Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(3), P. 1578 - 1578

Published: Jan. 27, 2024

Epipogium roseum, commonly known as one of the ghost orchids due to its rarity and almost transparent color, is a non-photosynthetic fully mycoheterotrophic plant. Given special nutritional strategies evolutionary significance, mitogenome was first characterized, three plastomes sampled from Asia were assembled. The found be smallest among Orchidaceae, with lengths ranging 18,339 19,047 bp, exhibited high sequence variety. For mitogenome, total 414,552 bp in length, comprising 26 circular chromosomes, identified. A 54 genes, including 38 protein-coding 13 tRNA 3 rRNA annotated. Multiple repeat sequences spanning length 203,423 (45.47%) discovered. Intriguingly, six plastid regions via intracellular gene transfer four horizontal observed. phylogenomics, incorporating 90 56 mitogenomes, consistently revealed sister relationship Gastrodia, bootstrap percentage 100%. These findings shed light on organelle evolution Orchidaceae plants.

Language: Английский

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

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

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Molecular characterization and phylogenetic analyses of the mitogenome of Wan-Xi white goose, a native goose breed in China

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

Published: May 13, 2025

Language: Английский

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Characteristics and Comparative Analysis of the Complete Plastomes of Apostasia fujianica and Neuwiedia malipoensis (Apostasioideae)

Horticulturae, Journal Year: 2024, Volume and Issue: 10(4), P. 383 - 383

Published: April 10, 2024

Apostasioideae, the early divergent subfamily of Orchidaceae, comprises Apostasia and Neuwiedia genera with approximately 20 species. Despite extensive research on previous studies have struggled to resolve taxonomic issues, particularly concerning position species within this subfamily. Here, we sequenced annotated plastomes fujianica malipoensis, unveiling their phylogenetic relationships shared plastome features other five published plastomes. We identified analyzed length, GC content, repeat sequences, RSCU values chloroplast genomes. It is noteworthy that genome N. malipoensis stands out as largest among all known genomes Apostasioideae subfamily, primarily due contributions from both LSC SSC regions. Furthermore, our analysis revealed three unique structural rearrangements located 10k–47k bp (ycf3–trnS-GCU) 58k–59k bp(accD) in region 118k–119k (ndhI) across genus, which presents a potential avenue for identifying distinctive genetic markers, setting them apart orchid plants. And total four mutational hotspots (rpoC2, atpH, rps4, ndhK, clpP) were identified. Moreover, study suggested formed monophyletic group, being sister Neuwiedia. Within classified into two major clades, represented follows: (A. odorata shenzhenica A. fujianica) ramifera wallichii)). These findings hold significance developing DNA barcoding contribute further understanding

Language: Английский

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Comparative Analysis of Malaxidinae (Orchidaceae) Plastome: Phylogenetic Relationship and Potential Molecular Marker

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

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Comparative Phylogenomic Study of Malaxidinae (Orchidaceae) Sheds Light on Plastome Evolution and Gene Divergence

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(20), P. 11181 - 11181

Published: Oct. 17, 2024

Malaxidinae is one of the most confusing groups in Orchidaceae classification. Previous phylogenetic analyses have revealed that relationships between taxa not yet been reliably established, using only a few plastome regions and nuclear ribosomal internal transcribed spacer (nrITS). In present study, complete plastomes

Language: Английский

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Comprehensive characterization and phylogenetic analysis of the complete plastomes of two ant–orchids, Caularthron bicornutum and Myrmecophila thomsoniana

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

Published: Nov. 29, 2024

Myrmecophytes, characterized by specialized structures like hollow stems that facilitate mutualistic relationships with ants, serve as an important system for studying ant-plant interactions and the adaptation mechanisms. Caularthron Myrmecophila are exemplary myrmecophytes within Orchidaceae. Previous studies suggested a genetic relationship between these two genera, placing them Laeliinae (Epidendreae), yet precise phylogenetic positioning remained uncertain. The absence of available plastome resources has hindered investigations into evolution phylogeny. In this study, we sequenced assembled complete plastomes bicornutum thomsoniana to elucidate their characteristics relationships. determined sizes were 150,557 bp C. 156,905 M. thomsoniana, GC contents 37.3% 37.1%, respectively. Notably, exhibited distinctive IR expansion SSC contraction, region measuring only 4532 containing five genes (ccsA, ndhD, rpl32, psaC, trnL-UAG), unique feature observed first time in Epidendreae. Comparative analyses species from related genus Epidendrum revealed conserved genome size, content, gene order. A total 32 33 long sequence repeats, 50 40 tandem 99 109 SSRs identified RSCU analysis demonstrated consistent pattern both plastomes, 29 out 30 codons values greater than 1 featuring A/U at third codon position. Leucine was most prevalent amino acid, while Cysteine least common. Four potential DNA barcoding regions Pi exceeding 0.07, namely ycf1, ccsA–psaC, petN–psbM, accD–psaI, subsequent reconstructions Laeliinae. Phylogenetic underscored close among Caularthron, Epidendrum, Myrmecophila. This study represents comprehensive thomsoniana. Through our characterization analyses, unveiled expansion/SSC contraction further elucidated positions. Our research contributes significant data insights dynamic ant–orchid phylogeny

Language: Английский

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The Complete Chloroplast Genome of an Epiphytic Leafless Orchid, Taeniophyllum complanatum: Comparative Analysis and Phylogenetic Relationships

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

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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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Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae)

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(17), P. 9538 - 9538

Published: Sept. 2, 2024

Vanda R.Br. is an epiphytic orchid genus with significant horticultural and ornamental value. Previous molecular studies expanded including some members from five other genera. However, the interspecific relationships of this recently radiated have remained unclear based on several DNA markers until now. In study, complete plastome has been used to infer phylogenetic s.l. The newly obtained plastomes ranged 146,340 bp 149,273 in length, a GC content ranging 36.5% 36.7%. contained 74 protein-coding genes (CDSs), 38 tRNAs, 8 rRNAs, their ndh underwent loss or pseudogenization. Comparative analyses 13 species revealed high conservation terms genome size, structure, gene order, except for large inversion trnGGCC ycf3 V. coerulea. Moreover, six CDSs non-CDSs were selected as candidate barcodes. Our demonstrated that monophyletic group supporting values different datasets (complete one IR, 68 CDSs, LSC, hypervariable non-CDSs, CDSs), while among fully resolved IR dataset. results confirmed great power resolving lineages.

Language: Английский

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