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Phylogenomics of Chenopodiaceae

Goal: Understanding phylogenomic relationship of diverse species of Chenopodiaceae in the aspect of organelle genomes

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Jongsun Park
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Atriplex gmelinii C. A. Mey. Ex Bong._1838 is an annual halophytic herb found in East Asia and North America. The chloroplast genome of A. gmelinii was successfully sequenced. The assembled genome (151,852bp; GC ratio, 37.3%) is composed of four subregions, with the large single copy (LSC; 83,872bp; 35.4%) and small single copy (SSC; 17,812bp; 30.9%) regions separated by two regions of inverted repeat regions (25,084 bp; 42.8%). A total of 130 genes were predicted with 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. The phylogenetic analyses inferred from whole chloroplast genomes of 35 species, including 34 species in Amaranthaceae and one outgroup species, suggest a close relation- ship between A. gmelinii and A. centralasiatica.
Jongsun Park
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Chenopodium album sensu stricto belonging to C. album aggregate is an annual cosmopolitan weed displaying the diversity of morphologies. We completed the six chloroplast genomes of C. album s. str. collected in Korea to understand the relationship between the diversity of chloroplast genomes and their morphological variations. All six C. album chloroplast genomes have a typical quadripartite structure with length ranging from 151,906 bp to 152,199 bp, similar to the previously sequenced C. album chloroplast genome (NC_034950). In total, 56 single nucleotide polymorphisms (SNPs) and 26 insertion and deletion (INDEL) regions (308 bp in total) were identified from the six chloroplast genomes, presenting a low level of intraspecific variations in comparison to the other angiosperm species. 376 normal simple sequence repeats were identified in all seven C. album chloroplast genomes. The phylogenetic analysis based on all available complete Amaranthaceae chloroplast genomes presents phylogenetic positions of six C. album samples as well as correlation with one of C. album morphological features. Our results provide the way to investigate intraspecific features of C. album chloroplast genomes and also the insights of understanding various intraspecific characteristics including morphological features.
Jongsun Park
added 2 research items
Suaeda japonica Makino is an annual herb in seashore in Korea and Japan. In this study, we presented the first complete chloroplast genome of S. japonica which is 152,109 bp long and has four subregions: 83,618 bp of large single copy (LSC) and 18,101 bp of small single copy (SSC) regions are separated by 25,195 bp of inverted repeat (IR) regions including 128 genes (83 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 36.4% and those in the LSC, SSC, and IR regions are 34.2%, 29.2%, and 42.7%, respectively. Phylogenetic trees show that two Suaeda chloroplast genomes were clustered and clade of Betoidae, Chenopodioidae, and Amarantheae are successfully resolved with high bootstrap supports. Our chloroplast genome will contribute for phylogeny of Amaranthaceae in detail.
Suaeda japonica Makino is an annual herb found in the seashore in Korea and Japan. In this study, we presented second complete chloroplast genome of S. japonica which is 152,112 bp long and has four subregions: 83,620 bp of large single-copy (LSC) and 18,102 bp of small single-copy (SSC) regions are separated by 25,195 bp of inverted repeat (IR) regions including 128 genes (83 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 36.4% and those in the LSC, SSC, and IR regions are 34.2%, 29.2%, and 42.7%, respectively. Phylogenetic trees show that two S. japonica is monophyletic. This chloroplast genome suggests further investigation to find the relationship between morphological variations and genetic diversity.
Jongsun Park
added a research item
Oxybasis glauca (L.) S. Fuentes, Uotila & Borsch is an annual halophyte. In this study, we presented complete chloroplast genome of O. glauca as the first chloroplast genome of genus Oxybasis, which is 151,655 bp long and has four subregions: 83,759 bp of large single-copy (LSC) and 17,914 bp of small single-copy (SSC) regions are separated by 24,991 bp of inverted repeat (IRs) regions including 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC, and IR regions are 34.7, 30.4, and 42.8%, respectively. Phylogenomic tree shows that O. glauca belongs to tribe Atripliceae forming a monophyletic clade with genus Chenopodium and Atriplex.
Jongsun Park
added a research item
Dysphania ambrosioides (L.) Mosyakin & Clemants which belongs to Chenopodiaceae/Amaranthaceae sensu in APG system has been known as a useful plant in various fields as well as an invasive species spreading all over the world. To understand its phylogenetic relationship with neighbour species, we completed chloroplast genome of D. ambrosioides collected in Korea. Its length is 151,689 bp consisting of four sub-regions: 83,421 bp of large single copy (LSC) and 18,062 bp of small single copy (SSC) regions are separated by 25,103 bp of inverted repeat (IR) regions. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC and IR regions are 34.9%, 30.3%, and 42.7%, respectively. Distribution of simple sequence repeats are similar to those of the other two Dysphania chloroplasts; however, different features can be utilized for population genetics. Nucleotide diversity of Dysphania chloroplast genomes 18 genes including two ribosomal RNAs contains high nucleotide diversity peaks, which may be genus or species-specific manner. Phylogenetic tree presents that D. ambrosioides occupied a basal position in genus Dysphania and phylogenetic relation of tribe level is presented clearly with complete chloroplast genomes.
Jongsun Park
added a research item
We completed chloroplast genome of Dysphania pumilio (R.Br.) Mosyakin & Clemants isolated in Anyang city in Korea. Its length is 151,960 bp consisting four subregions: 83,756 bp of large single copy (LSC) and 17,742 bp of small single copy (SSC) regions are separated by 25,231 bp of inverted repeat (IR) region. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content is 36.9% and those in LSC, SSC, and IR regions are 34.8%, 30.4%, and 42.7%, respectively. 25 single nucleotide polymorphisms and two insertions and deletions suggest multiple invasive origins in Korea.
Jongsun Park
added 2 research items
Dysphania pumilio (R.Br.) Mosyakin & Clemants which belongs to Amaranthaceae is an invasive species all over the world. In this study, we presented first complete chloroplast genome of D. pumilio of which length is 151,962 bp consisting four sub regions: 83,758 bp of large single copy (LSC) and 17,742 bp of small single copy (SSC) regions are separated by 25,231 bp of inverted repeat (IR) regions. One hundred and twenty-eight genes (84 coding genes, eight rRNAs, and 36 tRNAs) were annotated successfully. The overall GC contents of the chloroplast genome were 36.9% and in the LSC, SSC and IR regions were 34.8%, 30.4%, and 42.7%, respectively. First chloroplast genome of Dysphania will provide accurate phylogenetic position of Dysphania genus among neighbour genera.
Chenopodium ficifolium Sm. is an invasive weedy species, one of the main targets for weed control in Korea. In this study, we presented the first complete chloroplast genome of C. ficifolium which is 151,823 bp long and has four subregions: 83,668 bp of large single copy (LSC) and 17,937 bp of small single copy (SSC) regions are separated by 25,109 bp of inverted repeat (IR) regions including 129 genes (84 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.3% and those in the LSC, SSC, and IR regions are 35.3%, 31.0%, and 42.7%, respectively. Phylogenetic tree shows that C. ficifolium is clustered with C. album forming a monophyletic clade with other Chenopodium species.
Jongsun Park
added a project goal
Understanding phylogenomic relationship of diverse species of Chenopodiaceae in the aspect of organelle genomes