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Genus-wide investigations of Potentilleae

Goal: Project goal is for understanding genome-wide diversitication of Potentillcae species.

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131

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Jongsun Park
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The complete chloroplast genome of Agrimonia pilosa Ledeb. isolated in Korea is 155,125 bp long (GC ratio is 36.9%) and has four subregions: 84,458 bp of large single copy (34.9%) and 18,737 bp of small single copy (30.4%) regions are separated by 25,965 bp of inverted repeat (42.6%) regions including 129 genes (84 protein-coding genes, eight rRNAs, and 37 tRNAs). 258 SNPs and 542 INDELs were iden- tified as intraspecific variations against the partial genome (KY419942). Phylogenetic trees show that our chloroplast genome was clustered with the previous A. pilosa chloroplast genome.
Jongsun Park
added a project goal
Project goal is for understanding genome-wide diversitication of Potentillcae species.
 
Jongsun Park
added a research item
Potentilla freyniana Bornm. has radical leaves with petioles and trifoliolate distinguished from Potentilla fragarioides and Duchesnea indica. In this study, we presented first complete chloroplast genome of P. freyniana to understand its phylogenetic position. Its length is 156,381 bp long and has four subregions: 85,724 bp of large single copy (LSC) and 18,617 bp of small single copy (SSC) regions are separated by 26,020 bp of inverted repeat (IR) 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 34.8%, 30.7%, and 42.7%, respectively. Phylogenetic trees show that phylogenetic position of P. freyniana disagrees with three phylogenetic studies, showing that more Potentilla chloroplast genomes are required for clarifying Potentilla phylogeny.
Jongsun Park
added a research item
Potentilla stolonifera var. quelpaertensis Nakai has developed stolon in comparison to Potentilla fragarioides var. major. To uncover phylogenetic relations of two species, we presented complete chloroplast genome of P. stolonifera var. quelpaertensis which is 156,393 bp long and has four subregions: 85,763 bp of large single-copy (LSC) and 18,590 bp of small single-copy (SSC) regions are separated by 26,020 bp of inverted repeat (IR) 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 34.8%, 30.7%, and 42.7%, respectively. Phylogenetic trees show that P. stolonifera var. quelpaertensis is closely clustered with P. fragarioides var. major and Potentilla centigrana, of which morphological characteristics are clearly distinct with each other. Additional researches are strongly required to understand the relationship between morphological classification and phylogenetic relationship of these Potentilla species. © 2019, © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
Jongsun Park
added 2 research items
We conducted taxonomical investigations based on morphological characteristics, fruit morphology, and literature research on the tribe Potentilleae (Rosaceae) in Korea covering seven genera and 24 species. The style position on the ovary and the shape of style were useful characteristics for the classification of subtribal and generic levels in the tribe Potentilleae. The subtribe Fragariinae is characterized by subbasal or lateral style on the ovary and anthers with one theca. The subtribe Potentillinae has a subterminal style on the ovary, except for Argentina, which presents a subterminal and lateral style and anthers with two thecae. These results support the recent taxonomic recognition that i) the tribe Potentilleae consists of two subtribes, and ii) genera such as Dasiphora, Comarum, and Sibbaldianthe sometimes included in Potentilla s.l. are treated as independent genus. In the subtribe Potentillinae, Argentina, which has been treated as Potentilla, is supported as a distinct genus according to the characteristics of the subterminal and lateral style position and the ventral stipular auricles. In Fragaria, F. nipponica subsp. chejuensis, which has generally small leaves and a limited distribution only on Hallasan Mt., is supported by treatment as an endemic species. Duchesnea chrysantha is distinguished from D. indica by the characteristics of light green or yellowish green leaves, thin and somewhat membranous leaflets, and broad ovate or obovate leaflets. Each complex of P. dickinsii and P. chinensis remains unresolved with regard to controversy over the taxonomic circumscription due to their external morphological variations. Additional taxonomical research and molecular population studies are required for a more in-depth understanding of the tribe Potentilleae in Korea.
New candidate of variety of Potentilla, named as Potentilla freyniana var. chejuensis, was found in about 1,000–1,500 m elevations in Mt. Halla in Korea. To uncover its phylogenomic relationships with available chloroplast genomes, we presented complete chloroplast genome of P. freyniana var. chejuensis which is 156,739 bp long and has four subregions: 85,909 bp of large single copy (LSC) and 18,590 bp of small single copy (SSC) regions are separated by 25,940 bp of inverted repeat (IR) regions including 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs). The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC, and IR regions are 34.7, 30.7, and 42.8%, respectively. Phylogenomic trees based on whole chloroplast genomes show that P. freyniana var. chejuensis is clustered with three Potentilla species isolated in Korea which present enough differences of their morphologies. It indicates that P. freyniana var. chejuensis can be a new variety species.
Jongsun Park
added a research item
Potentilla fragarioides var. major Maxim. distributed in East Asia has been discussed about its scientific name. To clarify its phylogenetic position, we presented first complete chloroplast genome of P. fragarioides var. major which is 156,440 bp long and has four subregions: 85,784 bp of large single copy (LSC) and 18,616 bp of small single copy (SSC) regions are separated by 26,020 bp of inverted repeat (IR) regions including 129 genes (84 coding genes, eight 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 34.8%, 30.7%, and 42.7%, respectively. Phylogenetic trees show that P. fragarioides var. major is sister to P. freyniana with high bootstrap values, suggesting further phylogenetic and morphological researches about the two species.
Jongsun Park
added 4 research items
Duchesnea chrysantha (Zoll. & Moritzi) Miq. is a traditional medicinal species of genus Duchesnea nested in Potentilla genus but having a significant key to be independent genus. In this study, we presented first complete chloroplast genome of D. chrysantha which is 156,329 bp long and has four subregions: 85,568 bp of large single copy (LSC) and 18,757 bp of small single copy (SSC) regions are separated by 26,002 bp of inverted repeat (IR) regions including 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.0% and those in the LSC, SSC, and IR regions are 34.9%, 30.5%, and 42.8%, respectively. Phylogenetic trees show that D. chrysantha is clustered with D. indica and Duchesnea clade is nested in Potentilla clade with high bootstrap support.
Duchesnea indica (Andrews) Th.Wolf is a species of genus Duchesnea which is nested in Potentilla clade. Its fruit is developed enough to be compared with strawberry, which is a significant key to be independent genus Potentilla. In this study, we presented the first complete chloroplast genome of D. indica which length is 156,050 bp long and has four sub-regions: 85,352 bp of large single copy (LSC) and 18,572 bp of small single copy (SSC) regions are separated by 26,063 bp of inverted repeat (IR) regions including 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC contents of the chloroplast genome are 37.0% and in the LSC, SSC, and IR regions are 34.9%, 30.6%, and 42.7%, respectively.
Potentilla centigrana Maxim. is one of species in core Potentilla group. To clarify phylogenetic position of P. centigrana, we sequenced the complete chloroplast genome which is 156,392 bp long and has four subregions: 85,479 bp of large single copy (LSC) and 18,845 bp of small single copy (SSC) regions are separated by 26,034 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 37.0% and those in the LSC, SSC, and IR regions are 35.0%, 30.8%, and 42.7%, respectively. Phylogenetic trees show that P. centigrana is located far from core group of Potentilla, disagreeing with morphological classification.