Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences

BMC Plant Biology, Journal Year: 2022, Volume and Issue: 22(1)

Published: April 6, 2022

Abstract Background Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with center of diversity Africa. Previous studies on species this have not obtained complete chloroplast genomes, structures variations. Additionally, phylogenetic position Orchidaceae still controversial uncertain. Therefore, study, we sequenced plastomes six Kenya based genome skimming, subjected them to comparative genomic analysis, reconstructed relationships other species. Results The results exhibited that genomes had typical quadripartite structure conserved arrangement moderate divergence. ranged from 145,484 bp 149,274 length an almost similar GC content 36.9–37.0%. Gene annotation revealed 106–109 single-copy genes. In addition, 19 genes are duplicated inverted regions, 16 each possessd one or more introns. Although no structural variations were observed among plastomes, about 1 kb inversion was found modesta all 11 ndh lost pseudogenized. Comparative analysis overall sequence identity confirmed for both coding non-coding regions , SC exhibit higher variation than IRs. Furthermore, there various amplifications IR Most protein-coding these high degree codon preference. We screened out SSRs seven relatively highly variable loci. Moreover, 13 discovered significant positive selection. Phylogenetic showed formed monophyletic clade closely related tribe Vandeae. family inferred 85 sequences generally consistent previous robust. Conclusions Our study initial report species, elucidates characteristics filters can contribute development DNA markers use genetic variability evolutionary . strongly support part

Language: Английский

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Lineage‐Specific CYP80 Expansion and Benzylisoquinoline Alkaloid Diversity in Early‐Diverging Eudicots

Advanced Science, Journal Year: 2024, Volume and Issue: 11(19)

Published: March 13, 2024

Abstract Menispermaceae species, as early‐diverging eudicots, can synthesize valuable benzylisoquinoline alkaloids (BIAs) like bisbenzylisoquinoline (bisBIAs) and sinomenines with a wide range of structural diversity. However, the evolutionary mechanisms responsible for their chemo‐diversity are not well understood. Here, chromosome‐level genome assembly Menispermum dauricum is presented demonstrated occurrence two whole duplication (WGD) events that shared by Ranunculales specific to , providing model understanding chromosomal evolution in eudicots. The biosynthetic pathway diverse BIAs M. reconstructed analyzing transcriptome metabolome. Additionally, five catalytic enzymes – one norcoclaurine synthase (NCS) four cytochrome P450 monooxygenases (CYP450s) from formation skeleton, hydroxylated modification, C‐O/C‐C phenol coupling BIAs. Notably, novel leaf‐specific MdCYP80G10 enzyme catalyzes C2′‐C4a ( S )‐reticuline into sinoacutine, enantiomer morphinan compounds, predictable stereospecificity discovered. Moreover, it found ‐specific CYP80 gene expansion, tissue‐specific expression, has driven BIA diversity compared other species. This study sheds light on WGD occurrences eudicots biosynthesis.

Language: Английский

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An updated classification for the hyper‐diverse genusCorydalis(Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence

Journal of Integrative Plant Biology, Journal Year: 2023, Volume and Issue: 65(9), P. 2138 - 2156

Published: April 29, 2023

Abstract The genus Corydalis , with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on a few markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections subgenera. We have performed phylogenetic analyses related taxa, using 65 shared protein‐coding plastid genes from 313 accessions (including 280 samples 226 species ) 152 universal low‐copy nuclear 296 271 covering all 42 previously recognized five independent “series”. Phylogenetic trees inferred Bayesian Inference Maximum Likelihood. Eight selected morphological characters estimated ancestral state reconstructions. Results include: (i) the three subgenera two are fully supported by both data; third, subg. Cremnocapnos is weakly DNA only, whereas in data included form successive outgroups rest genus; (ii) among “series”, 25 one “series” resolved as monophyletic sets; (iii) common ancestor likely be perennial plant taproot, yellow flowers short saccate spur, linear fruits recurved fruiting pedicels, seeds elaiosomes; (iv) we provide new classification four (of which Bipapillatae here newly described), 39 sections, 16 consistent previous classification, recircumscribed, section reinstated six established. Characters associated lifespan, underground structures, floral fruit elaiosomes important for recognition sections. These combined character reconstructions uncovered unrecognized relationships, greatly improved our understanding evolution genus.

Language: Английский

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Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(4), P. 2278 - 2278

Published: Feb. 14, 2024

The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports such events have emerged in some lineages. In this study, we conducted a comprehensive comparison the complete plastomes from twenty-two species, covering seventeen genera three subfamilies (Fumarioideae, Hypecooideae, and Papaveroideae) Papaveraceae. Our results revealed high level variability genome size Papaveraceae, ranging 151,864 bp to 219,144 length, which might be triggered by expansion IR region large number repeat sequences. Moreover, detected numerous large-scale rearrangements, primarily occurring Fumarioideae Hypecooideae. Frequent gene loss or pseudogenization were also observed for ndhs, accD, clpP, infA, rpl2, rpl20, rpl32, rps16, several tRNA genes, particularly associated structural variation their plastomes. Furthermore, found that exhibited higher GC content more sequences than those Papaveroideae. showed Papaveroideae generally displayed relatively conserved plastome, exception Eomecon chionantha, while Hypecooideae harbored reconfigurable plastomes, showing size, content, order. This study provides insights into plastome evolution Papaveraceae may contribute development effective molecular markers.

Language: Английский

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RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Feb. 6, 2024

Corydalis saxicola , an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, date, the mitochondrial (mt) genome of C. has not been reported, which limits our understanding genetic biological mechanisms . Here, mt was assembled by combining Nanopore Illumina reads. The represented a circular chromosome 587,939 bp length, with overall GC content 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA three rRNA were identified. Codon usage PCGs investigated 167 simple sequence repeats Twelve homologous fragments identified between ct genomes accounting for 1.04% entire genome. Phylogenetic examination 30 taxa provided their evolutionary relationships. We also predicted 779 RNA editing sites C successfully validated 506 (65%) these using PCR amplification Sanger sequencing. In addition, we transcriptionally profiled 24 core roots treated different concentrations CaCl 2 as well organs. These investigations will be useful effective utilization molecular breeding, provide reference further studies genus

Language: Английский

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Dynamic changes in the plastid and mitochondrial genomes of the angiosperm Corydalis pauciovulata (Papaveraceae)

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

Published: April 22, 2024

Abstract Background Corydalis DC., the largest genus in family Papaveraceae, comprises > 465 species. Complete plastid genomes (plastomes) of show evolutionary changes, including syntenic arrangements, gene losses and duplications, IR boundary shifts. However, little is known about evolution mitochondrial genome (mitogenome) . Both organelle transcriptomes are needed to better understand relationships between patterns genomes. Results We obtained complete from pauciovulata using a hybrid assembly Illumina Oxford Nanopore Technologies reads assess parallels The mitogenome plastome C. had sizes 675,483 bp 185,814 bp, respectively. Three ancestral clusters were missing mitogenome, expanded (46,060 bp) miniaturized SSC (202 regions identified plastome. contained 41 67 protein-coding genes, respectively; loss genes was plastid-specific event. also generated draft transcriptome for A combination genomic transcriptomic data supported functional replacement acetyl-CoA carboxylase subunit β ( accD ) by intracellular transfer nucleus In contrast, our analyses suggested concurrent NADH-plastoquinone oxidoreductase ndh complex both nuclear Finally, we performed characterize DNA replication, recombination, repair (DNA-RRR) as well Liriodendron tulipifera Nelumbo nuicifera 25 DNA-RRR their structure Pairwise comparisons nonsynonymous d N synonymous S substitution rates revealed that several have higher values than those nuicifera. Conclusions here provide valuable resource understanding first Papaveraceae provides an example can be explored other researchers sequencing mitogenomes related plants. Our results fundamental information rate variation, which elucidates stability.

Language: Английский

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Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 12

Published: Aug. 4, 2021

With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack chloroplast genome (plastome) resources impedes better understanding its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, which 15 were newly sequenced. Phylogenomic comparative analyses 22 plastome sequences all four recognized subgenera within revealed that length in labile, presenting range variation 42 kb. Large-scale expansions inverted repeat (IR) region identified, at extreme opposite, near-complete loss IR (with only 355 bp left) was detected for first time Euphorbiaceae. Other structural variations, including gene inversion duplication, loss/pseudogenization, also observed. We screened most promising molecular markers both intergenic coding regions phylogeny-based utilities, estimated maximum likelihood Bayesian phylogenies datasets whole sequences. The monophyly supported, are recovered successive sister relationship. Our study constitutes comprehensive investigation on it provides phylogenetic research genus, facilitating further studies taxonomy, evolution, conservation.

Language: Английский

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Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: June 22, 2022

The species in the genus Cypripedium (Orchidaceae) are considered endangered, mainly distributed temperate regions of Northern Hemisphere, with high ornamental and economic value. Despite previous extensive studies based on both morphology molecular data, sections relationships within remain controversial. Here, we employed two newly generated chloroplast genomes five other published to elucidate their genomic characteristics. were 162,773–207,142 bp length contained 128–130 genes, including 82–84 protein-coding 38 tRNA 8 rRNA genes. We identified 2,192 simple sequence repeats, 786 large repeat sequences, 7,929 variable loci. increase sequences (simple repeats sequences) causes a significant amplification genome size . expansion IR region led pseudogenization or loss genes SSC region. In addition, 12 highly polymorphic loci (Pi > 0.09) suitable for inferring phylogeny species. Based data sets whole (IRa excluded) well-supported phylogenetic tree was reconstructed, strongly supporting subfamilies Orchidaceae as monophyletic taxa. Our findings also supported that C. palangshanense belonged sect. Palangshanensia rather than Retinervia This study enriched resources , which may help promote conservation efforts these endangered

Language: Английский

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Gastroprotective action of the extract of Corydalis yanhusuo in Helicobacter pylori infection and its bioactive component, dehydrocorydaline

Journal of Ethnopharmacology, Journal Year: 2023, Volume and Issue: 307, P. 116173 - 116173

Published: Jan. 19, 2023

Language: Английский

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Phylogenomic analyses sheds new light on the phylogeny and diversification of Corydalis DC. in Himalaya–Hengduan Mountains and adjacent regions

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 193, P. 108023 - 108023

Published: Feb. 10, 2024

Language: Английский

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