Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: June 24, 2022

Members of Polygonatum are perennial herbs that have been widely used in traditional Chinese medicine to invigorate Qi, moisten the lung, and benefit kidney spleen among patients. However, phylogenetic relationships intrageneric taxonomy within long controversial because complexity their morphological variations lack high-resolution molecular markers. The chloroplast (cp) genome is an optimal model for deciphering related families. In present study, complete cp 26 species Trib. Polygonateae were de novo assembled characterized; all exhibited a conserved quadripartite structure, is, two inverted repeats (IR) containing most ribosomal RNA genes, unique regions, large single sequence (LSC) small (SSC). A total 8 highly variable regions (rps16-trnQ-UUG, trnS-GCU-trnG-UCC, rpl32-trnL-UAG, matK-rps16, petA-psbJ, trnT-UGU-trnL-UAA, accD-psaI, trnC-GCA-petN) might be useful as potential markers identifying identified. clock analysis results showed divergence time occur at ∼14.71 Ma, verticillate leaf ancestral state this genus. Moreover, based on 88 genomes strongly supported monophyly Polygonatum. also suggested Heteropolygonatum may sister group Polygonatum, but Disporopsis, Maianthemum, Disporum diverged earlier. This study provides valuable information further identification, evolution, research

Language: Английский

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Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 11(12), P. 7810 - 7826

Published: May 6, 2021

Abstract The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues the phylogeny of due low polymorphism molecular markers. Therefore, suitable polymorphic regions need be identified. Here, we de novo assembled plastomes three species B . oxyodonta , B. tenella balsamifera compared them with 26 other Asteroideae after correction annotations. These quadripartite similar gene content, genome organization, inverted repeat contraction expansion comprising 113 genes, 80 protein‐coding, 29 transfer RNA, 4 ribosomal RNA genes. comparative analysis codon usage, amino acid frequency, microsatellite repeats, oligonucleotide transition transversion substitutions has revealed high resemblance among newly We identified 10 highly nucleotide diversity above 0.02, rps 16‐ trn Q, ycf 1, ndh F‐ rpl 32, pet N‐ psb M, 32‐ L, they may for development robust, authentic, cost‐effective markers barcoding inference Among these regions, five also co‐occurred repeats support use as a proxy identification loci. phylogenetic close relationship between Pluchea within tribe Inuleae. At level, our supports sister Astereae Anthemideae rooted Gnaphalieae, Calenduleae, Senecioneae. results are contradictory recent which reported “Senecioneae Anthemideae” “Astereae Gnaphalieae” or Gnaphalieae Anthemideae, then Senecioneae using nuclear sequences. conflicting signals observed at tribal level plastidt data require further investigation.

Language: Английский

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Complete chloroplast genome sequences of three aroideae species (Araceae): lights into selective pressure, marker development and phylogenetic relationships

BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)

Published: March 19, 2022

Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species subfamily Aroideae phylogenetically perplexing due to shared interspecific morphological traits variation.This study, for first time ever, assembled analyzed complete chloroplast genomes of C. X. with genome sizes 165,906 bp, 153,149 bp 165,169 length, respectively. The were composed conserved quadripartite circular structures a total 131 annotated genes, including 8 rRNA, 37 tRNA 86 protein-coding genes. A comparison within showed seven genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 matK) linked environmental adaptation. Phylogenetic analysis confirmed close relationship gigantea esculenta S. colocasiifolia, sagittifolium. Furthermore, DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI trnS-trnG, psaC-ndhE trnS-trnG) harbored highly variable regions distinguish subfamily.These results would be beneficial identification, phylogenetic relationship, genetic diversity, potential germplasm resources Aroideae.

Language: Английский

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Comparative and Phylogenetic Analysis Based on the Chloroplast Genome of Coleanthus subtilis (Tratt.) Seidel, a Protected Rare Species of Monotypic Genus

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Feb. 24, 2022

Coleanthus subtilis (Tratt.) Seidel (Poaceae) is an ephemeral grass from the monotypic genus Seidl, which grows on wet muddy areas such as fishponds or reservoirs. As a rare species with strict habitat requirements, it protected at international and national levels. In this study, we sequenced its whole chloroplast genome for first time using next-generation sequencing (NGS) technology Illumina platform, performed comparative phylogenetic analysis related in Poaceae. The complete of C. 135,915 bp length, quadripartite structure having two 21,529 inverted repeat regions (IRs) dividing entire circular into large single copy region (LSC) 80,100 small (SSC) 12,757 bp. overall GC content 38.3%, while contents LSC, SSC, IR are 36.3%, 32.4%, 43.9%, respectively. A total 129 genes were annotated genome, including 83 protein-coding genes, 38 tRNA 8 rRNA genes. accD gene introns both clpP rpoC1 missing. addition, ycf1, ycf2, ycf15, ycf68 pseudogenes. Although was found to be conserved stable general, 26 SSRs 13 highly variable loci detected, these have potential developed important molecular markers subfamily Pooideae. Phylogenetic Poaceae indicated that Phippsia sister groups, provided new insights relationship between Coleanthus, Zingeria, Colpodium. This study presents initial report subtilis, provides essential data reference further research origin.

Language: Английский

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The multi-chromosomal structure of mitogenomes provided new insights into the accurate authentication of medicinal Dendrobium species

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Feb. 15, 2025

The global prevalence of herbal-based health care rapidly promoted requirements for medicinal plant resources. Accurate classification and identification are crucial to assuring the safety these herbal sources. Here, we took Dendrobium (Orchidaceae), a famous horticultural taxon, as study focus establish an effective authentication approach plants based on new mtDNA barcodes. We first de novo assembled three complete mitogenomes using Illumina Nanopore data. These were 635,454 bp-831,745 bp long with multichromosomal structures. Moreover, compared other four published mitogenomes. results revealed great variations structure repeat contents among mitogenomes, while gene genomic sequences relatively conserved. analysis mutational hotspots showed eight mitochondrial DNA regions high sequence variability (> 5%) at interspecific level, which could provide abundant informatic loci phylogeny, genetic diversity, analyses. also newly obtained 45 individuals from 15 species analysis. successfully identified by whole mitogenome isoform combination (Mt17 + Mt19) respectively. Our findings that isoforms (chromosomes) be used super-barcodes authentication. multi-chromosomal provided insights into accurate medical plants.

Language: Английский

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Comparative analysis of chloroplast genomes in three Araceae species: genomic difference, genetic distance and species morphology association

Frontiers in Genetics, Journal Year: 2025, Volume and Issue: 16

Published: April 8, 2025

Many species in the Araceae have extremely high medicinal value, while chloroplast genome is relatively conserved, and encoded expressed bioactive substances are also abundant. Therefore, genomes can serve as one of basis for evolution important individual material accumulation. To study relationship between morphology target species, this selected three sequencing assembly, downloaded complete sequences another 11 species. Grouping based on genetic distance, we analyze association structure morphology. The results showed that there were significant differences size among but Relative Synonymous Codon Usage (RSCU) exhibited similarity; Based phylogenetic tree, these 14 be divided into branches, with genes such rrn4, rrn5, rrn23, trnN within each branch; Morphologically, length male inflorescence BranchⅢ significantly greater than BranchⅡ; There a strong positive correlation plant stem parameters (Length LSC, Length SSC genome) genome. This conducted research from perspective On hand, distance determined, other explored morphology, providing theoretical relationships

Language: Английский

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Lemnaceae and Orontiaceae Are Phylogenetically and Morphologically Distinct from Araceae

Plants, Journal Year: 2021, Volume and Issue: 10(12), P. 2639 - 2639

Published: Nov. 30, 2021

Duckweeds comprise a distinctive clade of pleustophytic monocots that traditionally has been classified as the family Lemnaceae. However, molecular evidence called into question their phylogenetic independence, with some authors asserting instead duckweeds should be reclassified subfamily Lemnoideae an expanded Araceae. Although close relationship traditional Araceae supported by multiple studies, taxonomic disposition must evaluated more critically to promote nomenclatural stability and utility. Subsuming morphologically incongruent lineage effectively eliminates category Lemnaceae widely used for many years. Instead, we suggest Orontioideae restored status Orontiaceae, which thereby would enable recognition three phylogenetically distinct lineages: Araceae, Lemnaceae, Orontiaceae.

Language: Английский

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Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: July 8, 2022

Tilia is a complex genus in the family Malvaceae that has high ecological and economical values. Owing to lack of sufficient distinguishable morphological molecular characteristics, interspecific relationships this are not clear. Chloroplast (cp) genomes small, meanwhile most angiosperms usually undergo matrilineal inheritance. Consequently, they can be used systematics phylogenetic analyses. Here, we sequenced assembled cp from T. endochrysea, tomentosa, miqueliana, americana cordata, compared them with those seven previously reported species. Similar gene contents, orders GC contents existed among 12 genomes, which ranged 162,564 162,855 bp encoded 113 unique genes. Abundant simple sequence repeats (119-127) dispersed (97-135) were detected genomes. In total, 11 hypervariable regions identified could suitable for species identification studies. A analysis based on 5 genes (matK + ndhF rpoB rpoC2+ycf1) revealed all eight subfamilies monophyletic groups. Additionally, was divided into three groups basis 521 variation loci. The current study provides valuable insights genomic evolution Tilia.

Language: Английский

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Comparative and phylogenetic analyses based on the complete chloroplast genome of Cornus subg. Syncarpea (Cornaceae) species

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: March 13, 2024

This study presents a comprehensive analysis of the chloroplast (cp) genomes Cornus species, including comparative and phylogenetic evaluations, as well examinations their genomic structure composition. The cp exhibit typical circular quadripartite demonstrate highly similar gene order structure. complete genome size 10 taxa in this is 156,965 bp to 157,383 bp, where length large single-copy (LSC) region 86,296 86,691 small (SSC) 18,386 18,454 inverted repeat (IR) 23,143 26,112 bp. A total 131 genes were found, 86 protein-coding (PCGs), eight rRNA genes, 37 tRNA genes. mean GC content 38.145%, LSC 36.396%, SSC 32.372%, IR 43.076%. Despite relatively conserved nature within species , 25–31 simple sequence repeats (SSRs) identified our study. SSRs found be distributed LSC, SSC, regions hongkongensis subsp. C. elegans gigantea tonkinensis while SSR was not other six taxa. Thus, whole genomics valuable tool for identification, taxonomic clarification, evolutionary analysis. Furthermore, findings reveal that along with kousa elliptica form sister groups. Notably, ferruginea melanotricha did affinity . Our furnishes essential data further research on classification provides novel insights into relationship subg. Syncarpea

Language: Английский

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Comparative Chloroplast Genomics in Phyllanthaceae Species

Diversity, Journal Year: 2021, Volume and Issue: 13(9), P. 403 - 403

Published: Aug. 26, 2021

Family Phyllanthaceae belongs to the eudicot order Malpighiales, and its species are herbs, shrubs, trees that mostly distributed in tropical regions. Here, we elucidate molecular evolution of chloroplast genome identify polymorphic loci for phylogenetic inference. We de novo assembled genomes three species, i.e., Phyllanthus emblica, Flueggea virosa, Leptopus cordifolius, compared them with six other previously reported genomes. All comprised two inverted repeat regions (size range 23,921–27,128 bp) separated large single-copy (83,627–89,932 small (17,424–19,441 Chloroplast contained 111–112 unique genes, including 77–78 protein-coding, 30 tRNAs, 4 rRNAs. The deletion/pseudogenization rps16 genes was found only species. High variability seen number oligonucleotide repeats, while guanine-cytosine contents, codon usage, amino acid frequency, simple sequence synonymous non-synonymous substitutions, transition transversion substitutions were similar. higher coding sequences than non-coding sequences. Phylogenetic analysis revealed polyphyletic nature genus Phyllanthus. protein-coding rpl22, ycf1, matK, ndhF, rps15, also determined, which may be helpful reconstructing high-resolution tree family Phyllanthaceae. Overall, study provides insight into

Language: Английский

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