The complete chloroplast genome of Zoysia japonica Steud. isolated in Korea (Poaceae): investigation of potential molecular markers on Z. japonica chloroplast genomes

Lee, Bumkyu; Park, Jongsun

doi:10.1007/s11816-021-00708-y

Cited by 11 publications

(7 citation statements)

References 55 publications

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“…Number of SNPs identified in Z. macrostachya is greater in number than that of Z. matrella (28 SNPs) (Lee and Park, 2021a); while number of the INDEL regions is smaller. In addition, both are smaller than those of Z. japonica (68 SNPs and 24 INDEL regions) (Lee and Park, 2021b), indicating that intraspecific variations of Z. macrostachya is the smallest among Zoysia species. These numbers are also smaller than those identified between the samples isolated in Korea: e.g., Campanula takesimana (Park et al, 2021a), Pseudostellaria palibiniana (Kim et al, 2019), Daphne genkwa (Yoo et al, 2021), Abeliophyllum distichum (Min et al, 2019;Park et al, 2019bPark et al, , 2019cPark et al, , 2021d, Chenopodium album (Park et al, 2021c), and Pyrus ussuriensis (Cho et al, 2019).…”

Section: Resultsmentioning

confidence: 85%

“…In addition, one SNP was in trnQ, displaying 20.51% SNPs are in genic region. Number of genes containing SNPs in Z. macrostachya is smaller than that of Z. japonica, exhibiting different genes: rpoB, rpoC2, atpB, and ndhA contain one synonymous SNP each, petA covers three synonymous SNPs, rpoC1 and atpF have one non-synonymous SNP each (Lee and Park, 2021b). This distribution of intraspecific SNPs in the genic region can be developed as intraspecific molecular markers with additional experiments of validation.…”

Section: Resultsmentioning

confidence: 95%

“…Because Z. macrostachva has more resistance to salt than Z. japonica and Z. matrella (Loch et al, 2017), it is highly valuable as a breeding copy for land reclamation or coastal areas. Due to recently sequenced chloroplast genomes of Zoysia (Tanaka et al, 2016;Lee and Park, 2021a;Lee and Park, 2021b), intraspecific variations which have been utilized for developing markers and understanding phylogenetic relationship (Park et al, 2020b;Park et al, 2021a) can be investigated along with Zoysia species. Here, we completed the complete chloroplast genome of Z. macrostachya to understand intraspecific variations as well as species boundary.…”

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confidence: 99%

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The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation of the Zoysia species

Lee

Yun

et al. 2021

Korean J. Pl. Taxon

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The complete chloroplast genome of Zoysia macrostachya Franch. & Sav. isolated in Korea is 135,902 bp long (GC ratio is 38.4%) and has four subregions; 81,546 bp of large single-copy (36.3%) and 12,586 bp of small single-copy (32.7%) regions are separated by 20,885 bp of inverted repeat (44.1%) regions, including 130 genes (83 protein-coding genes, eight rRNAs, and 39 tRNAs). Thirty-nine single nucleotide polymorphisms and 11 insertions and deletion (INDEL) regions were identified from two Z. macrostachya chloroplast genomes, the smallest among other Zoysia species. Phylogenetic trees show that two Z. macrostachya chloroplast genomes are clustered into a single clade. However, we found some incongruency with regard to the phylogenetic position of the Z. macrostachya clade. Our chloroplast genome provides insights into intraspecific variations and species delimitation issues pertaining to the Zoysia species.

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Section: Resultsmentioning

confidence: 85%

Section: Resultsmentioning

confidence: 95%

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confidence: 99%

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The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation of the Zoysia species

Lee

Yun

et al. 2021

Korean J. Pl. Taxon

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“…Intraspecific nucleotide diversity was calculated according to the method of Nei and Li (1979) based on three sets of complete Plantaginaceae chloroplast genomes. The Perl script applied here (500‐bp and 200‐bp window and step size, respectively) was utilized in previous studies (Kim et al 2021b; Lee & Park 2021; Park et al 2020d; Park & Xi 2021).…”

Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of the complete mitochondrial genome of Melanoplus differentialis (Acrididae: Melanoplinae) captured in Korea

Kim

Lee

et al. 2023

Entomological Research

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In this study, we determined the complete mitochondrial genome of the invasive insect species Melanoplus differentialis captured in Korea. The complete mitochondrial genome of M. differentialis is 15,625 bp long and comprises 13 protein‐coding genes, two ribosomal RNA genes, and 22 transfer RNAs, with a GC ratio of 25.2%. In total, 353 SNPs and 11 INDEL regions (total length 67 bp) were found against the previously sequenced M. differentialis mitochondrial genome recorded as public genome data. The number of interspecific variations was greater than the number of intraspecific variations in this insect. Phylogenetic tree analysis showed that the mitochondrial genome clustered the Melanoplus clade with two previously reported Melanoplus sequences. However, the sequences were not divided at the species‐level clade possibly as a consequence of misidentification caused by an error in the public database. Our results extend the molecular database status of Melanoplus by providing a novel complete mitochondrial genome sequence for M. differentialis that could serve as reference for further molecular studies.

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“… 2009 ) in the Genome Information System (GeIS) environment ( http://geis.infoboss.co.kr/ ), which has been used in previous studies (Heo et al. 2020 ; Lee and Park 2021 ; Park, Kim, et al. 2021 ; Park, Min, et al.…”

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The complete chloroplast genome of Utricularia tenuicaulis Miki (Lentibulariaceae) isolated in Korea

Park¹,

Xi²,

Kim

2022

Mitochondrial DNA Part B

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Utricularia tenuicaulis Miki 1935 is an aquatic carnivorous plant species found in East Asia including Korea and Japan. In this study, the chloroplast genome of U. tenuicaulis was successfully sequenced. The assembled genome (153,976 bp; GC ratio, 37.0%) contains four subregions, with the large single copy (LSC; 84,596 bp; 34.9%) and small single copy (SSC; 17,946 bp; 30.5%) regions separated by 25,718 bp of inverted repeat regions (42.7%), and includes 126 genes (81 protein-coding genes, 8 rRNAs, and 37 tRNAs). Phylogenetic analyses based on the whole-chloroplast genomes of 18 species, including 17 Lentibulariaceae species and one outgroup species, suggest a close relationship between U. tenuicaulis and Utricularia macrorhiza Leconte 1824. A comparison of genomic variation between U. tenuicaulis and U. macrorhiza confirmed the validity of the specific discrimination of U. tenuicaulis.

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The complete chloroplast genome of Zoysia japonica Steud. isolated in Korea (Poaceae): investigation of potential molecular markers on Z. japonica chloroplast genomes

Cited by 11 publications

References 55 publications

The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation of the Zoysia species

The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation of the Zoysia species

Comprehensive analysis of the complete mitochondrial genome of Melanoplus differentialis (Acrididae: Melanoplinae) captured in Korea

The complete chloroplast genome of Utricularia tenuicaulis Miki (Lentibulariaceae) isolated in Korea

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