The complete chloroplast genome of ornamental coffee tree,Coffea arabicaL. (Rubiaceae)

Park, Jongsun; Kim, Yongsung; Xi, Hong; Heo, Kyeong-In

doi:10.1080/23802359.2019.1584060

Cited by 19 publications

(21 citation statements)

References 8 publications

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“…Alternatively, the insertion of nucleotides in gap region 2 may have occurred in V. amplificatum and in an ancestor of the V. dilatatum complex independently. These long gaps on the chloroplast genome are also found in Coffea arabica (Park et al, 2019e), Duchesnea chrysantha (Park et al, 2019c), and Illicium anisatum (Park et al, 2019d). This type of gap was also identified on the mitochondrial genomes of Liriodendron tulipifera (Park et al, 2019b) and Populus alba × glandulosa (Park et al, 2019f).…”

Section: Nucleotide Diversity Among Six Viburnum Speciesmentioning

confidence: 62%

Comparative chloroplast genomics and phylogenetic analysis of the Viburnum dilatatum complex (Adoxaceae) in Korea

Park¹,

Xi²,

2020

Korean J. Pl. Taxon

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Complete chloroplast genome sequences provide detailed information about any structural changes of the genome, instances of phylogenetic reconstruction, and molecular markers for fine-scale analyses. Recent developments of next-generation sequencing (NGS) tools have led to the rapid accumulation of genomic data, especially data pertaining to chloroplasts. Short reads deposited in public databases such as the Sequence Read Archive of the NCBI are open resources, and the corresponding chloroplast genomes are yet to be completed. The V. dilatatum complex in Korea consists of four morphologically similar species: V. dilatatum, V. erosum, V. japonicum, and V. wrightii. Previous molecular phylogenetic analyses based on several DNA regions did not resolve the relationship at the species level. In order to examine the level of variation of the chloroplast genome in the V. dilatatum complex, raw reads of V. dilatatum deposited in the NCBI database were used to reconstruct the whole chloroplast genome, with these results compared to the genomes of V. erosum, V. japonicum, and three other species in Viburnum. These comparative genomics results found no significant structural changes in Viburnum. The degree of interspecific variation among the species in the V. dilatatum complex is very low, suggesting that the species of the complex may have been differentiated recently. The species of the V. dilatatum complex share large unique deletions, providing evidence of close relationships among the species. A phylogenetic analysis of the entire genome of the Viburnum showed that V. dilatatum is a sister to one of two accessions of V. erosum, making V. erosum paraphyletic. Given that the overall degree of variation among the species in the V. dilatatum complex is low, the chloroplast genome may not provide a phylogenetic signal pertaining to relationships among the species.

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Section: Nucleotide Diversity Among Six Viburnum Speciesmentioning

confidence: 62%

Comparative chloroplast genomics and phylogenetic analysis of the Viburnum dilatatum complex (Adoxaceae) in Korea

Park¹,

Xi²,

2020

Korean J. Pl. Taxon

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“…It is caused by 6 bp deletion on ycf2 located in the IR region compared to the rest five A. thaliana chloroplast genomes. Interestingly, Tsu0 shows the longest length of chloroplast genome, caused by an insertion of approximately 500 bp between trnL and trnF , which is similar to the cases of Coffea arabica with one continuous insertion region [ 50 ], Duchesnea chrysantha showing three continuous insertion regions [ 21 ], Viburnum amplificatum showing two continuous insertion regions [ 32 ], and mitochondrial genomes of Populus tremula x Populus glandulosa and Liriodendron tulipifera with four and thirty-three continuous insertion regions, respectively [ 51 , 52 ].…”

Section: Resultsmentioning

confidence: 99%

“…This is also caused by the inserted region of the Tsu0 chloroplast genome. Other plant chloroplasts of which intraspecific variations of the GC contents are identical to those of A. thaliana are Goodyera schlechtendaliana (37.1% and 37.2%) [ 53 – 55 ] and Gastrodia elata (26.7% and 26.8%) [ 56 – 58 ] which are same to those of Arabidopsis thaliana , while Coffea arabica [ 50 , 59 – 63 ], Viburnum erosum [ 64 , 65 ], Duchesnea chrysantha [ 20 , 21 ], Salix koriyanagi [ 66 , 67 ], Pseudostellaria palibiniana [ 23 , 25 ], and Pyrus ussuriensis [ 68 , 69 ] present no difference in the intraspecific GC contents.…”

Section: Resultsmentioning

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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“…Coffea arabica; Cold resistance; Jeju island chloroplast genome lowlevel sequence variations Coffea arabica L. is one of the major economical plants occupying 70% of world coffee production (Lashermes et al 1999;O'brien and Kinnaird 2003). Seven coffee chloroplast genomes are available presenting low level of intraspecies variations (Samson et al 2007;Park, Kim, Xi, Heo 2019a. Cold resistance feature of coffee tree can expand cultivation area beyond 'Bean Belt' (Bentley and Baker 2000).…”

mentioning

confidence: 99%

The complete chloroplast genomes of two cold hardness coffee trees, Coffea arabica L. (Rubiaceae)

Park¹,

Kim²,

Xi³

et al. 2020

Mitochondrial DNA Part B

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We presented two complete chloroplast genomes of cold resistance coffee trees (Coffea arabica L.), named as CH1 and CH2 cultivated in Jeju island, Korea. Their length is 155,187 bp long (GC ratio is 37.4%) and has four subregions: 85,160 bp of large single copy (LSC; 35.4%) and 18,135 bp of small single copy (SSC; 31.3%) regions are separated by 25,946 bp of inverted repeat (IR; 43.0%) regions including 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). Like sequenced coffee chloroplast genomes, number of sequence variations of CH1 and CH2 against TY1 chloroplast genomes are zero and two, respectively.

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The complete chloroplast genome of ornamental coffee tree,Coffea arabicaL. (Rubiaceae)

Cited by 19 publications

References 8 publications

Comparative chloroplast genomics and phylogenetic analysis of the <i>Viburnum dilatatum</i> complex (Adoxaceae) in Korea

Comparative chloroplast genomics and phylogenetic analysis of the <i>Viburnum dilatatum</i> complex (Adoxaceae) in Korea

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 chloroplast genomes of two cold hardness coffee trees, Coffea arabica L. (Rubiaceae)

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