The complete chloroplast genome sequence of <i>Asarum sieboldii</i> Miq. (Aristolochiaceae), a medicinal plant in Korea

Lim, Chae Eun; Lee, Sang-Choon; So, Soonku; Han, Su-Min; Choi, Jieun; Lee, Byoung-Yoon

doi:10.1080/23802359.2018.1424577

Cited by 8 publications

(12 citation statements)

References 3 publications

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“…Syntenically disrupted and otherwise divergent plastomes have been reported in some American Asarum species, which were suggested as contigs of the sequence, but not a completely circularized map [42]. The structural change was supported based on the complete plastome map of A. sieboldii, a member of the section Asiasarum [43]. However, it remains unclear whether changes in the IRs boundary would be present throughout the section.…”

Section: Introductionmentioning

confidence: 93%

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

Yoo

Jin

Lee

et al. 2021

Plants

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The genus Asarum (Aristolochiaceae) is a well-known resource of medicinal and ornamental plants. However, the taxonomy of Korean Asarum is ambiguous due to their considerable morphological variations. Previously, a unique plastome structure has been reported from this genus. Therefore, we investigated the structural change in the plastomes within three Korean Asarum species and inferred their phylogenetic relationships. The plastome sizes of Asarum species assembled here range from 190,168 to 193,356 bp, which are longer than a typical plastome size (160 kb). This is due to the incorporation and duplication of the small single copy into the inverted repeat, which resulted in a unique tripartite structure. We first verified this unique structure using the Illumina Miseq and Oxford Nanopore MinION platforms. We also investigated the phylogeny of 26 Aristolochiaceae species based on 79 plastid protein-coding genes, which supports the monophyly of Korean Asarum species. Although the 79 plastid protein-coding gene data set showed some limitations in supporting the previous classification, it exhibits its effectiveness in delineating some sections and species. Thus, it can serve as an effective tool for resolving species-level phylogeny in Aristolochiaceae. Last, we evaluated variable sites and simple sequence repeats in the plastome as potential molecular markers for species delimitation.

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Section: Introductionmentioning

confidence: 93%

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

Yoo

Jin

Lee

et al. 2021

Plants

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“…The average chloroplast genome (plastome) size of land plants is 151 kb, with most species ranging from 130–170 kb in length, and the average GC content is 36.3% (NCBI database, 4,281 land plant plastomes, March 17, 2020) ( Supplementary Table 1 ). However, previous studies documented that the plastome size of some lineages was extremely enlarged ( Chumley et al, 2006 ; Kim et al, 2015 ; Blazier et al, 2016 ; Weng et al, 2017 ; Lim et al, 2018 ; Gruzdev et al, 2019 ; Li H. et al, 2020 ). The largest chloroplast genome of angiosperm is Pelargonium transvaalense (242, 575 bp), with the inverted repeat (IR) region of the species expanding to 87,724 bp ( Weng et al, 2017 ).…”

Section: Introductionmentioning

confidence: 96%

Chloroplast Genomes of Two Species of Cypripedium: Expanded Genome Size and Proliferation of AT-Biased Repeat Sequences

Guo

Yang

et al. 2021

Front. Plant Sci.

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The size of the chloroplast genome (plastome) of autotrophic angiosperms is generally conserved. However, the chloroplast genomes of some lineages are greatly expanded, which may render assembling these genomes from short read sequencing data more challenging. Here, we present the sequencing, assembly, and annotation of the chloroplast genomes of Cypripedium tibeticum and Cypripedium subtropicum. We de novo assembled the chloroplast genomes of the two species with a combination of short-read Illumina data and long-read PacBio data. The plastomes of the two species are characterized by expanded genome size, proliferated AT-rich repeat sequences, low GC content and gene density, as well as low substitution rates of the coding genes. The plastomes of C. tibeticum (197,815 bp) and C. subtropicum (212,668 bp) are substantially larger than those of the three species sequenced in previous studies. The plastome of C. subtropicum is the longest one of Orchidaceae to date. Despite the increase in genome size, the gene order and gene number of the plastomes are conserved, with the exception of an ∼75 kb large inversion in the large single copy (LSC) region shared by the two species. The most striking is the record-setting low GC content in C. subtropicum (28.2%). Moreover, the plastome expansion of the two species is strongly correlated with the proliferation of AT-biased non-coding regions: the non-coding content of C. subtropicum is in excess of 57%. The genus provides a typical example of plastome expansion induced by the expansion of non-coding regions. Considering the pros and cons of different sequencing technologies, we recommend hybrid assembly based on long and short reads applied to the sequencing of plastomes with AT-biased base composition.

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“…However, extensive studies have also found that atypical genome structures and gene contents frequently occur among several distantly related families [20]. Among fully photosynthetic angiosperms, the variation in their genome structures is largely attributable to the expansion and contraction of IRs, the most extreme examples being the complete deletion of one copy (e.g., the IR-lacking clade of Fabaceae) and the expansion to an entire single-copy region shown from the genus Asarum L. within Aristolochiaceae [21–22]. Genome rearrangements via large inversions and reductions in gene numbers have been reported from Campanulaceae [23–24], Geraniaceae [25–27], and Oleaceae [28].…”

Section: Introductionmentioning

confidence: 99%

Plastid genome evolution in tribe Desmodieae (Fabaceae: Papilionoideae)

Jin

Choi

2019

PLoS ONE

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Recent plastid genome (plastome) studies of legumes (family Fabaceae) have shown that this family has undergone multiple atypical plastome evolutions from each of the major clades. The tribe Desmodieae belongs to the Phaseoloids, an important but systematically puzzling clade within Fabaceae. In this study, we investigated the plastome evolution of Desmodieae and analyzed its phylogenetic signaling. We sequenced six complete plastomes from representative members of Desmodieae and from its putative sister Phaseoloid genus Mucuna . Those genomes contain 128 genes and range in size from 148,450 to 153,826 bp. Analyses of gene and intron content revealed similar characters among the members of Desmodieae and Mucuna . However, there were also several distinct characters identified. The loss of the rpl2 intron was a feature shared between Desmodieae and Mucuna , whereas the loss of the rps12 intron was specific to Desmodieae. Likewise, gene loss of rps16 was observed in Mucuna but not in Desmodieae. Substantial sequence variation of ycf4 was detected from all the sequenced plastomes, but pseudogenization was restricted to the genus Desmodium . Comparative analysis of gene order revealed a distinct plastome conformation of Desmodieae compared with other Phaseoloid legumes, i.e., an inversion of an approximately 1.5-kb gene cluster ( trnD-GUC , trnY-GUA , and trnE-UUC ). The inversion breakpoint suggests that this event was mediated by the recombination of an 11-bp repeat motif. A phylogenetic analysis based on the plastome-scale data set found the tribe Desmodieae is a highly supported monophyletic group nested within the paraphyletic Phaseoleae, as has been found in previous phylogenetic studies. Two subtribes (Desmodiinae and Lespedezinae) of Desmodieae were also supported as monophyletic groups. Within the subtribe Lespedezinae, Lespedeza is closer to Kummerowia than Campylotropis .

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The complete chloroplast genome sequence of Asarum sieboldii Miq. (Aristolochiaceae), a medicinal plant in Korea

Cited by 8 publications

References 3 publications

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

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

Chloroplast Genomes of Two Species of Cypripedium: Expanded Genome Size and Proliferation of AT-Biased Repeat Sequences

Plastid genome evolution in tribe Desmodieae (Fabaceae: Papilionoideae)

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