Complete Plastome of Three Korean Asarum (Aristolochiaceae): Confirmation Tripartite Structure within Korean Asarum and Comparative Analyses

Yoo, Mi‐Jeong; Jin, Dong-Pil; Lee, Hyun-Oh; Lim, Chae Eun

doi:10.3390/plants10102056

Cited by 3 publications

(2 citation statements)

References 54 publications

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“…heterotropoides and Asa. sieboldii (both section Asiasarum ) likely maintain the tripartite structure, supporting a previous study (Yoo et al, 2021). Due to the close relationships of the various accessions, indicated by the extremely short branch lengths, we were not able to confidently reconstruct the relationships within the two species (Figure 1).…”

Section: Discussionsupporting

confidence: 90%

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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: Discussionsupporting

confidence: 90%

“…Notable differences are reported in Asarum (hereafter shortened to “ Asa .”). Multiple accessions are tripartite, with significantly increased plastome size, along SSC loss and a partial LSC inversion (Sinn et al, 2018; Yoo et al, 2021).…”

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confidence: 99%

A comparative analysis of plastome evolution in autotrophic Piperales

Jost,

Wanke

2024

American J of Botany

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Complete chloroplast genome of Asarum chungbuensis (C.S. Yook & J.G. Kim) B.U. Oh 2005 (Aristolochiaceae), a Korean endemic species

Choi,

Kim,

Kim

et al. 2024

Mitochondrial DNA Part B

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Asarum chungbuensis , a species endemic to Korea, has a limited distribution across the Korean Peninsula and is used in traditional medicine. Despite its importance, the genome structure, genetic composition, and phylogenetic relationships based on its chloroplast genome have not been documented. In this study, the complete chloroplast genome of A. chungbuensis was newly assembled. The chloroplast genome is 190,179 base pairs (bp) long, and the overall GC content (%) of the plastid was 36.8%. The chloroplast genome size of A. chungbuensis is longer than that of the normal chloroplast genome (160 kb) because of an inverted small single-copy (SSC) duplication that incorporates the SSC into an inverted repeat (IR) region. By extension, this duplication event causes this chloroplast genome to lack an SSC, unlike other formal structures. The chloroplast genome, with a tripartite structure, consisted of a single-copy region of 93,351 bp with a 34.6% GC content and two IR regions, each with a length of 48,414 bp and a 38.8% GC content. Additionally, it was found to have 113 genes, including 79 PCG genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis revealed that A. chungbuensis was grouped with A. heterotropoides var. seoulense , which diverged from the clade comprising A. koreanum and A. patens . The newly sequenced A. chungbuensis chloroplast genome could provide valuable genomic information for determining unique genome structures, especially for the assessment of genetic diversity, phylogenetic relationships, species conservation, and biogeographic studies of the genus Asarum .

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Application of third-generation sequencing to herbal genomics

Gao

Xu²,

Xin³

et al. 2023

Front. Plant Sci.

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There is a long history of traditional medicine use. However, little genetic information is available for the plants used in traditional medicine, which limits the exploitation of these natural resources. Third-generation sequencing (TGS) techniques have made it possible to gather invaluable genetic information and develop herbal genomics. In this review, we introduce two main TGS techniques, PacBio SMRT technology and Oxford Nanopore technology, and compare the two techniques against Illumina, the predominant next-generation sequencing technique. In addition, we summarize the nuclear and organelle genome assemblies of commonly used medicinal plants, choose several examples from genomics, transcriptomics, and molecular identification studies to dissect the specific processes and summarize the advantages and disadvantages of the two TGS techniques when applied to medicinal organisms. Finally, we describe how we expect that TGS techniques will be widely utilized to assemble telomere-to-telomere (T2T) genomes and in epigenomics research involving medicinal plants.

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Complete Plastome of Three Korean Asarum (Aristolochiaceae): Confirmation Tripartite Structure within Korean Asarum and Comparative Analyses

Cited by 3 publications

References 54 publications

A comparative analysis of plastome evolution in autotrophic Piperales

A comparative analysis of plastome evolution in autotrophic Piperales

Complete chloroplast genome of Asarum chungbuensis (C.S. Yook & J.G. Kim) B.U. Oh 2005 (Aristolochiaceae), a Korean endemic species

Application of third-generation sequencing to herbal genomics

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