A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 2, 2025

Peucedanum japonicum (PJ), a member of the Apiaceae family, is widely distributed and cultivated in East Asian countries for edible functional foods. In this study, we compared plastid genomes (plastomes) 45S nuclear ribosomal DNA (45S nrDNA) simultaneously from 10 PJ collections. Plastome-based phylogenetic analysis showed that accessions were monophyletic within genus Peucedanum. However, ten plastomes classified into two different groups according to their length inverted repeat (IR) block, short-type (S-type) plastome group containing 18.6 kbp original IR long-type (L-type) 35.7 expanded by duplication 17.1 large single copy region. A total nine nucleotide polymorphisms eight insertions or deletions identified among five L-type plastomes, whereas variations S-type plastomes. Calculation synonymous substitution rates divergence time estimation suggested 17 expansion occurred recently. Molecular markers developed validated classify 55 germplasm types. Our study would be useful unraveling dynamic evolution family molecular breeding PJ.

Language: Английский

---

Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution

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

Published: Feb. 26, 2022

Abstract Background The large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists 10 tribes, > 90 genera, 2000 species. Previous molecular phylogenetics using limited numbers markers were often unable to fully resolve the phylogenetic relationships at tribal generic levels. Also, structural variations plastomes (PSVs) within tribes have been poorly investigated in previous studies. To understand PSVs clade, highly reliable sufficient sampling with superior next-generation analysis techniques is required. In this study, 71 (40 newly sequenced assembled rest from GenBank) comparatively analyzed decipher four data matrices. Results All are typically quadripartite size ranging 153,055 155,908 bp contained 111 unique genes. inverted repeat (IR) regions experienced multiple contraction expansion; five types detected but most abundant was SSR. its elements affected by IR boundary shifts types. However, emerging had no taxonomic implications. Eight divergent identified plastome ndhF, ccsA, ndhD, ndhA, ndhH, ycf1 , rps16-trnQ-UUG, psbM-trnD . These variable may be potential for further species delimitation population genetic analyses clade. Our phylogenomic yielded a well-resolved phylogeny tree well-support levels alliance. Conclusions Plastome could indispensable resolving tribes. Therefore, study provides deep insights into Rubiaceae family as whole.

Language: Английский

---

The evolution of ephemeral flora in Xinjiang, China: insights from plastid phylogenomic analyses of Brassicaceae

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

Published: Feb. 15, 2024

Abstract Background The ephemeral flora of northern Xinjiang, China, plays an important role in the desert ecosystems. However, evolutionary history this remains unclear. To gain new insights into its origin and dynamics, we comprehensively sampled plants Brassicaceae, one essential plant groups flora. Results We reconstructed a phylogenetic tree using plastid genomes estimated their divergence times. Our results indicate that species began to colonize arid areas north Xinjiang during Early Miocene there was greater dispersal from surrounding community Middle Late Miocene, contrast or Pliocene periods. Conclusions findings, together with previous studies, suggest originated assembly became rapid onwards, possibly attributable global climate changes regional geological events.

Language: Английский

---

Large seeds as a defensive strategy against partial granivory in the Fagaceae

Journal of Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 16, 2025

Abstract Large seeds interact with a wide range of animals (e.g. predators) and are dispersed via certain small animals' foraging behaviours, such as caching. Some the most iconic species large‐seeded plants have long fascinated ecologists studying biotic interactions, oaks their relatives in Fagaceae family. The acorns through synzoochory, specific dispersal mode which animal partners act both seed dispersers granivores. Although granivory (i.e. herbivory) can profoundly impact survival plant offspring, partial damage on reserves is prevalent phenomenon that does not always result mortality. However, previous single‐species studies resulted mixed evidence across treatments traits, leaving regeneration unclear. Using artificial experiments 1185 20 species, here we quantify how loss reserve affects germination, seedling growth biomass allocation gradient from 0% to 96% loss. We show that, although reduces total number leaves), it significantly affect germination or overall seedlings leaf mass fraction root:shoot ratio). Seedlings more preyed upon higher area, indicating they tend grow larger but less protected leaves against herbivores, perhaps compete for light. Synthesis . As scatter‐hoarding granivores evolved relatively large sizes, like acorns, our findings demonstrate this type may tolerate exchange high efficiency. This study opens new perspectives understanding size diversity evolution. conclude per se defensive trait, counteract potential losses escape full predation allow germination.

Language: Английский

---

Plastome structure, phylogenomics, and divergence times of tribe Cinnamomeae (Lauraceae)

BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)

Published: Sept. 8, 2022

Tribe Cinnamomeae is a species-rich and ecologically important group in tropical subtropical forests. Previous studies explored its phylogenetic relationships historical biogeography using limited loci, which might result biased molecular dating due to insufficient parsimony-informative sites. Thus, 15 plastomes were newly sequenced combined with published study plastome structural variations, gene evolution, relationships, divergence times of this tribe.Among the generated plastomes, 14 ranged from 152,551 bp 152,847 bp, remaining one (Cinnamomum chartophyllum XTBGLQM0164) was 158,657 bp. The inverted repeat (IR) regions XTBGLQM0164 contained complete ycf2, trnICAU, rpl32, rpl2. Four hypervariable plastid loci (ycf1, ndhF-rpl32-trnLUAG, petA-psbJ) identified as candidate DNA barcodes. Divergence based on few primarily determined by prior age constraints rather than data. In contrast, protein-coding genes (PCGs) data constraints. Dating analyses PCGs showed that Cinnamomum sect. Camphora diverged C. late Oligocene (27.47 Ma).This reports first case drastic IR expansion tribe Cinnamomeae, indicates have sufficient sites for dating. Besides, provide preliminary insights into time within can facilitate future biogeography.

Language: Английский

---

Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae)

Annals of Botany, Journal Year: 2024, Volume and Issue: 133(4), P. 585 - 604

Published: Feb. 13, 2024

Abstract Background and Aims Kalanchoideae is one of three subfamilies within Crassulaceae contains four genera. Despite previous efforts, the phylogeny remains inadequately resolved with persistent issues including low support, unstructured topologies polytomies. This study aimed to address two central objectives: (1) resolving pending phylogenetic questions by using organelle-scale ‘barcodes’ (plastomes) nuclear data; (2) investigating interspecific diversity patterns among plastomes. Methods To explore plastome evolution in Kalanchoideae, we newly sequenced 38 plastomes representing all constituent genera (Adromischus, Cotyledon, Kalanchoe Tylecodon). We performed comparative analyses plastomic features, GC gene contents, distributions at IR (inverted repeat) boundaries, nucleotide divergence, tRNA (pttRNA) structures codon aversions. Additionally, inferences were inferred both dataset (79 genes) (1054 genes). Key Results Significant heterogeneities observed lengths strongly correlated LSC (large single copy) lengths. Informative diversities existed content SSC/IRa (small copy/inverted repeat a), unique individually identified Adromischus leucophyllus major clade. The ycf1 was assessed as a shared hypervariable region genera, containing nine lineage-specific indels. Three pttRNAs exhibited specific Kalanchoe. Moreover, 24 coding sequences revealed total 41 unused codons across phyloplastomic clearly depicted internal branching Kalanchoideae. Most notably, plastid- nuclear-based phylogenies, our research offers first evidence that section Eukalanchoe not monophyletic. Conclusions conducted comprehensive on reported Importantly, results only reconstructed well-resolved phylogenies but also highly informative markers subfamily, genus species levels. These findings significantly enhance understanding evolutionary history

Language: Английский

---

Characterization, comparison, and phylogenetic analyses of chloroplast genomes of Euphorbia species

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: July 4, 2024

The genus Euphorbia (Euphorbiaceae) has near-cosmopolitan distribution and serves as a significant resource for both ornamental medicinal purposes. Despite its economic importance, Euphorbia's taxonomy long been challenged by the intricate nature of morphological traits exhibiting high levels convergence. While molecular markers are essential phylogenetic studies, their availability limited. To address this gap, we conducted comparative analyses focusing on chloroplast (CP) genomes nine species, incorporating three newly sequenced annotated accessions. In addition, informativeness nucleotide diversity were computed to identify candidate among closely related taxa in genus. Our investigation revealed relatively conserved sizes structures CP across studied with notable interspecific variations observed primarily non-coding regions IR/SC borders. By leveraging diversity, identified rpoB gene optimal species delimitation shallow-level inference within Through comprehensive analysis multiple taxa, our study sheds light evolutionary dynamics taxonomic intricacies Euphorbia, offering valuable insights into genome evolution taxonomy.

Language: Английский

---

Plastome evolution and phylogenomics of Trichosporeae (Gesneriaceae) with its morphological characters appraisal

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: May 9, 2023

Trichosporeae is the largest and most taxonomically difficult tribe of Gesneriaceae due to its diverse morphology. Previous studies have not clarified phylogenetic relationships within this on several DNA markers, including generic subtribes. Recently, plastid phylogenomics been successfully employed resolve at different taxonomic levels. In study, were used explore Trichosporeae. Eleven plastomes Hemiboea newly reported. Comparative analyses, phylogeny morphological character evolution conducted 79 species representing seven The range from 152,742 bp 153,695 in length. Within Trichosporeae, sampled 152,196 156,614 GC content 37.2% 37.8%. A total 121-133 genes annotated each species, 80-91 protein-coding genes, 34-37 tRNA 8 rRNA genes. contraction expansion IR borders detected, gene rearrangements inversions did occur. 13 hypervariable regions proposed as potential molecular markers for identification. 24,299 SNPs 3,378 indels inferred, functionally missense silent variations. There 1968 SSRs, 2055 tandem repeats 2802 dispersed repeats. RSCU ENC values indicated that codon usage pattern was conserved Both frameworks based whole plastome 80 CDSs basically concordant. sister between Loxocarpinae Didymocarpinae confirmed, Oreocharis a group with high support. characters showed complex evolutionary Our findings may contribute future research genetic diversity, patterns, conservation

Language: Английский

---

Evolution of 101 Apocynaceae plastomes and phylogenetic implications

Molecular Phylogenetics and Evolution, Journal Year: 2022, Volume and Issue: 180, P. 107688 - 107688

Published: Dec. 26, 2022

Language: Английский

---

Phylogenomics and plastome evolution of Indigofera (Fabaceae)

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: June 6, 2023

Indigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, soil water conservation. The taxonomically difficult due to high level of overlap morphological characters interspecies, fewer reliability states classification, extensive adaptive evolution. Previous characteristic-based taxonomy nuclear ITS-based phylogenies have contributed our understanding However, lack chloroplast genomic resources limits comprehensive phylogenetic relationships evolutionary processes Indigofera.Here, we newly assembled 18 genomes Indigofera. We performed a series analyses genome structure, nucleotide diversity, analysis, pairwise Ka/Ks ratios, positive selection analysis by combining with allied Papilionoideae.The exhibited highly conserved structures ranged size from 157,918 160,040 bp, containing 83 protein-coding genes, 37 tRNA eight rRNA genes. Thirteen variable regions were identified, which trnK-rbcL, ndhF-trnL, ycf1 considered as candidate DNA barcodes identification Phylogenetic using maximum likelihood (ML) Bayesian inference (BI) methods based on complete genes (PCGs) generated well-resolved phylogeny species. monophyly was strongly supported, four monophyletic lineages (i.e., Pantropical, East Asian, Tethyan, Palaeotropical clades) resolved within genus. ratios showed values lower than 1, 13 significant posterior probabilities codon sites identified branch-site model, associated photosynthesis. Positive accD suggested experienced evolution pressures imposed their herbivores pathogens. Our study provided insight into structural variation genomes, relationships, These results will facilitate future studies identification, interspecific intraspecific delimitation, evolution,

Language: Английский

---