The complete chloroplast genome of candidate new species from <i>Rosa rugosa</i> in Korea (Rosaceae)

Kim, Yongsung; Heo, Kyeong-In; Nam, Suhwan; Xi, Hong; Lee, Sang‐Tae; Park, Jongsun

doi:10.1080/23802359.2019.1637296

Cited by 14 publications

(20 citation statements)

References 22 publications

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“…Additional mitochondrial genomes of Rosa species will provide better result to understand phylogenetic relationship of these two Rosa species using mitochondrial genomes. This complete mitochondrial genome supports R. angusta is a new species together with its chloroplast genome sequences (Kim, Heo, et al 2019).…”

supporting

confidence: 64%

“…Rosa rugosa, one of the firstly reported Rosa species in Korea, is distributed in Korea, Japan, China, and Russia (Rehder 1949). One population of R. rugosa was identified in 2013 by Suhwan Nam, one of the authors, showing significant differences of leaves and flowers (Kim, Heo, et al 2019), named as Rosa augusta . Its chloroplast genome was successfully deciphered presenting 40 single nucleotide polymorphisms (SNPs) and 224 insertions and deletions (INDELs) between R. augusta and Chinese R. rugosa (Kim, Heo, et al 2019).…”

mentioning

confidence: 99%

“…One population of R. rugosa was identified in 2013 by Suhwan Nam, one of the authors, showing significant differences of leaves and flowers (Kim, Heo, et al 2019), named as Rosa augusta . Its chloroplast genome was successfully deciphered presenting 40 single nucleotide polymorphisms (SNPs) and 224 insertions and deletions (INDELs) between R. augusta and Chinese R. rugosa (Kim, Heo, et al 2019). For understanding genetic background of this species, we successfully assembled its complete mitochondrial genome.…”

mentioning

confidence: 99%

“…One population of R. rugosa was identified in 2013 by Suhwan Nam, one of the authors, showing significant differences of leaves and flowers (Kim, Heo, et al. 2019 ), named as Rosa augusta (Kim, Park, et al. 2019 ).…”

mentioning

confidence: 99%

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The complete mitochondrial genome of new species candidate of Rosa rugosa (Rosaceae)

Park¹,

Xi²,

Kim³

et al. 2020

Mitochondrial DNA Part B

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Completed mitochondrial genome of a new species candidate of Rosa rugosa, named as Rosa angusta, is 303,484 bp long. The overall GC content of this mitochondrial genome is 45.2%. It contains 52 genes covering 31 protein-coding genes, 17 tRNAs, and 3 rRNAs. In comparison to R. rugosa mitochondrial genome assembled from the public NGS raw reads, 124 SNPs and 769 INDELs were identified. Phylogenetic trees suggest that more Rosa mitochondrial genomes will be needed to understand phylogenetic relationship of the two Rosa species.

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supporting

confidence: 64%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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The complete mitochondrial genome of new species candidate of Rosa rugosa (Rosaceae)

Park¹,

Xi²,

Kim³

et al. 2020

Mitochondrial DNA Part B

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“…However, chloroplast genomes are occasionally useful for unravelling corresponding phylogenetic relationships based on the maternal lineage: e.g., Lindera genus [ 13 ], Fagopyrum genus [ 14 ], Potentilla genus [ 15 – 21 ], Pseudostellaria genus [ 22 – 26 ], and Dysphania genus [ 27 – 30 ]. Moreover, several studies that described assembled organelle genomes from NGS raw sequences generated with different purposes have been conducted [ 31 , 32 ].…”

Section: Introductionmentioning

confidence: 99%

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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A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics

Chen

et al. 2021

Hortic Res

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Rosa rugosa, commonly known as rugged rose, is a perennial ornamental shrub. It produces beautiful flowers with a mild fragrance and colorful seed pods. Unlike many other cultivated roses, R. rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity, alkaline, shade, drought, high humidity, and frigid temperatures. Here, we produced and analyzed a high-quality genome sequence for R. rugosa to understand its ecology, floral characteristics and evolution. PacBio HiFi reads were initially used to construct the draft genome of R. rugosa, and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes. We obtained a 382.6 Mb genome encoding 39,704 protein-coding genes. The genome of R. rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication (WGT), which occurred ~100 million years ago in the ancestor of core eudicots. Based on a comparative analysis of the high-quality genome assembly of R. rugosa and other high-quality Rosaceae genomes, we found a unique large inverted segment in the Chinese rose R. chinensis and a retroposition in strawberry caused by post-WGT events. We also found that floral development- and stress response signaling-related gene modules were retained after the WGT. Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2 (DRIP2) and PEPTIDE TRANSPORTER 3 (PTR3) were found to be positively selected in evolution, which may have contributed to the unique ability of this plant to adapt to harsh environments. In summary, the high-quality genome sequence of R. rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.

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The complete chloroplast genome of candidate new species from Rosa rugosa in Korea (Rosaceae)

Cited by 14 publications

References 22 publications

The complete mitochondrial genome of new species candidate of Rosa rugosa (Rosaceae)

The complete mitochondrial genome of new species candidate of Rosa rugosa (Rosaceae)

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

A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics

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