Toward a phylogenomic classification of magnoliids

American Journal of Botany, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 14, 2025

Magnoliids are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses limited number mostly plastid markers have led to the current classification magnoliids into four orders and 18 families. However, uncertainty remains regarding placement several For first comprehensive phylogenomic analysis as whole, we sampled 235 species from 199 (74%) genera representing all families most subfamilies tribes. We analyzed newly generated data Angiosperms353 probe set using both coalescent concatenation testing impact multiple filtering alignment strategies. While our results generally provide further support for previously established relationships in whole large including Annonaceae Lauraceae, they also new evidence ambiguous relationships. In particular, found position Hydnoraceae sister remainder Piperales, though was conflicting, resolved backbone among Myristicaceae. Different analytical strategies tended rather small effects branch topology. Although some by low gene recovery taxa significant tree conflict relationships, this study represents step toward reconstructing evolutionary history major lineage Based these results, present an updated magnoliids, recognizing 21 families, summarizing tribes, describing tribes

Language: Английский

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Hundreds of nuclear and plastid loci yield novel insights into orchid relationships

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1166 - 1180

Published: July 1, 2021

PREMISE The inference of evolutionary relationships in the species‐rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust phylogenetic framework, which was used to classify orchids investigate drivers orchid diversification. However, extent based genome is congruent with nuclear been only poorly assessed. METHODS We inferred higher‐level likelihood ASTRAL analyses 294 low‐copy genes sequenced using Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) concatenated analysis 78 264 (117 18 28 subtribes). compared informativeness support hypotheses. RESULTS Phylogenetic data sets provides well‐supported that are highly between analyses. Comparisons gene trees supermatrix tree showed mostly congruent, but revealed instances strongly supported incongruence both shallow deep time. individual general better than most genes. CONCLUSIONS Our study first phylogenomic framework an assessment intragenomic discordance, plastid‐nuclear incongruence, across family. results also demonstrate what long known rarely thoroughly documented: can contain discordances, this must be reconciled prior interpretation studies, such as taxonomy, biogeography, character evolution.

Language: Английский

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Can plastid genome sequencing be used for species identification in Lauraceae?

Botanical Journal of the Linnean Society, Journal Year: 2021, Volume and Issue: 197(1), P. 1 - 14

Published: Jan. 26, 2021

Abstract Using DNA barcoding for species identification remains challenging many plant groups. New sequencing approaches such as complete plastid genome may provide some increased power and practical benefits beyond standard barcodes. We undertook a case study comparing to discrimination in the ecologically economically important family Lauraceae, using 191 genomes 131 from 25 genera, representing largest plastome data set Lauraceae date. found that sequences were useful correcting errors finding new cryptic species. However, overall only able discriminate c. 60% of our sample, with this modest improvement 40 50% success Beyond discrimination, revealed complex relationships family, 12/25 genera being non-monophyletic extensive incongruence relative nuclear ribosomal DNA. These results highlight although improving phylogenetic resolution providing species-level insights, partially improve reinforces need large-scale among closely related

Language: Английский

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Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(11), P. 2850 - 2868

Published: Feb. 27, 2023

The evergreen versus deciduous leaf habit is an important functional trait for adaptation of forest trees and has been hypothesized to be related the evolutionary processes component species under paleoclimatic change, potentially reflected in dynamic history broadleaved forests (EBLFs) East Asia. However, knowledge about shift with impact change using genomic data remains rare. Here, we focus on Litsea complex (Lauraceae), a key lineage dominant EBLFs, gain insights into how shifted, providing origin historical dynamics EBLFs Asia Cenozoic climate change. We reconstructed robust phylogeny genome-wide single-nucleotide variants (SNVs) eight clades resolved. Fossil-calibrated analyses, diversification rate shifts, ancestral habit, ecological niche modelling reconstruction were employed estimate its pattern. Taking account studies other plant lineages dominating Asia, it was revealed that prototype probably emerged Early Eocene (55-50 million years ago [Ma]), facilitated by greenhouse warming. As response cooling drying Middle Late (48-38 Ma), habits evolved Up Miocene (23 prevailing Asian monsoon increased extreme seasonal precipitation accelerated emergence lineages, ultimately shaped vegetation resembling today.

Language: Английский

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Comparative genomics and phylogenetic analysis of mitochondrial genomes of Neocinnamomum

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: March 6, 2025

Neocinnamomum plants are considered a promising feedstock for biodiesel in China, due to the richness long-chain fatty acids (LCFAs) found their seeds. However, mitochondrial genome (mitogenome) of this genus has not yet been systematically described, and exploration species relationships within using mitogenome sequences is also an uncharted territory. This hindered our understanding diversity evolutionary Neocinnamomum. In study, total 24 individuals representing seven distinct taxa from were subjected Illumina sequencing, N. delavayi was sequenced Oxford Nanopore sequencing technology. We successfully assembled delavayi, which 778,066 bp size exhibits single circular structure. The analysis identified 659 dispersed repeats, 211 simple sequence repeats (SSRs), 30 tandem mitogenome. Additionally, 37 homologous fragments, totaling 9929 bp, between plastid (plastome). codons 41 protein-coding genes (PCGs) had preference ending A/T, codon usage bias majority these influenced by natural selection pressures. Comparative genomic revealed low collinearity significant gene rearrangements species. Phylogenetic resulted classification into six clades, contradicting previous findings based on complete plastomes nuclear ribosomal cistron (nrDNA). PCGs individuals, 86 mutation events identified, included three indels 83 SNPs. Notably, ccmC underwent positive pairwise comparisons pairs. Furthermore, 748 RNA editing sites predicted study enriches knowledge mitogenomes family Lauraceae, provides valuable data foundation evolution research, genetic resource conservation, molecular breeding

Language: Английский

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A comparative analysis of complete chloroplast genomes of seven Ocotea species (Lauraceae) confirms low sequence divergence within the Ocotea complex

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Jan. 21, 2022

The genus Ocotea (Lauraceae) includes about 450 species, of which 90% are Neotropical, while the rest is from Macaronesia, Africa and Madagascar. In this study we present first complete chloroplast genome sequences seven six Neotropical one Macaronesia. Genome sizes range 152,630 (O. porosa) to 152,685 bp aciphylla). All plastomes contain a total 131 (114 unique) genes, among 87 (80 encode proteins. order genes (if present) same in all Lauraceae examined so far. Two hypervariable loci were found LSC region (psbA-trnH, ycf2), three SSC (ycf1, ndhH, trnL(UAG)-ndhF). pairwise cp genomic alignment between taxa showed that regions more variable compared IR regions. protein coding comprise 25,503-25,520 codons examined. most frequent amino acids encoded leucine, isoleucine, serine. SSRs be two dioecious species than four bisexual gynodioecious (87 vs. 75-84 SSRs). A preliminary phylogenetic analysis based on 69 shows as sister group Cinnamomum sensu lato. Sequence divergence appears much lower closely related, likewise species-rich genera Cinnamomum, Lindera Litsea.

Language: Английский

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Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests

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

Published: Jan. 13, 2022

Abstract Background The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain new insights into the of this biome, we generated a molecular phylogeny one its essential plant groups, tribe Perseeae (Lauraceae). Results Our plastid tree topologies were robust to analyses based on different regions and strategies for data partitioning, nucleotide substitution saturation, gap handling. We found that comprised six major clades began colonize EBLFs Asia in early Miocene. diversification rates accelerated twice late Conclusions findings suggest intensified precipitation Miocene may have facilitated range expansions establishment within biome. By Miocene, species had become rapid.

Language: Английский

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Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae)

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

Published: July 7, 2023

The genus Neocinnamomum is considered to be one of the most enigmatic groups in Lauraceae, mainly distributed tropical and subtropical regions Southeast Asia. contains valuable oilseed medicinal tree species. However, there are few studies on at present, its interspecific relationship still unclear. In order explore genetic structure evolutionary characteristics chloroplast genome resolve species relationships within genus, comparative genomic phylogenetic analyses were performed whole sequences 51 samples representing seven taxa. size ranged from 150,753-150,956 bp, with a GC content 38.8%-38.9%. A total 128 genes annotated genome, including 84 protein coding genes, 8 rRNA 36 tRNA genes. Between 71-82 SSRs detected, among which A/T base repeats common. contained 31 preferred codons. Three highly variable regions, trnN - GUU ndhF , petA psbJ ccsA ndhD identified Pi values > 0.004. Based tree, taxa determined. N. delavayi fargesii closely related species, lecomtei was as basal taxon. this study, sequence variation genomes revealed, clarified. results study will provide reference for subsequent molecular marker development research .

Language: Английский

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Leaf phenotypic plasticity coupled with integration facilitates the adaptation of plants to enhanced N deposition

Environmental Pollution, Journal Year: 2023, Volume and Issue: 327, P. 121570 - 121570

Published: April 4, 2023

Language: Английский

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LC-MS/DIA-based strategy for comprehensive flavonoid profiling: an Ocotea spp. applicability case

RSC Advances, Journal Year: 2024, Volume and Issue: 14(15), P. 10481 - 10498

Published: Jan. 1, 2024

We introduce a liquid chromatography - mass spectrometry with data-independent acquisition (LC-MS/DIA)-based strategy, specifically tailored to achieve comprehensive and reliable glycosylated flavonoid profiling. This approach facilitates in-depth simultaneous exploration of all detected precursors fragments during data processing, employing the widely-used open-source MZmine 3 software. It was applied dataset six Ocotea plant species. framework suggested 49 flavonoids potentially newly described for these species, alongside 45 known features within genus. Flavonols kaempferol quercetin, both exhibiting O-glycosylation patterns, were particularly prevalent. Gas-phase fragmentation reactions further supported findings. For first time, apigenin flavone backbone also annotated in most examined Apigenin derivatives found mainly C-glycoside form, O. porosa displaying highest : flavonol ratio. The allowed an unprecedented detection quercetin it has underscored untapped potential LC-MS/DIA broad Our study more than 50 backbones each surpassing current literature.

Language: Английский

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