Long-read assemblies reveal structural diversity in genomes of organelles - an example with<i>Acacia pycnantha</i>

Syme, Anna; McLay, Todd G. B.; Udovicic, Frank; Cantrill, David J.; Murphy, Daniel J.

doi:10.1101/2020.12.22.423164

Cited by 2 publications

(3 citation statements)

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“…2 ). This hybrid approach has shown improved assembly accuracy to determine the plastome structure and sequence in flowering plants ( Wu et al, 2014 ; Wang et al, 2018 ; Syme et al, 2020 ; Guo et al, 2021 ). Although the long reads obtained from the Pacbio platform have a higher error rate than short reads sequenced on Illumina platforms, the use of both technologies can help to reveal striking features regarding structural complexity in plastomes ( Guo et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine

Fonseca

Nazareno

Thode

et al. 2022

PeerJ

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The plastid genome of flowering plants generally shows conserved structural organization, gene arrangement, and gene content. While structural reorganizations are uncommon, examples have been documented in the literature during the past years. Here we assembled the entire plastome of Bignonia magnifica and compared its structure and gene content with nine other Lamiid plastomes. The plastome of B. magnifica is composed of 183,052 bp and follows the canonical quadripartite structure, synteny, and gene composition of other angiosperms. Exceptionally large inverted repeat (IR) regions are responsible for the uncommon length of the genome. At least four events of IR expansion were observed among the seven Bignoniaceae species compared, suggesting multiple expansions of the IRs over the SC regions in the family. A comparison with 6,231 other complete plastomes of flowering plants available on GenBank revealed that the plastome of B. magnifica is the longest Lamiid plastome described to date. The newly generated plastid genome was used as a source of selected genes. These genes were combined with orthologous regions sampled from other species of Bignoniaceae and all gene alignments concatenated to infer a phylogeny of the family. The tree recovered is consistent with known relationships within the Bignoniaceae.

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Section: Introductionmentioning

confidence: 99%

Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine

Fonseca

Nazareno

Thode

et al. 2022

PeerJ

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“…To date, there are several tools available to assemble organelle genomes using long-read data and hybrid data (both short-and long-read data), including organelle_pba (Soorni et al, 2017), canu (Koren et al, 2017), unicycler (Wick et al, 2017) and flye (Kolmogorov et al, 2019;Syme et al, 2021). However, these pipelines have some drawbacks.…”

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confidence: 99%

“…organelle_pba was designed exclusively for PacBio data; the Sprai (Miyamoto et al, 2014) and Celera (Miller et al, 2008) assemblers in organelle_pba are no longer maintained, limiting its extension to assembly with hybrid data sets. The approach of Syme et al (2021) requires an extra step to manually filter a subset of raw reads matching the plastome (~250× coverage) and sometimes generates multiple contigs in the assembly result. canu can yield different results depending on different read coverages (Wang, Schalamun, et al, 2018).…”

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confidence: 99%

Plastid Genome Assembly Using Long‐read data

Zhou

Armijos

Lee

et al. 2023

Molecular Ecology Resources

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Although plastid genome (plastome) structure is highly conserved across most seed plants, investigations during the past two decades have revealed several disparately related lineages that experienced substantial rearrangements. Most plastomes contain a large inverted repeat and two single‐copy regions, and a few dispersed repeats; however, the plastomes of some taxa harbour long repeat sequences (>300 bp). These long repeats make it challenging to assemble complete plastomes using short‐read data, leading to misassemblies and consensus sequences with spurious rearrangements. Single‐molecule, long‐read sequencing has the potential to overcome these challenges, yet there is no consensus on the most effective method for accurately assembling plastomes using long‐read data. We generated a pipeline, plastid Genome Assembly Using Long‐read data (ptGAUL), to address the problem of plastome assembly using long‐read data from Oxford Nanopore Technologies (ONT) or Pacific Biosciences platforms. We demonstrated the efficacy of the ptGAUL pipeline using 16 published long‐read data sets. We showed that ptGAUL quickly produces accurate and unbiased assemblies using only ~50× coverage of plastome data. Additionally, we deployed ptGAUL to assemble four new Juncus (Juncaceae) plastomes using ONT long reads. Our results revealed many long repeats and rearrangements in Juncus plastomes compared with basal lineages of Poales. The ptGAUL pipeline is available on GitHub: https://github.com/Bean061/ptgaul.

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Long-read assemblies reveal structural diversity in genomes of organelles - an example withAcacia pycnantha

Cited by 2 publications

References 48 publications

Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine

Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine

Plastid Genome Assembly Using Long‐read data

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