Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15
Published: Oct. 29, 2024
Thunb. is a genus in the family Caprifoliaceae. All species this have high ornamental and medicinal value. However, genetic divergence between phylogeny within
Language: Английский
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
Citations
0
Plants, Journal Year: 2024, Volume and Issue: 13(10), P. 1332 - 1332
Published: May 12, 2024
The family Chenopodiaceae Vent. (Amaranthaceae
Language: Английский
Citations
3
BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)
Published: June 3, 2024
Abstract Background The disputed phylogenetic position of Aerides flabellata Rolfe ex Downie, due to morphological overlaps with related species, was investigated based on evidence complete chloroplast (cp) genomes. structural characterization cp genomes A. and rosea Lodd. Lindl. & Paxton were analyzed compared those six species in “ Vanda - alliance” provide genomic information taxonomy phylogeny. Results exhibited conserved quadripartite structures, 148,145 bp 147,925 length, similar GC content (36.7 ~ 36.8%). Gene annotations revealed 110 single-copy genes, 18 duplicated inverted regions, ten introns. Comparative analysis across confirmed stable sequence identity higher variation regions. However, there are notable differences the IR regions between two Lour. other species. CDS from indicated that except formed a monophyletic clade nested subtribe Aeridinae, being sister group Renanthera Lour., consistent previous studies. Meanwhile, separate consisted R. Br. formed, as taxon Holcoglossum Schltr. Conclusions This research first report . results provided insights into understanding plastome evolution relationships showed should be placed rather than
Language: Английский
Citations
2
International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(23), P. 16629 - 16629
Published: Nov. 22, 2023
Hydrocotyle, belonging to the Hydrocotyloideae of Araliaceae, consists 95 perennial and 35 annual species. Due lack stable diagnostic morphological characteristics high-resolution molecular markers, phylogenetic relationships Hydrocotyle need be further investigated. In this study, we newly sequenced assembled 13 whole plastid genomes performed comparative genomic analyses with four previously published plastomes phylogenomic within Araliaceae. The exhibited typical quadripartite structures lengths from 152,659 bp 153,669 bp, comprising a large single-copy (LSC) region (83,958-84,792 bp), small (SSC) (18,585-18,768 pair inverted repeats (IRs) (25,058-25,145 bp). Each plastome encoded 113 unique genes, containing 79 protein-coding 30 tRNA rRNA genes. Comparative showed that IR boundaries were highly similar, coding regions more conserved than non-coding (SC) regions. A total 2932 simple sequence 520 long identified, specificity in number distribution repeat sequences. Six hypervariable screened SC region, including intergenic spacers (IGS) (ycf3-trnS, trnS-rps4, petA-psbJ, ndhF-rpl32) two genes (rpl16 ycf1). Three (atpE, rpl16, ycf2) subjected positive selection only few species, implying most relatively during evolutionary process. Plastid supported treatment Apiaceae topologies high resolution indicated data can used comprehensive research Hydrocotyle. currently may not accurately reflect genus, new taxonomic evaluated selected combination results.
Language: Английский
Citations
6
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
Published: Dec. 29, 2023
Dendrobium Sw have multiple photosynthetic pathways but due to the lack of identification, influence CAM pathway on plastid genomic evolution and origin are still poorly understood. In this study, based results δ13C, net rates (Pn) titratable acid value, we identified species into three pathways. Then chloroplast whole genome characteristics 10 were analyzed with next-generation sequencing technology. The quadripartite-structure plastomes ranged from 151,673 bp 160,375 included 127 132 genes. Five noncoding mutational hotspots (rbcL-accD, atpB-rbcL, rbcL, trnLUAA, accD, Pi > 0.10) identified. A total 41–60 SSRs recognized, average trinucleotide content was only about 4%, which is probably a more conserved SSR. Among pathways, apparent differences in IR junctions SSC/IRB (JSBs) measured within genomes, size constitutive plants shorter because their ndh gene loss or pseudogenization, phenomenon accounts for decreasing proportion CAM, facultative obligate C3 plants, so that may be speculated closely related pathway. Phylogenetic analyses showed there independent origins selected species, ancestral plastome possessed full ORFs all study aims clarify features different enrich data provide genetic information perspectives further systematic Dendrobium.
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(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
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