Plastid Genome Assembly Using Long‐read data

Zhou, Wenbin; Armijos, Carolina; Lee, Chaehee; Lu, Ruisen; Wang, Jeremy; Ruhlman, Tracey A.; Jansen, Robert K.; Jones, Alan M.; Jones, Corbin D.

doi:10.1111/1755-0998.13787

Cited by 14 publications

(7 citation statements)

References 124 publications

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“…Starting with high‐molecular‐weight DNA, different sequencing approaches may be used in combination to create an ideal foundation for plastome assembly. In addition to short‐read sequencing, long‐read approaches can be applied for lineages with long stretches of low nucleotide diversity or plastomes with substantial rearrangements (Scheunert et al, 2020; Zhou et al, 2023). Appropriate sequencing depth should be estimated based on genome size information and closely related lineages.…”

Section: Discussionmentioning

confidence: 99%

A comparative analysis of plastome evolution in autotrophic Piperales

Jost,

Wanke

2024

American J of Botany

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PremiseMany plastomes of autotrophic Piperales have been reported to date, describing a variety of differences. Most studies focused only on a few species or a single genus, and extensive, comparative analyses have not been done. Here, we reviewed publicly available plastome reconstructions for autotrophic Piperales, reanalyzed publicly available raw data, and provided new sequence data for all previously missing genera. Comparative plastome genomics of >100 autotrophic Piperales were performed.MethodsWe performed de novo assemblies to reconstruct the plastomes of newly generated sequence data. We used Sanger sequencing and read mapping to verify the assemblies and to bridge assembly gaps. Furthermore, we reconstructed the phylogenetic relationships as a foundation for comparative plastome genomics.ResultsWe identified a plethora of assembly and annotation issues in published plastome data, which, if unattended, will lead to an artificial increase of diversity. We were able to detect patterns of missing and incorrect feature annotation and determined that the inverted repeat (IR) boundaries were the major source for erroneous assembly. Accounting for the aforementioned issues, we discovered relatively stable junctions of the IRs and the small single‐copy region (SSC), whereas the majority of plastome variations among Piperales stems from fluctuations of the boundaries of the IR and the large single‐copy (LSC) region.ConclusionsThis study of all available plastomes of autotrophic Piperales, expanded by new data for previously missing genera, highlights the IR‐LSC junctions as a potential marker for discrimination of various taxonomic levels. Our data indicates a pseudogene‐like status for cemA and ycf15 in various Piperales. Based on a review of published data, we conclude that incorrect IR‐SSC boundary identification is the major source for erroneous plastome assembly. We propose a gold standard for assembly and annotation of high‐quality plastomes based on de novo assembly methods and appropriate references for gene annotation.

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Section: Discussionmentioning

confidence: 99%

A comparative analysis of plastome evolution in autotrophic Piperales

Jost,

Wanke

2024

American J of Botany

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“…Gene loss is frequent in Poales, particularly the loss of ndh genes in some species of Juncaceae [ 60 ]. The loss of ndh genes reported previously mostly occurred in the non-autotrophic plants [ 2 ] such as Epijagus virginiana [ 78 ], Cuscuta [ 15 , 79 ], Hypopitys monotropa [ 4 ], and Triantha occidentalis [ 71 , 80 ].…”

Section: Discussionmentioning

confidence: 99%

“…Recent sequencing of 37 plastomes from Bromeliaceae also found new lineage-specific rearrangements, including significant shift of IR boundary and large inversions in Tillandsioideae [ 58 ]. Many large repeats and rearrangements were also found in the four plastomes of Juncus (Juncaceae) [ 60 ]. Nevertheless, large-scale study about the general evolutionary pattern of plastome in the Poales as a whole is still lacking.…”

Section: Introductionmentioning

confidence: 99%

Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales

Wu,

Li,

2024

BMC Biol

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Background The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. Results We acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern. Extensive variation including the largest one in monocots with 225,293 bp in size, heterogeneous GC content, and a wide variety of gene duplication and loss were revealed. Moreover, rare occurrences of three inverted repeat (IR) copies in angiosperms and one IR loss were observed, accompanied by short IR (sIR) and small direct repeat (DR). Widespread structural heteroplasmy, diversified inversions, and unusual genomic rearrangements all appeared in Poales, occasionally within a single species. Extensive repeats in the plastomes were found to be positively correlated with the observed inversions and rearrangements. The variation all showed a “small-large-moderate” trend along the evolution of Poales, as well as for the sequence substitution rate. Finally, we found some positively selected genes, mainly in C4 lineages, while the closely related lineages of those experiencing gene loss tended to have undergone more relaxed purifying selection. Conclusions The variation of plastomes in Poales may be related to its successful diversification into diverse habitats and multiple photosynthetic pathway transitions. Our order-scale analyses revealed unusual evolutionary scenarios for plastomes in the photoautotrophic order of Poales and provided new insights into the plastome evolution in angiosperms as a whole.

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“…Pre-existing chloroplast genome assembly tools largely make use of short read data [ 13 ]. However, Zhou et al [ 28 ] introduce ptGAUL as a plastid genome assembly tool that makes use of long reads. While ptGAUL and CLAW share the common objective of chloroplast genome assembly from long reads their implementation methodologies markedly differ.…”

Section: Discussionmentioning

confidence: 99%

CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data

Phillips,

Ferguson,

Burton

et al. 2024

PLoS Comput Biol

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Chloroplasts are photosynthetic organelles in algal and plant cells that contain their own genome. Chloroplast genomes are commonly used in evolutionary studies and taxonomic identification and are increasingly becoming a target for crop improvement studies. As DNA sequencing becomes more affordable, researchers are collecting vast swathes of high-quality whole-genome sequence data from laboratory and field settings alike. Whole tissue read libraries sequenced with the primary goal of understanding the nuclear genome will inadvertently contain many reads derived from the chloroplast genome. These whole-genome, whole-tissue read libraries can additionally be used to assemble chloroplast genomes with little to no extra cost. While several tools exist that make use of short-read second generation and third-generation long-read sequencing data for chloroplast genome assembly, these tools may have complex installation steps, inadequate error reporting, poor expandability, and/or lack scalability. Here, we present CLAW (Chloroplast Long-read Assembly Workflow), an easy to install, customise, and use Snakemake tool to assemble chloroplast genomes from chloroplast long-reads found in whole-genome read libraries (https://github.com/aaronphillips7493/CLAW). Using 19 publicly available reference chloroplast genome assemblies and long-read libraries from algal, monocot and eudicot species, we show that CLAW can rapidly produce chloroplast genome assemblies with high similarity to the reference assemblies. CLAW was designed such that users have complete control over parameterisation, allowing individuals to optimise CLAW to their specific use cases. We expect that CLAW will provide researchers (with varying levels of bioinformatics expertise) with an additional resource useful for contributing to the growing number of publicly available chloroplast genome assemblies.

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Plastid Genome Assembly Using Long‐read data

Cited by 14 publications

References 124 publications

A comparative analysis of plastome evolution in autotrophic Piperales

A comparative analysis of plastome evolution in autotrophic Piperales

Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales

CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data

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