Chloroplast Genome Sequencing and Comparative Analysis of Six Medicinal Plants of Polygonatum

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 1, 2025

ABSTRACT The genus Polygonatum boasts abundant germplasm resources and comprises numerous species. Among these, medicinal plants of this genus, which have a long history, garnered attention scholars. This study sequenced analyzed the chloroplast genomes six species ( P. zanlanscianense , kingianum sibiricum cyrtonema filipes odoratum respectively) to explore their interspecific relationships. sequence length (154, 578–155, 807 bp) genome structure were conserved among species, with typical tetrad structure. 127–131 genes contained in genomes, 84–85 are protein‐coding genes, 37–38 transfer RNA 6–8 ribosomal genes. 64–76 simple repeats (SSRs) 36–62 repetitive sequences. Codon bias patterns tended use codons ending A/T. In 30 types RSCU > 1, 93.3% ended A/T Twenty‐one highly variable plastid regions identified plants. Furthermore, phylogenetic analysis encompassing these 53 other revealed that clustered together on one clade, whereas formed separate clades. Notably, emerged as standalone our tree reinforces classification forming monophyly. provides novel basis for intragenus taxonomy DNA barcoding molecular identification within

Language: Английский

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Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(4), P. 2193 - 2193

Published: Feb. 12, 2024

The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains China, have high medicinal ornamental value. diversity of plant morphology this genus poses significant challenges for identification, given their propensity highland dwelling, which makes it a question worth exploring how they cope with harsh surroundings. In study, we recently generated chloroplast (cp) genomes two species, paniculata (M. paniculata) M. pinnatifolia, compared them those ten cp to comprehend genomic features, phylogenetic relationships, what part might play plateau adaptation. These shared great deal similarities terms genome size, structure, gene content, GC codon usage patterns. were between 151,864 bp 154,997 length, contain 133 predictive genes. Through sequence divergence analysis, identified three highly variable regions (trnD-psbD, ccsA-ndhD, ycf1 genes), could be used as potential markers or DNA barcodes analysis. Between 22 38 SSRs some long repeat sequences from 12 species. Our analysis confirmed that clustered into monophyletic clade Papaveraceae, corroborated intrageneric relationships. results indicated pinnatifolia sister tree. addition, atpA ycf2 genes positively selected high-altitude functions these involved adaptation extreme environment cold low CO2 concentration conditions at plateau.

Language: Английский

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Comparative chloroplast genomes of Incarvillea species (Bignoniaceae) unveiled genomic diversity and shed light on phylogenetic relationships

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

Published: March 29, 2025

Juss. is a small herbaceous genus within the Bignoniaceae family. It comprises 16 species, which are subdivided into five subgenera. The species distributed mainly in Himalaya-Hengduan Mountains, although there exceptions, including I. sinensis, algae, semiretschenskia, and potaninii. Phylogenetic analyses based on trnL-F nr ITS sequences provided support for monophyly of its However, interspecific relationships among subgenera remain unresolved, further investigation necessary to elucidate these relationships. In this study, we sequenced assembled 34 chloroplast genomes from 12 Incarvillea representing all subgenera, explored phylogeny cp. genome data. results demonstrated that newly exhibited lengths between 159,132 169,244 bp, encoded total 129-141 genes. These included 84-95 protein-coding genes, 37 or 38 tRNA eight rRNA A comparative analysis revealed structural rearrangements expansions/contractions IR regions species. mutation hotspot were identified Incarvillea, encompassing six genes (atpI, psaI, rps18, trnQ-UUG, infA ycf1) intergenic spacer (psbT-psbf1, rps11-rpl36, infA-rps8, trnN-GUU-ycf1, ndhE-ndhG ndhI-ndhA). Pi values highly variable exceeded 0.06. phylogenetic corroborated elucidated subgenere, namely ((Niedzwedzkia, Incarvillea), ((Amphicome, Olgaea),Pteroscleris)). comprehensive comparison genomic diversity terms size, gene content order genomes. Based data, robust tree was generated through analysis, with well resolved. study enhance understanding evolutionary history genus, will facilitate studies resource protection genus.

Language: Английский

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Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(4), P. 2278 - 2278

Published: Feb. 14, 2024

The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports such events have emerged in some lineages. In this study, we conducted a comprehensive comparison the complete plastomes from twenty-two species, covering seventeen genera three subfamilies (Fumarioideae, Hypecooideae, and Papaveroideae) Papaveraceae. Our results revealed high level variability genome size Papaveraceae, ranging 151,864 bp to 219,144 length, which might be triggered by expansion IR region large number repeat sequences. Moreover, detected numerous large-scale rearrangements, primarily occurring Fumarioideae Hypecooideae. Frequent gene loss or pseudogenization were also observed for ndhs, accD, clpP, infA, rpl2, rpl20, rpl32, rps16, several tRNA genes, particularly associated structural variation their plastomes. Furthermore, found that exhibited higher GC content more sequences than those Papaveroideae. showed Papaveroideae generally displayed relatively conserved plastome, exception Eomecon chionantha, while Hypecooideae harbored reconfigurable plastomes, showing size, content, order. This study provides insights into plastome evolution Papaveraceae may contribute development effective molecular markers.

Language: Английский

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Comparative Analysis of Complete Chloroplast Genomes and Phylogenetic Relationships of 21 Sect. Camellia (Camellia L.) Plants

Genes, Journal Year: 2025, Volume and Issue: 16(1), P. 49 - 49

Published: Jan. 3, 2025

Background: Section Camellia is the most diverse group in genus L., and this of plants has a long history cultivation China as popular ornamental flowers oil plants. Sect. present morphological variations complexity among species, resulting uncertainty classification which resulted degree inconvenience confusion use plant resources research. Methods: Here, We sequenced assembled chloroplast genomes 6 sect. performed comparative genome analysis phylogenetic studies combined with 15 existing Results: The 21 species were quadripartite length 156,587–157,068 bp base pairs (bp), highly conserved moderately differentiated arrangement. similar to those angiosperms, high consistency gene number, content structure. After annotation process, we identified total 132 genes, specifically 87 sequences coding for proteins (CDS), 37 transfer RNA (tRNA) 8 ribosomal (rRNA) genes. ycf1 was only small single-copy/inverted repeat (SSC/IRa) region. Sequence variation greater large single-copy (LSC) region than IR region, majority protein-coding genes presented codon preferences. exhibit relatively SC (single copy region)/IR (inverted region) boundaries. detected 2975 single sequence repeats (SSRs) well 833 dispersed nuclear elements (INEs). Among these SSRs, A/T AT/AT dominated, while INEs, forward palindromic predominated. Codon usage frequencies largely similar, 30 high-frequency codons detected. Comparative revealed five hotspot regions (rps16, psaJ, rpl33, rps8, rpl16) two intervals (atpH-atpI petD-rpoA) cp genome, can be used potential molecular markers. In addition, tree constructed from that oleifera aggregated into branch, further subdivided evolutionarily independent sub-branches. Conclusions: It confirmed C. Abel are closely related genus. These findings will enhance our knowledge plants, deepen understanding their genetic characteristics pathways, provide strong support scientific development rational utilization Camellia.

Language: Английский

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Comparative Analysis of Complete Chloroplast Genomes and Phylogenetic Relationships in Medicinally Important Pantropical Genus Bauhinia s.s. (Leguminosae) from Southern Africa and Eastern Asia

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(1), P. 397 - 397

Published: Jan. 5, 2025

Bauhinia s.s. belongs to the Cercidoideae subfamily, located at base of Leguminosae family. It displays a variety growth habits and morphologies, is widely utilized as both ornamental medicinal plants globally. The objective this research uncover chloroplast genomes species from Eastern Asia Southern Africa, thereby advancing our understanding diversity within genus. This study sequenced purpurea, brachycarpa var. microphylla, variegata candida, galpinii, monandra using Illumina platform conducted construction phylogenetic trees well estimation divergence times. Compared Asian species, IR regions African underwent contraction approximately 100–400 bp. analysis indicated that clustered into two distinct clades, with high support. occurred in late Paleocene, rps18 cemA genes were under positive selection. Six hypervariable screened for evolutionary studies super-barcode data used delimitation. results revealed certain differences between their species.

Language: Английский

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Comprehensive Chloroplast Genome Analysis of Four Callitriche (Plantaginaceae) Species for Phylogenetic and Conservation Insights

Horticulturae, Journal Year: 2025, Volume and Issue: 11(1), P. 66 - 66

Published: Jan. 10, 2025

Callitriche species are capable of purifying water, promoting wetland restoration, and providing natural shelters. Moreover, they can be utilized as horticultural plants for landscape greening. However, due to the threats climate change environmental degradation, some within this genus have been listed endangered. This study utilizes chloroplast genome analysis provide molecular evidence classification conservation these species. We conducted a comprehensive sequencing characterization complete genomes four Callitriche: C. cophocarpa, hermaphroditica, palustris, stagnalis. The sizes ranged from 150,042 150,879 bp, with GC content 37.5–37.8% between 131 132 genes. Comparative genomic revealed several highly variable intergenic regions (e.g., rps16–psbK, trnS-GCU–trnG-UCC, ccsA–ndhD, ndhF–rpl32, trnN-UGG) ycf1 gene, highlighting their potential phylogenetic markers. Phylogenetic analyses confirmed monophyly supported hermaphroditica an early-diverging lineage genus. Notably, phylogeny also resolved Hemiphragma Veronicastrum sister taxa, contributing insights into evolutionary relationships Plantaginaceae. provides data Callitriche, offering valuable markers research, taxonomic clarification, ecologically significant

Language: Английский

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Complete chloroplast genome of eight Phaius (Orchidaceae) species from China: comparative analysis and phylogenetic relationship

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

Published: Jan. 10, 2025

Phaius Lour. (Collabieae, Orchidaceae) is a small genus consisting of about 45 species, with highly ornamental and medicinal values. However, the phylogenetic relationship among Calanthe s. l. has been debated based on morphological molecular data. The complete chloroplast (cp) genome widely used as useful marker for resolving problems, while few genomic data was available. Therefore, cp genomes eight species were sequenced characterized in detail to provide better understanding its phylogenetics investigated exhibited conserved quadripartite structures varied lengths ranging between 157,997 bp 158,735 bp. overall GC content these ranged 36.82 36.97%. Gene annotation revealed 136 genes all genomes, which 21 duplicated inverted regions 15 introns. Comparative analysis stable sequence identity greater variation single-copy regions, alongside notable differences at LSC/IRb IRb/SSC junctions, well number SSRs. CDS from 49 Collabieae indicated that together other two P. philippinensis hainanensis, clustered into monophyletic clade divided subclades strong supports. Additionally, it also supported should be five genera supports, including s., Cephalantheropsis, Styloglossum, Phaius, Preptanthe. It first report six (P. columnaris, mishmensis, takeoi, tonkinensis, wallichii wenshanensis) comparatively analyzed flavus tancarvilleae. provided comprehensive investigation various features implications, structure, codon usage, repeat sequences, IR boundaries, DNA polymorphisms, reconstruction. suggested treated independent genera. concept new Paraphaius not confirmed by here. intergeneric alliance group could understood more

Language: Английский

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Comparative Chloroplast Genomes and Phylogenetic Relationships of True Mangrove Species Brownlowia tersa and Brownlowia argentata (Malvaceae)

Current Issues in Molecular Biology, Journal Year: 2025, Volume and Issue: 47(2), P. 74 - 74

Published: Jan. 23, 2025

Brownlowia tersa and argentata are two true mangroves in the genus Malvaceae, they a near-threatened data-deficient species, respectively. However, genomic resources of have not been reported for studying their phylogeny evolution. Here, we report chloroplast genomes B. based on stLFR data that were 159,478 159,510 base pairs length, Both contain 110 unique genes one infA pseudogene. Sixty-eight RNA-editing sites detected 26 argentata. A comparative analysis with related species showed similar genome sizes, structures, gene contents as well high sequence divergence non-coding regions. Abundant SSRs dispersed repeats identified. Five hotspots, psbI-trnS, trnR-atpA, petD-rpoA, rpl16-rps3, trnN-ndhF, among four Brownlowioideae. One hotspot, rps14-psaB, was observed species. Additionally, phylogenetic supported has close relationship Pentace triptera. Moreover, rpoC2 candidate adaptive evolution compared to P. Thus, these present valuable further evolutionary studies plant Malvaceae.

Language: Английский

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Complete chloroplast genomes of 13 species of the Impatiens genus for genomic features and phylogenetic relationships studies

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Feb. 4, 2025

Impatiens spp. are well-known ornamental and medicinal plants that widely distributed in the highlands mountains of southwestern China. This area is one hotspots for distribution species, with typical karst landforms abundant wild resources. Many these species endemic to a narrow area, but their classification relationships relatively unclear because insufficient field investigations, diverse morphological characteristics lack molecular information. In this study, chloroplast genome analysis 13 (including 2 synonyms) habitats was conducted study phylogenetic relationships. The results revealed genomes all had double-stranded tetrad structures ranging length from 151,284 bp 152,421 bp, including total 113 genes, 80 protein-coding 29 transfer RNAs, 4 ribosomal RNAs. SSRs mainly consist A/T repeats AT/AT repeats, while INEs positive palindromic repeats. frequency codon usage essentially same, 31 high-frequency codons detected, vast majority ending A/U. Five mutation were detected: rps16-trnQ-UUG, ndhF, ccsA-ndhD, ycf1, trnN-GUU, among which ycf1 highest Pi value greatest potential as DNA barcode marker. Our tree shows belong Section Impatiens. And supported I. reptans rhombifolia should synonyms (BS = 100/PP 1.00). comprehensively analyzed cp different taxa, sheds light on taxonomic intricacies provide valuable information into its taxonomy.

Language: Английский

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