Decoding the Chloroplast Genome of Bitterwood (Picrasma quassioides): Structure, Variability, and Evolutionary Relationships

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

The chloroplast genome of Picrasma quassioides, a medicinally significant plant in traditional Asian medicine, was sequenced and analyzed to understand its genetic architecture evolutionary relationships within Simaroubaceae. High-throughput sequencing revealed 160,013-bp circular with typical quadripartite structure, encoding 132 genes including 87 protein-coding genes, 37 tRNA 8 rRNA genes. Comparative analysis other Simaroubaceae species identified distinct patterns nucleotide diversity between single-copy repeat regions, while examination IR boundaries dynamic processes. Analysis 101 SSR loci 48 sequences provided insights into organization potential molecular markers for identification. Selective pressure across 78 demonstrated predominant purifying selection (average K a/K s ratio 0.23), evidence positive specific Phylogenetic reconstruction using 77 confirmed Simaroubaceae's monophyly close relationship Rutaceae. These findings advance our understanding evolution providing tools authentication breeding this valuable medicinal species. comprehensive genomic characterization establishes foundation investigating the basis therapeutic properties P. quassioides facilitating conservation.

Language: Английский

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Comparative chloroplast genomic analysis of Pithecellobium dulce (Roxb.) Benth 1844 and related species within Caesalpinioideae

Genetica, Journal Year: 2025, Volume and Issue: 153(1)

Published: May 6, 2025

Language: Английский

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The Complete Chloroplast Genome Sequence of the Medicinal Moss Rhodobryum giganteum (Bryaceae, Bryophyta): Comparative Genomics and Phylogenetic Analyses

Genes, Journal Year: 2024, Volume and Issue: 15(7), P. 900 - 900

Published: July 10, 2024

(Bryaceae, Bryophyta), a rare medicinal bryophyte, is valued for its cardiovascular therapeutic properties in traditional Chinese medicine. This study presents the first complete chloroplast genome sequence of

Language: Английский

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Exploring the Evolutionary History and Phylogenetic Relationships of Giant Reed (Arundo donax) through Comprehensive Analysis of Its Chloroplast Genome

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(14), P. 7936 - 7936

Published: July 20, 2024

Giant reed (

Language: Английский

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Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis

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

Published: Nov. 5, 2024

Habenaria, a genus in the family Orchidaceae, are nearly cosmopolitan orchids, and most species have significant medicinal ornamental values. Despite morphological molecular data that been studied recent years, phylogenetic relationship is still unclear. We sequenced, assembled, annotated chloroplast (cp) genomes of two (Habenaria aitchisonii Rchb.f. Habenaria tibetica Schltr.ex Limpricht) grown on Qinghai-Tibetan Plateau (QTP), compared them with seven previously published cp which may aid genomic profiling these species. The ranged from 155,259–155,269 bp length both included 132 genes, encoding 86 proteins, 38 tRNAs 8 rRNAs. In genomes, tandem repeats (797), SSRs (2195) diverse loci (3214) were identified. Comparative analyses codon usage, amino frequency, microsatellite, oligo transition transversion substitutions revealed similarities between Moreover, we identified 16 highly polymorphic regions nucleotide diversity above 0.02, be suitable for robust authentic barcoding inferring phylogeny Among regions, positive selection was significantly exerted several such as cemA, petA, ycf1. This finding suggest an important adaptation strategy QTP. H. more closely related to each other than species, clustered three groups. addition, estimated divergence time suggested separated others approximately 0.39 Mya Neogene period. Our findings also can divided into different sections. results this study enriched genomics resources SSR marker conservation management endangered

Language: Английский

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Plastome Evolution, Phylogenomics, and DNA Barcoding Investigation of Gastrochilus (Aeridinae, Orchidaceae), with a Focus on the Systematic Position of Haraella retrocalla

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(15), P. 8500 - 8500

Published: Aug. 4, 2024

Gastrochilus is an orchid genus containing about 70 species in tropical and subtropical Asia with high morphological diversity. The phylogenetic relationships among this have not been fully resolved, the plastome evolution has investigated either. In study, five plastomes of were newly reported, sixteen used to conduct comparative analyses. Our results showed that ranged from 146,183 148,666 bp, a GC content 36.7-36.9%. There 120 genes annotated, consisting 74 protein-coding genes, 38 tRNA 8 rRNA genes. No contraction expansion IR borders, gene rearrangements, or inversions detected. Additionally, repeat sequences codon usage bias highly conserved. Twenty hypervariable regions selected as potential DNA barcodes. within well resolved based on whole plastome, especially main clades. Furthermore, both molecular data strongly supported Haraella retrocalla member (G. retrocallus).

Language: Английский

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