Plastid Phylogenetics, Biogeography and Character Evolution of the Chinese Endemic Genus Sinojackia Hu.

Published: May 13, 2024

Sinojackia Hu. comprises five to eight Chinese endemic species with high ornamental and medicinal value. However, the generic limits, interspecific relationships evolutionary history of genus remain unresolved. In this study, we newly sequenced assembled three plastomes S. oblongicarpa compared them those other congeneric explore taxonomic delimitation genus. Plastomes structure were extremely conserved in terms number genes, sequence length GC content. Codon usage patterns revealed that natural selection may be main factor shaping codon bias. Our phylogenetic tree shows is monophyletic can divided into two clades. as a distinct supported for it distantly related sarcocarpa. The analysis morphological features indicates woody mesocarp an ancestral feature, while undeveloped, spongy fleshy are later derived. originated Central-Southeast China during early Miocene. period, experienced elevated diversification migrated from Hunan Province Sichuan development Asian monsoon East flora. at intraspecies levels mainly occurred Quaternary. Glacial-interglacial interactions climate provide favorable expansion conditions on small-scale.

Language: Английский

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Comparative and phylogenetic analysis of the chloroplast genomes of four commonly used medicinal cultivars of Chrysanthemums morifolium

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Oct. 22, 2024

Language: Английский

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Complete Chloroplast Genome of Hypericum perforatum and Dynamic Evolution in Hypericum (Hypericaceae)

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(22), P. 16130 - 16130

Published: Nov. 9, 2023

Hypericum perforatum (St. John's Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced whole chloroplast genome of H. and compared variation among five species to discover dynamic changes elucidate mechanisms that lead rearrangements in genomes. The 139,725 bp, exhibiting circular quadripartite structure with two copies inverted repeats (IRs) separating large single-copy region small region. encodes 106 unique genes, including 73 protein-coding 29 tRNAs, 4 rRNAs. genomes exhibit rearrangement significant variations species. size was remarkably associated expansion or contraction IR regions gene losses. Three genes-trnK-UUU, infA, rps16-were lost, three genes-rps7, rpl23, rpl32-were pseudogenized Hypericum. All lost introns clpP, intron rps12, second ycf3. contain many long repeat sequences, suggesting role facilitating rearrangements. Most according molecular evolution assessments, are under purifying selection.

Language: Английский

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The first complete mitochondrial genome of Carex (C. breviculmis): a significantly expanded genome with highly structural variations

Planta, Journal Year: 2023, Volume and Issue: 258(2)

Published: July 14, 2023

Language: Английский

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Comparative insights into genomic variability and adaptation in the chloroplast genomes of Salvia japonica and Salvia rosmarinus

Turkish Journal of Food and Agriculture Sciences, Journal Year: 2025, Volume and Issue: 7(1), P. 1 - 13

Published: Jan. 13, 2025

Chloroplast genomes provide important information about phylogenetics, plant evolution, and adaptive processes. This study examines the chloroplast of Salvia japonica rosmarinus. We conducted structural functional annotations to identify significant variations in gene content organization. found that S. rosmarinus has fewer photosystem II (psb) genes a greater abundance hypothetical (ycf). may help maintain genomic stability while facilitating species evolution. There are big differences insertion-deletion events (indels) single nucleotide polymorphisms (SNPs) families, like NADH dehydrogenase ribosomal proteins. determined this organizational difference by applying Principal Component Analysis (PCA) two species, which belong different distinct categories. Sequence alignment revealed gaps inconsistencies related RNA polymerase photosynthesis. The fact have lot adapted live environments suggests they had evolutionary paths. These results give us how evolved way think change ecological settings. provides basis for understanding evolution genome genus Salvia. been clarifying role photosynthetic controlling environmental responses. Future must use transcriptome data enhance our impact genetic variants on functionality.

Language: Английский

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Using RAD-seq to identify and differentiate the medicinal herb Scrophularia ningpoensis and its adulterants

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 4, 2025

Language: Английский

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Report on the complete organelle genomes of Orobanche Filicicola Nakai ex Hyun, Y. S. Lim & H. C. Shin (Orobanchaceae): insights from comparison with Orobanchaceae plant genomes

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 17, 2025

Abstract Background Orobanche is a parasitic plant distributed in the temperate zone of Northern Hemisphere, with approximately 200 species found worldwide. In Republic Korea, two , namely O. coerulescens Stephan ex Willd. and filicicola Nakai Hyun, Y. S. Lim & H. C. Shin, are present, being endemic. Genome analysis this has not yet been performed, characterizing its complete organelle genome will provide valuable insights into phylogeny evolution plants. Results The chloroplast mitochondrial genomes were analyzed, revealing distinct characteristics. 91,529 bp long GC content 33.6%, containing 33 protein-coding, 30 tRNA, 4 rRNA genes. contrast, 1,058,991 45.5%, featuring 31 16 3 over three times more simple sequence repeats longer than genome. Analysis synonymous codon usage protein-coding genes from nine Orobanchaceae revealed significant differences between chloroplasts mitochondria, codons ending A or T exhibiting higher coding rates. Ka/Ks ratio calculations indicated that psbI atpB had smallest largest ratios chloroplasts, respectively, while ccmFC was identified as only gene under positive selection mitochondria genomes. Sequence alignment homologous fragments genomes, totaling 7,247 bp. Comparison ’s related showed loss conserved inverted repeat sequences. Numerous collinear blocks species, but some regions lacked homology. Phylogenetic identical topologies for forming strong monophyletic group. Conclusions Characterizing enabled comprehensive genome, providing important baseline data structure evolution.

Language: Английский

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Sequencing, de novo assembly of Ludwigia plastomes, and comparative analysiswithin the Onagraceae family

Peer Community Journal, Journal Year: 2025, Volume and Issue: 5

Published: April 23, 2025

The Onagraceae family, which belongs to the order Myrtales, consists of approximately 657 species and 17 genera. This family includes genus Ludwigia L., is comprised 82 species. In this study, we focused on two aquatic invasive grandiflora subsp. hexapetala ( Lgh ) peploides montevidensis Lpm largely distributed in environments North America Europe. Both have been found degrade major watersheds leading ecological economical damages. Genomic resources for are limited, with only octovalvis (Lo) plastid genome available L. at time our study. scarcity constrains phylogenetic, population genetics, genomic studies. To brush up ressources, new complete genomes subps . were generated using a combination MiSeq (Illumina) GridION (Oxford Nanopore) sequencing technologies. These plastomes then compared published Lo genome, was re-annotated by authors. We initially sequenced assembled chloroplast (cp) hybrid strategy combining short long reads sequences. observed existence haplotypes potential haplotypes. , Lpm, similar terms size (around 159 Kb), gene number, structure, inverted repeat (IR) boundaries, comparable other Myrtales order. A total 45 65 SSRs simple sequence repeats), detected, depending species, majority consisting solely T, common among angiosperms. Four genes matK accD ycf2 ccsA) under positive selection pressure, commonly associated plant development, especially plants such as Lgh, Lpm. Our approach revealed presence plastome will help advance phylogenetic evolutionary studies, not specifically but also enhance robustness findings, larger dataset would be beneficial.

Language: Английский

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Comparative and phylogenetic analysis of complete chloroplast genomes of Phrynium s. s. and Stachyphrynium (Marantaceae) in China, including a new species

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: May 1, 2025

Plants of the genera Phrynium and Stachyphrynium traditionally used as ethnomedicine or for wrapping sticky rice dumpling in tropical south subtropical Asia, have a long history ethnobotanical use. China represents northernmost distribution Marantaceae Asia. Due to notably similar leaf morphology between these genera, herbarium specimens are frequently misidentified, especially during vegetative stages. Their morphological uniformity unclear interspecific genetic relationships pose significant challenges taxonomic classification species identification. To date, systematic revisions phylogeny their indigenous remain lacking. In this study, we conducted comparative chloroplast genomes analyses seven two China. The exhibited conserved structure, gene content, order codon usage bias, but diverged size SC/IR boundaries. Four variable regions were identified potential molecular markers Phylogenetic using CDS nrDNA strongly support distinct monophyletic groups, with subdivided into clades. These findings advance our understanding provide critical insights identification, utilization, conservation medicinal plants. Finally, describe illustrate new pyramidale Y. Tong & Z. Lin.

Language: Английский

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Plastid Phylogenetics, Biogeography, and Character Evolution of the Chinese Endemic Genus Sinojackia Hu

Diversity, Journal Year: 2024, Volume and Issue: 16(5), P. 305 - 305

Published: May 18, 2024

Sinojackia Hu. comprises five to eight Chinese endemic species with high ornamental and medicinal value. However, the generic limits, interspecific relationships evolutionary history of genus remain unresolved. In this study, we newly sequenced three plastomes S. oblongicarpa compared them those other congeneric explore taxonomic delimitation genus. The plastome structure was extremely conserved in terms number genes, sequence length, GC content. codon usage patterns revealed that natural selection may be main factor shaping bias. Our phylogenetic tree shows is monophyletic can divided into two clades. as a distinct supported for it distantly related sarcocarpa. analysis morphological features indicates woody mesocarp an ancestral feature. originated central Southeast China during early Miocene. period, experienced elevated diversification migrated from Hunan Province Sichuan development Asian monsoon East flora. Glacial–interglacial interactions climate provide favorable expansion conditions on small scale.

Language: Английский

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