Comparative Analysis of Luisia (Aeridinae, Orchidaceae) Plastomes Shed Light on Plastomes Evolution and Barcodes Investigation DOI Open Access
Liang Ma, Cheng‐Yuan Zhou, Jinliao Chen

et al.

Genes, Journal Year: 2023, Volume and Issue: 15(1), P. 20 - 20

Published: Dec. 22, 2023

Luisia, a genus of the subtribe Aeridinae Orchidaceae, comprises ca. 40 species. Members Luisia exhibit unique morphological characteristics and represent valuable ornamental orchid genus. However, due to scarcity distinct characters, species identification within this is ambiguous controversial. In present study, next-generation sequencing (NGS) methods were used assemble plastomes five compare them with one publicly available plastid genome data. The possessed quadripartite structure, sizes ranging from 146,243 bp 147,430 bp. six contained total 120 genes, comprising 74 protein-coding 38 tRNA genes eight rRNA genes. Notably, all ndh pseudogenized or lost. An analysis codon usage bias showed that leucine (Leu) exhibited highest frequency, while cysteine (Cys) lowest frequency. A 57 64 SSRs 42 49 long repeats identified. Five regions coding sequences identified for DNA barcodes, based on nucleotide diversity (Pi) analysis. constituted monophyletic group sister Paraphalaenopsis strong support. Our study deepens understanding identification, plastome evolution phylogenetic positions Luisia.

Language: Английский

Complete Chloroplast Genomes and Comparative Analyses of Three Paraphalaenopsis (Aeridinae, Orchidaceae) Species DOI Open Access
Jinliao Chen, Fei Wang, Zhuang Zhao

et al.

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

Citations

18
Comparative Phylogenetic Analysis for Aerides (Aeridinae, Orchidaceae) Based on Six Complete Plastid Genomes DOI Open Access
Jinliao Chen, Fei Wang, Chengyuan Zhou

et al.

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

Citations

12
Applying DNA barcoding to identify the cultivated provenance of Fritillaria taipaiensis P. Y. Li and its related species DOI

Yuze Liang,

Jie Zhang, Xue Wang

et al.

Journal of Applied Research on Medicinal and Aromatic Plants, Journal Year: 2024, Volume and Issue: 39, P. 100530 - 100530

Published: Jan. 21, 2024

Language: Английский

Citations

4
Plastomes of Seven Coelogyne s.l. (Arethuseae, Orchidaceae) Species: Comparative Analysis and Phylogenetic Relationships DOI Creative Commons

Shan Lin,

Ruyi Li,

Shu‐Hua Tang

et al.

Horticulturae, Journal Year: 2025, Volume and Issue: 11(2), P. 144 - 144

Published: Jan. 30, 2025

The Coelogyne s.l. is one of the emblematic genera Asian orchids, with high horticultural and medicinal values. However, phylogenetic relationships genus inferred from previous studies based on a limited number DNA markers remain ambiguous. In this study, we newly sequenced assembled complete plastomes seven species: C. bulleyia, fimbriata, flaccida, prolifera, tricallosa, uncata, an unknown taxa, sp. exhibited typical quadripartite structure, varying in length between 157,476 bp 160,096 bp, accompanied by GC content spanning 37.3% to 37.5%. A total 132 genes were annotated for each plastome, including 86 protein-coding genes, eight rRNA 38 tRNA genes. Among these, 19 underwent duplication within inverted repeat (IR) regions, 18 presence introns. Additionally, detected 54 69 simple sequence repeats (SSRs) 30 49 long repeats. terms codon usage frequency, leucine (Leu) emerged highest while cysteine (Cys) lowest occurrence. Furthermore, hypervariable regions (atpB-rbcL, psbK-psbI, rps8-rpl14, rps16-trnQUUG, psaC-ndhE, ndhF-rpl32, psbB-psbT, ycf1) identified. Phylogenetic analyses using indicated that was monophyletic. Moreover, results robustly supported division into five clades. This study provides comprehensive analysis structural variation plastome data. findings offer significant insights plastid genomic characteristics s.l., contributing deeper understanding its evolutionary history.

Language: Английский

Citations

0
Characterization and Comparative Analysis of the Complete Plastomes of Five Epidendrum (Epidendreae, Orchidaceae) Species DOI Open Access
Zhuang Zhao,

Meng-Yao Zeng,

Yuwei Wu

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(19), P. 14437 - 14437

Published: Sept. 22, 2023

Epidendrum, one of the three largest genera Orchidaceae, exhibits significant horticultural and ornamental value serves as an important research model in conservation, ecology, evolutionary biology. Given ambiguous identification germplasm complex relationships within genus, complete plastome this genus (including five species) were firstly sequenced assembled to explore their characterizations. The plastomes exhibited a typical quadripartite structure. lengths ranged from 147,902 bp 150,986 bp, with GC content 37.16% 37.33%. Gene annotation revealed presence 78-82 protein-coding genes, 38 tRNAs, 8 rRNAs. A total 25-38 long repeats 130-149 SSRs detected. Analysis relative synonymous codon usage (RSCU) indicated that leucine (Leu) was most cysteine (Cys) least. consistent robust phylogenetic Epidendrum its closely related taxa established using 43 plastid genomes tribe Epidendreae. supported monophyletic group sister Cattleya. Meanwhile, four mutational hotspots (trnCGCA-petN, trnDGUC-trnYGUA, trnSGCU-trnGUCC, rpl32-trnLUAG) identified for further studies. Our analysis demonstrates promising utility inferring Epidendrum.

Language: Английский

Citations

9
Characteristics and Comparative Analysis of Seven Complete Plastomes of Trichoglottis s.l. (Aeridinae, Orchidaceae) DOI Open Access
Cheng‐Yuan Zhou,

Meng-Yao Zeng,

Xu-Yong Gao

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(19), P. 14544 - 14544

Published: Sept. 26, 2023

Trichoglottis exhibits a range of rich variations in colors and shapes flower is valuable ornamental orchid genus. The genus has been expanded by the inclusion Staurochilus, but this sensu lato (s.l.) was recovered as non-monophyletic based on molecular sequences from one or few DNA regions. Here, we present phylogenomic data sets, incorporating complete plastome seven species (including five sequenced study) s.l. two formerly treated Staurochilus), to compare structure reconstruct phylogenetic relationships plastomes possessed typical quadripartite angiosperms ranged 149,402 bp 149,841 with GC content 36.6-36.7%. These contain 120 genes, which comprise 74 protein-coding 38 tRNA 8 rRNA all ndh genes were pseudogenized lost. A total 98 (T. philippinensis) 134 ionosma) SSRs 33 subviolacea) 46 long repeats detected. consistent robust established using 25 plastid genomes Aeridinae subtribe. strongly supported monophyletic group, Staurochilus revealed successively basal lineages. In addition, mutational hotspots (trnNGUU-rpl32, trnLUAA, trnSGCU-trnGUCC, rbcL-accD, trnTGGU-psbD) identified ranking PI values. Our research indicates that source for identification evolutionary studies its related genera.

Language: Английский

Citations

8
The complete chloroplast genome sequence and phylogenetic relationship analysis of Eomecon chionantha, one species unique to China DOI
Zhang Zhi, Guoshuai Zhang, Xinke Zhang

et al.

Journal of Plant Research, Journal Year: 2024, Volume and Issue: 137(4), P. 575 - 587

Published: April 23, 2024

Language: Английский

Citations

2
A species unique to China—The complete chloroplast genome sequence of Eomecon chionantha Hance and phylogenetic relationships analysis DOI Creative Commons
Linfang Huang,

Yujing Miao,

Guoshuai Zhang

et al.

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: May 12, 2023

Abstract Eomecon chionantha Hance ( EC ) is a unique species in China with high medicinal value. Ethnic minorities China, such as the Miao and Tujia ethnic groups, have long history of using blood herbs for treatment, has been used this purpose centuries. However, despite its use, we no knowledge chloroplast genome Therefore, study reports 's complete information to better develop protect plant China. The genomic indicates that DNA (CPDNA) (178,808 bp) contains 99 protein-coding genes, including 8 rRNAs, 37 tRNAs. We discovered 54 SSRs, most which are single nucleotide adenine-thymidine (A-T) repeats. Comparative analysis codons, repeats, sequences found CPDNA highly conserved. According our phylogenetic tree results, closely related four species. Through K2-P analysis, identified five hypervariable regions, ycf 4- cem A, 3- trn S-GGA, C-GCA- pet N, rpl 32- L-UAG, psb I- S-UGA. In summary, reported, first time, genus This provides more scientific basis further development utilization conducive an in-depth understanding diversity from perspective.

Language: Английский

Citations

1
Comparative Analysis of Malaxidinae (Orchidaceae) Plastome: Phylogenetic Relationship and Potential Molecular Marker DOI Open Access

Meng-Yao Zeng,

Ming-He Li,

Jingshan Shi

et al.

Published: Dec. 26, 2023

Malaxidinae is one of the confusing groups with classification in Orchidaceae. Previous phylogenetic analysis reveals that relationships among taxa have not yet been reliably established using a few plastome regions or nuclear ribosomal internal transcribed spacer (nrITS). In present study, complete plastomes Oberonia integerrima and Crepidium purpureum were assembled high-throughput sequencing. Combined publicly available data, this resulted data set 19 plastomes, including 17 species Malaxidinae. The feature relationship compared analyzed. results showed that: (1) possessed quadripartite structure typical angiosperms, sizes ranging from 142,996 bp to 158,787 encoding 125 133 genes. ndh genes lost pseudogenized varying degrees six species. An unusal inversion was detected Large Single-Copy region (LSC) Oberonioides microtatantha. (2) A total 8 regions, ycf1, matK, rps16, rpl32, ccsA-ndhD, clpP-psbB, trn-FGAA-ndhJ, trnSGCU-trnGUCC, identified as mutational hotspots. (3) Based on 68 protein-coding 51 intergenic respectively, analyses resolved genera-level subtribe strong support. Liparis supported polyphyletic.

Language: Английский

Citations

1
The Complete Chloroplast Genome of an Epiphytic Leafless Orchid, Taeniophyllum complanatum: Comparative Analysis and Phylogenetic Relationships DOI Creative Commons
Zhuang Zhou, Jinliao Chen, Fei Wang

et al.

Horticulturae, Journal Year: 2024, Volume and Issue: 10(6), P. 660 - 660

Published: June 20, 2024

Taeniophyllum is a distinct taxon of epiphytic leafless plants in the subtribe Aeridinae Orchidaceae. The differences chloroplast genomes between extremely degraded orchids and other leafy orchids, as well their origins evolution, raise intriguing questions. Therefore, we report genome sequence complanatum, including an extensive comparative analysis with types orchids. T. complanatum exhibited typical quadripartite structure, its overall structure gene content were relatively conserved. entire was 141,174 bp length, making it smallest known It encoded total 120 genes, repetitive comprising 74 protein-coding 38 transfer RNA (tRNA) 8 ribosomal (rRNA) genes. A phylogenetic conducted on 43 species belonging to five subfamilies results showed that monophyly, nearly all segments having 100% bootstrap value. Chiloschista clustered together sister group Phalaenopsis occupied highest position Epidendroideae. Phylogenetic suggested within Orchidaceae evolved independently. This study may provide foundation for research structural diversity thereby enhancing resources available studies

Language: Английский

Citations

0