The complete chloroplast genome of <i>Scapania ampliata</i> Steph., 1897 (Scapaniaceae, Jungermanniales)

Choi, Seung Se; Kwon, Woochan; Park, Jongsun

doi:10.1080/23802359.2020.1791011

Cited by 8 publications

(9 citation statements)

References 16 publications

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“…In addition, Scapaniaceae clade is located outside of the rest families except Schistochilaceae family, which is different from the previous study (Choi et al. 2020 ), displaying relatively low supportive values ( Figure 1 ; see gray star). It requires more chloroplast genomes of Jungermanniales species.…”

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confidence: 93%

“… Neighbor joining (bootstrap repeat is 10,000), maximum likelihood (bootstrap repeat is 1000), and Bayesian Inference phylogenetic trees of twelve complete chloroplast genomes: Douinia plicata (MT898431 in this study), Scapania ampliata (MT644123; Choi et al. 2020 ), Scapania ciliata (NC_043786), Bazzania praerupta (NC_043785), Calypogeia fissa (NC_043787), Gymnomitrion concinnatum (NC_040133; Myszczyński et al. 2018 ), Heteroscyphus argutus (NC_043788), Plagiochila chinensis (NC_043784), Schistochila macrodonta (NC_043779), Calypogeia fissa (MK293995), Calypogeia integristipula (MK293996), Calypogeia muelleriana (MK294000), and Ptilidium pulcherrimum (NC_015402; Forrest et al.…”

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confidence: 88%

“…Geneious R11 11.0.5 (Biomatters Ltd, Auckland, New Zealand) was used for annotation based on S. amplicata chloroplast genome (MT644123; Choi et al. 2020 ).…”

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confidence: 99%

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The complete chloroplast genome of Douinia plicata (Lindb.) Konstant. & Vilnet (Scapaniaceae, Jungermanniales)

Bum

Kim

et al. 2020

Mitochondrial DNA Part B

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We completed chloroplast genome of Douinia plicata (Lindb.) Konstant. & Vilnet., presenting morphological features including denticulate leaf margin, verrucose cuticle on base of leaves, and 80–100° keel angle with stem at the midleaf. It is 118,797 bp long (GC ratio is 33.9%) and has four subregions: 81,142 bp of large single copy (31.9%) and 19,611 bp of small single copy (31.0%) regions are separated by 9,017 bp of inverted repeat (46.3%) regions including 130 genes (86 protein-coding genes, eight rRNAs, and 36 tRNAs). Phylogenetic trees show D. plicata is clustered with two Scapania species.

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confidence: 93%

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confidence: 88%

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The complete chloroplast genome of Douinia plicata (Lindb.) Konstant. & Vilnet (Scapaniaceae, Jungermanniales)

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Kim

et al. 2020

Mitochondrial DNA Part B

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“…In addition, A. thaliana and Arabidopsis suecica are clustered because the maternal origin of A. suecica is A. thaliana [ 101 ] ( Figure 7 ). Moreover, the topology of BI tree for the remaining Arabidopsis species, except for A. thaliana and A. suecica , is somewhat inconsistent to those of NJ and ML trees ( Figure 7 ), which has also been found in various plant chloroplast genomes [ 15 , 20 , 28 , 51 , 67 , 69 , 72 , 79 , 91 , 92 , 102 – 109 ]. This suggests that detailed investigations of phylogenetic relationships among Arabidopsis species with various methods should be done in near future.…”

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confidence: 92%

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

Park¹,

Xi²,

Kim³

2020

International Journal of Genomics

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Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.

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“…Here, we completed the mitogenome of S. ampliata for understanding its intraspecific variations and phylogenetic features together with its chloroplast genome already sequenced (Choi, Kwon, et al. 2020 ).…”

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confidence: 99%

The complete mitochondrial genome of Scapania ampliata Steph., 1897 (Scapaniaceae, Jungermanniales)

Choi

Min²,

Kwon³

et al. 2021

Mitochondrial DNA Part B

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The complete chloroplast genome of Scapania ampliata Steph., 1897 (Scapaniaceae, Jungermanniales)

Cited by 8 publications

References 16 publications

The complete chloroplast genome of Douinia plicata (Lindb.) Konstant. & Vilnet (Scapaniaceae, Jungermanniales)

The complete chloroplast genome of Douinia plicata (Lindb.) Konstant. & Vilnet (Scapaniaceae, Jungermanniales)

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

The complete mitochondrial genome of Scapania ampliata Steph., 1897 (Scapaniaceae, Jungermanniales)

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