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Plastid Genome Assembly Using Long-read data (ptGAUL)
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  • Wenbin Zhou,
  • Carolina Armijos,
  • Chaehee Lee,
  • Ruisen Lu,
  • Jeremy Wang,
  • Tracey Ruhlman,
  • Robert Jansen,
  • Alan Jones,
  • Corbin Jones
Wenbin Zhou
The University of North Carolina at Chapel Hill

Corresponding Author:wenbin.evolution@gmail.com

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Carolina Armijos
Universidad San Francisco de Quito
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Chaehee Lee
University of California Davis
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Ruisen Lu
Institute of Botany Jiangsu Province and Chinese Academy of Sciences
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Jeremy Wang
The University of North Carolina at Chapel Hill
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Tracey Ruhlman
University of Texas at Austin
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Robert Jansen
The University of Texas at Austin
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Alan Jones
The University of North Carolina at Chapel Hill
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Corbin Jones
The University of North Carolina at Chapel Hill
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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 have experienced substantial rearrangements. Most plastomes have two inverted repeat regions and two single-copy regions with few dispersed repeats. However, the plastomes of some taxa do harbor long repeat sequences (>300 bp). These long repeats make it difficult to assemble complete plastomes using short read data, leading to misassemblies and consensus sequences that have spurious rearrangements. Long read sequencing can potentially overcome these challenges. However, there is no consensus as to the most effective method for accurately assembling plastomes using long read data. Here, we generated a pipeline, plastid Genome Assembly Using Long-read data (ptGAUL) to address the problem of assembling of plastomes using long read data from Oxford Nanopore Technologies (ONT) or Pacific Biosciences (Pacbio) platforms. We demonstrated the efficacy of the ptGAUL pipeline using 16 published long read datasets. We showed that ptGAUL produces accurate and unbiased assemblies. Additionally, we applied ptGAUL to assemble four Juncus (Juncaceae) plastomes using ONT long reads. Our results revealed many long repeats and rearrangements in Juncus plastomes compared with basal lineages of Poales.
19 Nov 2022Submitted to Molecular Ecology Resources
02 Dec 2022Submission Checks Completed
02 Dec 2022Assigned to Editor
02 Dec 2022Review(s) Completed, Editorial Evaluation Pending
13 Dec 2022Reviewer(s) Assigned
26 Jan 2023Editorial Decision: Revise Minor
24 Feb 20231st Revision Received
24 Feb 2023Submission Checks Completed
24 Feb 2023Assigned to Editor
24 Feb 2023Review(s) Completed, Editorial Evaluation Pending
27 Feb 2023Reviewer(s) Assigned
16 Mar 2023Editorial Decision: Accept