plastomic sequences to reconstruct the phylogeny of Dipsacales, of which 28 were newly generated. Two primary clades were recovered that form the phylogenetic backbone of Dipsacales. Seven of the primary clades correspond to the recognized families Adoxaceae, Caprifoliaceae s. str., Diervillaceae, Dipsacaceae, Linnaeaceae, Morinaceae, and Valerianaceae, and one corresponds to Zabelia, which was found to be the closest relative of Morinaceae in all analyses. Additionally, our results, with greatly increased confidence in most branches, show that Heptacodium and Triplostegia are members of Caprifoliaceae s. str. and Dipsacaceae, respectively. The results of our study indicate that the complete plastomic sequences provide a fully‐resolved and well‐supported representation of the phylogenetic relationships within Dipsacales.

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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%

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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GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

Cited by 322 publications

References 56 publications

The complete chloroplast genome sequence of the Chinese endemic species Sorbus setschwanensis (Rosaceae) and its phylogenetic analysis

The complete chloroplast genome sequence of the Chinese endemic species Sorbus setschwanensis (Rosaceae) and its phylogenetic analysis

Revisiting the phylogeny of Dipsacales: New insights from phylogenomic analyses of complete plastomic sequences

A systematic comparison of chloroplast genome assembly tools

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