The Complete Chloroplast Genome Sequence and Intra-Species Diversity of <i>Rhus chinensis</i>

Kim, Inseo; Park, Jee Young; Lee, Yun Sun; Joh, Ho Jun; Kang, Sung Goon; Jayakodi, Murukarthick; Lee, Hyun Oh; Hur, Young-Jin; Kim, Yong; Kim, Kyung Hoon; Lee, Sang-Choon; Yang, Tae-Jin

doi:10.9787/pbb.2017.5.3.243

Cited by 6 publications

(5 citation statements)

References 23 publications

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“…Both species show very similar morphology and also very low sequence level genetic diversity for complete chloroplast genomes. Relatively abundant intra-species polymorphisms are identified in Pedicularis chamissonis, Panax ginseng, Scutellaria baicalensis and Rhus chinensis (Fujii et al 1997;Kim et al 2015a;Jiang et al 2017;Kim et al 2017). We found very low diversity between both species with their sequence variations, suggesting an on-going genome divergence of the two species.…”

Section: Authentication Of Eclipta Products With Three Indel-based Mamentioning

confidence: 83%

Discrimination and Authentication of Eclipta prostrata and E. alba Based on the Complete Chloroplast Genomes

Kim

Park

Lee

et al. 2017

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. prostrata is more widely used than E. alba. Morphological semblances have confounded identification of either species. Here, we report the complete chloroplast genomes of both species to provide an authentication system between the two species and understand their diversity. Both chloroplast genomes were 151,733-151,757 bp long and composed of a large single copy (83,285-83,300 bp), a small single copy (18,283-18,346 bp), and a pair of inverted repeats (25,075-25,063 bp). Gene annotation revealed 80 protein coding genes, 30 tRNA genes and four rRNA genes. A phylogenetic analysis revealed that the genus Eclipta is grouped with Heliantheae tribe species in the Asteraceae family. A comparative analysis verified 29 InDels and 58 SNPs between chloroplast genomes of E. prostrata and E. alba. The low chloroplast genome sequence diversity indicates that both species are really close to each other and are not completely diverged yet. We developed six DNA markers that distinguish E. prostrata and E. alba based on the polymorphisms of chloroplast genomes between E. prostrata and E. alba. The chloroplast genome sequences and the molecular markers generated in this study will be useful for further research of Eclipta species and accurate classification of medicinal herbs.

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Section: Authentication Of Eclipta Products With Three Indel-based Mamentioning

confidence: 83%

Discrimination and Authentication of Eclipta prostrata and E. alba Based on the Complete Chloroplast Genomes

Kim

Park

Lee

et al. 2017

Plant Breed. Biotech.

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“…Gray (24), Rhus aromatica L. (18) (https://www.ncbi.nlm.nih.gov/, accessed on the 4 August 2022). Moreover, the chloroplast genome of Rhus chinensis is available [84]. Studies dealing with the genetic diversity of sumac are also limited in number and in terms of geographical representation.…”

Section: Genetic Characterizationmentioning

confidence: 99%

Phytochemical, Antioxidant, Anti-Microbial, and Pharmaceutical Properties of Sumac (Rhus coriaria L.) and Its Genetic Diversity

et al. 2022

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Rhus coriaria L., commonly known as sumac, is a shrub of the Anacardiaceae family present in various subtropical and temperate regions of the world. Considering the rich array of functional and nutraceutical ingredients, sumac extracts are an underutilized source of health-promoting dietary ingredients. For example, sumac is a spice with remarkable antioxidant activity thanks to the high presence of phenolic compounds. In addition, sumac extracts also possess antimicrobial activity and exhibit antidiabetic and hypoglycemic properties. Based on the scientific records retrieved in reliable citation databases (Scopus and Web of Science), this review comprehensively offers research results on sumac with a focus on the phytochemical profiles, the antimicrobial and antioxidant properties of the extracts, the pharmaceutical uses, and the genetic diversity. We discuss that the use of sumac as a climate-resilient tree should be promoted to diversify the food basket by leveraging on its multiple health benefits and also to reverse the abandonment of marginal lands under low irrigation.

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“…Despite these previous studies, Rhus are poorly studied from a genomic perspective. To date, plastid genomes are available for only two representatives of Rhus: R. chinensis Mill., and R. typhina L. (Lee et al, 2016;Kim et al, 2017;Zuo et al, 2019). Interestingly, plastomes of the Asian R. chinensis range in size from 149,011-158,809 bp, while the North American R. typhina has a plastome of 160,204 bp, revealing striking variation in plastome size within Rhus.…”

Section: Introductionmentioning

confidence: 99%

Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.

Barrett¹

2020

PeerJ

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Plastid genomes (plastomes) represent rich sources of information for phylogenomics, from higher-level studies to below the species level. The genus Rhus (sumac) has received a significant amount of study from phylogenetic and biogeographic perspectives, but genomic studies in this genus are lacking. Rhus integrifolia and R. ovata are two shrubby species of high ecological importance in the southwestern USA and Mexico, where they occupy coastal scrub and chaparral habitats. They hybridize frequently, representing a fascinating system in which to investigate the opposing effects of hybridization and divergent selection, yet are poorly characterized from a genomic perspective. In this study, complete plastid genomes were sequenced for one accession of R. integrifolia and one each of R. ovata from California and Arizona. Sequence variation among these three accessions was characterized, and PCR primers potentially useful in phylogeographic studies were designed. Phylogenomic analyses were conducted based on a robustly supported phylogenetic framework based on 52 complete plastomes across the order Sapindales. Repeat content, rather than the size of the inverted repeat, had a stronger relative association with total plastome length across Sapindales when analyzed with phylogenetic least squares regression. Variation at the inverted repeat boundary within Rhus was striking, resulting in major shifts and independent gene losses. Specifically, rps19 was lost independently in the R. integrifolia-ovata complex and in R. chinensis, with a further loss of rps22 and a major contraction of the inverted repeat in two accessions of the latter. Rhus represents a promising novel system to study plastome structural variation of photosynthetic angiosperms at and below the species level.

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The Complete Chloroplast Genome Sequence and Intra-Species Diversity of Rhus chinensis

Cited by 6 publications

References 23 publications

Discrimination and Authentication of Eclipta prostrata and E. alba Based on the Complete Chloroplast Genomes

Discrimination and Authentication of Eclipta prostrata and E. alba Based on the Complete Chloroplast Genomes

Phytochemical, Antioxidant, Anti-Microbial, and Pharmaceutical Properties of Sumac (Rhus coriaria L.) and Its Genetic Diversity

Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.

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