Identification and phylogenetic analysis of the genus Syringa based on chloroplast genomic DNA barcoding

Yao, Ruihong; Runfang, Guo; Liu, Yuguang; Kou, Ziqian; Shi, Baosheng

doi:10.1371/journal.pone.0271633

Cited by 3 publications

(2 citation statements)

References 30 publications

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“…CPGs can significantly enhance resolution at lower taxonomic levels and facilitate recovery of monophyletic lineages 17 , and are therefore considered ideal material in phylogenetics and population genetics 14 , 18 – 20 . In recent years, DNA sequencing technology has shifted to high-throughput, and CPGs of a large number of plants have been sequenced and published 21 , which was in turn used to identification and classification of plant 22 – 24 , lineage geography 25 and phylogenetic relationship researches 26 – 28 . Due to the existence of overlap and mosaicism in important taxonomic morphological traits among the species of Quercus section Cyclobalanopsis 5 , molecular means such as chloroplast genomes can be used to explore intragroup interspecific relationships, identify species, and inform the implementation of species conservation strategies.…”

Section: Introductionmentioning

confidence: 99%

Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis

Chen,

Li,

Zhang

2023

Sci Rep

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The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.

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Section: Introductionmentioning

confidence: 99%

Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis

Chen,

Li,

Zhang

2023

Sci Rep

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“…CPGs can signi cantly enhance resolution at lower taxonomic levels and facilitate recovery of monophyletic lineages 16 , and are therefore considered ideal material in phylogenetics and population genetics 13 ; [17][18][19] . In recent years, DNA sequencing technology has shifted to high-throughput, and CPGs of a large number of plants have been sequenced and published 20 , which was in turn used to identi cation and classi cation of plant [21][22][23] , lineage geography 24 and phylogenetic relationship researches [25][26][27] . Due to the existence of overlap and mosaicism in important taxonomic morphological traits among the species of Quercus section Cyclobalanopsis 5 , molecular means such as chloroplast genomes can be used to explore intragroup interspeci c relationships, identify species, and inform the implementation of species conservation strategies.…”

Section: Introductionmentioning

confidence: 99%

Comparison of Chloroplast Genomes and Phylogenetic Analysis of Four Species in Quercus section Cyclobalanopsis

Xiao-li

Xue-mei

2023

Preprint

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The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana ), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160715 bp ~ 160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; the Quercus genus were distincted to two clades, including five sections. All CTB species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six CTB species gathered together in pairs to form one branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxology and phylogenetics.

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Comparative Plastomics of Plantains (Plantago, Plantaginaceae) as a Tool for the Development of Species-Specific DNA Barcodes

Mehmood,

Li,

Bertolli

et al. 2024

Plants

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Plantago (plantains, Plantaginaceae) is a cosmopolitan genus including over 250 species used as functional foods, forage, and traditional medicine. Among them, Plantago lanceolata is commonly used as an ingredient of herbal products, but the close similarity to other Plantago species can cause misidentifications with potentially serious consequences for product safety/quality. To test the possibility of developing species-specific barcoding markers, we de novo assembled plastome sequences of individuals of Plantago argentea, Plantago atrata, P. lanceolata, and Plantago maritima. These genomes were characterized in comparison with both previously sequenced conspecific accessions and other publicly available plastomes, thus providing an assessment of both intraspecific and interspecific genetic variation in Plantago plastomes. Additionally, molecular evolutionary analyses indicated that eleven protein-coding genes involved in different plastid functions in Plantago plastomes underwent positive selection, suggesting they might have contributed to enhancing species’ adaptation during the evolutionary history of Plantago. While the most variable mutational hotspots in Plantago plastomes were not suitable for the development of species-specific molecular markers, species-specific polymorphisms could discriminate P. lanceolata from its closest relatives. Taken together, these results highlight the potential of plastome sequencing for the development of molecular markers to improve the identification of species with relevance in herbal products.

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Identification and phylogenetic analysis of the genus Syringa based on chloroplast genomic DNA barcoding

Cited by 3 publications

References 30 publications

Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis

Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis

Comparison of Chloroplast Genomes and Phylogenetic Analysis of Four Species in Quercus section Cyclobalanopsis

Comparative Plastomics of Plantains (Plantago, Plantaginaceae) as a Tool for the Development of Species-Specific DNA Barcodes

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