Complete Chloroplast Genomes and Comparative Analyses of Three Paraphalaenopsis (Aeridinae, Orchidaceae) Species

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(13), P. 11167 - 11167

Published: July 6, 2023

Paraphalaenopsis, a genus of perennial herbs from the family Orchidaceae, contains number ornamental species. However, there is no information on chloroplast genomes which limits our studies this genus. In study, we reported three species Paraphalaenopsis (P. labukensis, P. denevel, and laycockii ‘Semi-alba’) performed comprehensive comparative analysis. These showed typical quadripartile structure. Their lengths ranged 147,311 bp to 149,240 bp. Each genome contained 120 unique genes, including 74 protein-coding 38 tRNA 8 rRNA genes. Comparative analysis revealed major differences in sequence divergence genomes. addition, six hypervariable regions were identified (psbM-trnDGUC, psbB, ccsA, trnKUUU, trnSGCU-trnGUCC, rps16-trnQUUG) that can be used as DNA molecular markers. Phylogenetic relationships determined using 28 12 genera Aeridinae. Results suggested was clade Aeridinae sister Holcoglossum-Vanda clade, with 100% bootstrap support within The findings study provided foundation for future phylogenetic

Language: Английский

---

Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(19), P. 11617 - 11617

Published: Oct. 1, 2022

Uncaria, a perennial vine from the Rubiaceae family, is typical Chinese traditional medicine. Currently, uncertainty exists over Uncaria genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four species mentioned in Pharmacopoeia scandens (an easily confused counterfeit) were sequenced annotated. findings demonstrated that whole genome genus 153,780–155,138 bp full length, encoding total 128–131 genes, containing 83–86 protein-coding eight rRNAs 37 tRNAs. These regions, which include eleven highly variable loci 31–49 SSRs, can be used to create significant molecular markers for genus. phylogenetic tree was constructed according genes sequences five using methods. topology two trees showed no difference. U. rhynchophylla are clustered one group, while hirsuta macrophylla another group. sessilifructus together with above small clades. New insights on relationship revealed via research species. This study will provide theoretical basis identifying its counterfeits, as well provides initial report contributes elucidating evolution China.

Language: Английский

---

Comparative and phylogenetic analysis of the complete chloroplast genomes of six Polygonatum species (Asparagaceae)

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: May 4, 2023

Abstract Polygonatum Miller belongs to the tribe Polygonateae of Asparagaceae. The horizontal creeping fleshy roots several species in this genus serve as traditional Chinese medicine. Previous studies have mainly reported size and gene contents plastomes, with little information on comparative analysis plastid genomes genus. Additionally, there are still some whose chloroplast genome has not been reported. In study, complete plastomes six were sequenced assembled, among them, P. campanulatum was for first time. Comparative phylogenetic analyses then conducted published three related species. Results indicated that whole plastome length ranged from 154,564 bp ( multiflorum ) 156,028 stenophyllum having a quadripartite structure LSC SSC separated by two IR regions. A total 113 unique genes detected each revealed content GC these highly identical. No significant contraction or expansion observed boundaries all except sibiricum 1, which rps19 pseudogenized owing incomplete duplication. Abundant long dispersed repeats SSRs genome. There five remarkably variable regions 14 positively selected identified Heteropolygonatum. Phylogenetic results based strongly supported placement alternate leaves sect. Verticillata , group characterized whorled leaves. Moreover, verticillatum cyrtonema displayed paraphyletic. This study characters Heteropolygonatum maintained high degree similarity. Five found be potential specific DNA barcodes . suggested leaf arrangement suitable basis delimitation subgeneric groups definitions require further study.

Language: Английский

---

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

---

Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships

Life, Journal Year: 2022, Volume and Issue: 12(1), P. 92 - 92

Published: Jan. 9, 2022

Fagus longipetiolata Seemen is a deciduous tree of the genus in Fagaceae, which endemic to China. In this study, we successfully sequenced cp genome F. longipetiolata, compared genomes genus, and reconstructed phylogeny Fagaceae. The results showed that was 158,350 bp, including pair inverted repeat (IRA IRB) regions with length 25,894 bp each, large single-copy (LSC) region 87,671 small (SSC) 18,891 bp. encoded 131 unique genes, 81 protein-coding 37 transfer RNA genes (tRNAs), 8 ribosomal (rRNAs), 5 pseudogenes. addition, 33 codons 258 simple sequence repeats (SSRs) were identified. relatively conserved, especially IR regions, best conservation, no inversions or rearrangements found. five largest variations rps12, rpl32, ccsA, trnW-CCA, rps3 spread over LSC SSC. comparison gene selection pressure indicated purifying main selective pattern maintaining important biological functions genomes. However, ndhD, rpoA, ndhF affected by positive selection. Phylogenetic analysis revealed engleriana formed close relationship, partially overlapped their distribution Our would provide genetic information for further research into classification, evolution Fagus.

Language: Английский

---

Comparative Phylogenetic Analysis for Aerides (Aeridinae, Orchidaceae) Based on Six Complete Plastid Genomes

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(15), P. 12473 - 12473

Published: Aug. 5, 2023

Aerides Lour. (Orchidaceae, Aeridinae) is a group of epiphytic orchids with high ornamental value, mainly distributed in tropical and subtropical forests, that comprises approximately 20 species. The species are great value floriculture garden designing because their beautiful flower shapes colors. Although the morphological boundaries clearly defined, relationship between other closely related genera still ambiguous terms phylogeny. To better understand phylogenetic relationships, this study used next-generation sequencing technology to investigate phylogeny DNA barcoding taxonomic unit using genetic information from six plastid genomes. quadripartite-structure plastomes ranged 147,244 bp 148,391 included 120 genes. Among them, 74 were protein coding genes, 38 tRNA genes 8 rRNA while ndh pseudogenized or lost. Four non-coding mutational hotspots (rpl20–rpl33, psbM, petB, rpoB–trnCGCA, Pi > 0.06) identified. A total 71–77 SSRs 19–46 long repeats (>30 bp) recognized plastomes, which mostly located large single-copy region. Phylogenetic analysis indicated was monophylic sister Renanthera. Moreover, our results confirmed can be divided into three major clades. These findings provide assistance for identification investigation Aerides, as well contributes future research on phylogenomics Orchidaceae.

Language: Английский

---

Characterization of Firmiana danxiaensis plastomes and comparative analysis of Firmiana: insight into its phylogeny and evolution

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Feb. 22, 2024

Abstract Background Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations Danxia or Karst habitats northern Guangdong Province, China. The specialized habitat preference makes it an ideal model species for study of adaptive evolution. Meanwhile, the phylogenetic relationships F. under two landforms are unclear. Therefore, we sequenced its complete chloroplast (cp.) genomes conducted comprehensive interspecific intrageneric plastome studies. Results plastomes showed typical quadripartite circular structure that ranged from 160,832 to 161,206 bp size, with 112 unique genes encoded. Comparative genomics were relatively conserved high similarity genome organization, gene number, GC content SSRs. While revealed higher biased codon preferences than those habitats. Eighteen 11 divergent hotpots identified at levels identification further Seven (clpP, accD, ccsA, ndhH, rpl20, rpoC2, rps4) positive selection may be related adaptation. Phylogenetic analysis sister major simplex . However, not consistent types. Conclusions characteristics relationship provide new insights into integration geographical factors, environmental genetic variations on genomic Together, our will contribute identification, population genetics, conservation biology

Language: Английский

---

The complete chloroplast genome sequence of Enkianthus perulatus (Miq.) C.K.Schneid. (Ericaceae)

Mitochondrial DNA Part B, Journal Year: 2025, Volume and Issue: 10(5), P. 366 - 371

Published: April 5, 2025

Enkianthus perulatus (Miq.) C.K.Schneid. is a popular ornamental plant in Japan, for which the chloroplast genome has not been previously reported. Its complete was therefore determined, using high-throughput sequencing technique. The total length of E. 157,256 bp, comprising large single copy region 89,680 bp and small 20,472 separated by pair 23,552 inverted repeat regions. A phylogenetic analysis, based on genome, indicated that earliest diverged species within Ericaceae. structure similar to from families Ericales, but other presented will be useful further systematic analyses planning conservation strategies.

Language: Английский

---

Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales

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

Published: Jan. 6, 2022

Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in Sapindaceae family. The phylogenetic relationship of these endangered species bodinieri (Lévl.) Rehd. cavaleriei et with other members s.l. is not well resolved. A previous study concluded that genus Aesculus might be paraphyletic because was nested within it based on small DNA fragments. Thus, their chloroplast genomic information comparative analysis necessary crucial to understand circumscription plastome evolution this family.The genome sizes 151,271 158,690 bp, respectively. Results showed a total 114 unique genes were annotated H. E. cavaleriei, ycf1 gene contained abundant SSRs both genomes. Comparative revealed content, PCGs, GC content remarkably similar or identical 13 from Sapindaceae, size four generally smaller family, including Acer, Dipteronia, Aesculus, Handeliodendron. IR boundaries significant contraction, whereas presented notable expansion cp genome. Ycf1, ndhC-trnV-UAC, rpl32-trnL-UAG-ccsA divergent regions species. Analysis selection pressure there few positively selected genes. Phylogenetic different datasets, whole sequences, coding large single-copy, inverted repeat regions, consistently demonstrated sister clade consisting chinensis A. wangii strongly support as Dodonaea viscosa.This Hippocastanoideae compared subfamilies three highly could used specific barcodes Sapindaceae. results subdivision Aesculus.

Language: Английский

---

Comparative genomics and phylogenomics of the genus Glycyrrhiza (Fabaceae) based on chloroplast genomes

Frontiers in Pharmacology, Journal Year: 2024, Volume and Issue: 15

Published: March 7, 2024

Glycyrrhiza (Fabaceae) species are rich in metabolites and widely used medicine. Research on the chloroplast genome of is important for understanding its phylogenetics, biogeography, genetic diversity, identification, medicinal properties. In this study, comparative genomics phylogenomics were analyzed based genome. The genomes six obtained using various assembly annotation tools. final assembled sizes ranged from 126,380 bp to 129,115 bp, with a total 109–110 genes annotated. Comparative results showed that typically lacking inverted repeat regions, length, structure, GC content, codon usage, gene distribution highly similar. Bioinformatics analysis revealed presence 69–96 simple sequence repeats 61–138 long genomes. Combining mVISTA nucleotide four variable regions screened identification relationship studies. Selection pressure indicated overall purifying selection , few positively selected potentially linked environmental adaptation. Phylogenetic analyses involving all tribes Fabaceae published elucidated evolutionary relationships, divergence time estimation estimated chronological order differentiations within family. phylogenetic subfamilies formed distinct clusters, consistent classification scheme subfamilies. addition, repeat-lacking clade subfamily Papilionoideae clustered together, it was last differentiate. Co-linear confirmed conserved nature genomes, instances rearrangements inversions observed Papilionoideae.

Language: Английский

---