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
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
Citations
8
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
Gene, Journal Year: 2024, Volume and Issue: 912, P. 148349 - 148349
Published: March 7, 2024
Language: Английский
Citations
2
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
Citations
1
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
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
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
Citations
0
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
Citations
0