Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

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

Published: Jan. 24, 2024

Abstract Background The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on provided us with good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, evolutionary history of this also remains inadequately understood. plastid genomes possessing highly conserved structure limited rate proved be an effective tool studying plant phylogeny evolution. Results In current study, we newly sequenced assembled fifteen complete plastomes. Combined two previously reported plastomes, performed comprehensively phylogenomics analyses gain novel insights into genus. comparative results indicated seventeen plastomes exhibited high degree conservation similarity in terms their structure, size, GC content, gene order, IR borders, codon bias patterns SSRs profiles. Such as all them displayed typical quadripartite including large single copy region (LSC: 85,074–86,197 bp), small (SSC: 17,047–17,132 bp) separated by pair inverted repeat regions (IRs: 26,176–26,334 bp). And had similar boundaries adjacent genes were identical. rps 19 was located at junction LSC/IRa, IRa/SSC between trn N ndh F gene, ycf 1 appeared SSC/IRb IRb/LSC boundary rpl 12 H gene. Twelve specific mutation hotspots ( atp F, cem A, acc D, 22, rbc L, mat K, 1, -psb 4 -cem L -acc E -trn T G R) identified can serve potential DNA barcodes species identification within . Furthermore, data Internal Transcribed Spacer (ITS) sequences reconstruct Sanicula. tree topologies incongruent, both strong evidence supporting monophyly Saniculoideae Apioideae. addition, sister groups Apioideae strongly suggested. involved study clustered clade, Eryngium together. However, it clearly observed sections respectively recovered monophyletic group. Molecular dating analysis explored origin occurred during late Eocene period, approximately 37.84 Ma (95% HPD: 20.33–52.21 Ma) years ago diversification early Miocene 18.38 10.68–25.28 Ma). Conclusion plastome-based ITS-based generated incongruences, which may attributed event hybridization/introgression, incomplete lineage sorting (ILS) chloroplast capture. Our highlighted power plastome significantly improve phylogenetic supports resolutions, efficiently explore Miocene, largely influenced prevalence East Asian monsoon uplift Hengduan Mountains (HDM). summary, our provides evolution, relationships, framework evolution

Language: Английский

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The giant genome of lily provides insights into the hybridization of cultivated lilies

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 2, 2025

Lilies are economically important monocots known for their ornamental flowers, bulbs, and large genomes. The absence of genomic information has impeded evolutionary studies genome-based breeding efforts. Here, we present reference genomes Lilium sargentiae (lily, 35.66 Gb) Gloriosa superba (flame lily, 5.09 Gb). giant lily genome is shaped by recent long terminal repeat retroelements. Phylogenetic analysis reveals diverse, independent origins cultivars. Gene families involved in sucrose starch metabolism significantly expanded the genome. Key homologs XTH22, SOC1, AP1/FUL-like genes regulate development, bud growth transition, floral transition bulbs. Colchicine biosynthetic gene clusters identified G. but absent L. sargentiae, highlighting colchicine evolution Colchicaceae. These insights enhance understanding Liliales evolution, providing a foundation future molecular research. perennial plants with flowers authors assemble two species, analyze phylogeny, flower stem development (bulbs lilies, rhizomes flame lilies), bulb transitions, biosynthesis.

Language: Английский

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Lilium liangiae, a new species in the genus Lilium (Liliaceae) that reveals parallel evolution within morphology

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

Published: March 27, 2024

The former genus Nomocharis , which has been merged as a clade within the Lilium (Liliaceae), represents one of most complicated and unclear groups included in latter. Research on members quite limited due to sampling difficulties caused by its selective environmental preferences. In this study, we propose new species clade, liangiae further bridge connecting with other Lilium. We conducted morphological clustering, phylogenetic, comparative genomics analyses nuclear internal spacers newly generated complete chloroplast genome, conjunction previously published sequences, performed ancestral state reconstruction clarify evolutionary pattern important traits . clustering results 38 indicated that is allied Nomocharis, increasing polymorphism phylogenetic both supported L. belonging subclade Ecristata closest affinity being gongshanense Inconsistencies relationships were detected between plastid datasets, possibly ancient hybridization ongoing introgression. Comparative revealed conservation similarity their genomes, variations observed expansion contraction IR regions. A/T palindromic repeat sequences abundant. Seven highly variable regions (Pi≥0.015) identified potential molecular markers based genomes 47 Both genes exhibited very low variability contrasting appearance. analysis suggests campanulate flower form, arose at least three times revealing parallel evolution Overall, study adds genetic evidence for understanding patterns

Language: Английский

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Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution

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

Published: June 7, 2022

Lilium ledebourii (Baker) Boiss is a rare species, which exhibits valuable traits. However, before its genetic diversity and evolutionary were uncovered, wild resources jeopardized. Moreover, some ambiguities in phylogenetic relationships of this genus remain unresolved. Therefore, obtaining the whole chloroplast sequences L. comparative analysis along with other species crucial pivotal to understanding evolution as well populations. A multi-scale genome-level analysis, especially selection pressure, was conducted. Detailed third‑generation sequencing revealed genome 151,884 bp, an ordinary quadripartite protected structure comprising 37.0% GC. Overall, 113 different genes recognized genome, consisting 30 distinct tRNA genes, four ribosomal RNAs 79 unique protein-encoding genes. Here, 3234 SSRs 2053 complex repeats identified, comprehensive performed for IR expansion contraction, codon usage bias. genome-wide sliding window variability rpl32-trnL-ccsA, petD-rpoA, ycf1, psbI-trnS-trnG, rps15-ycf1, trnR, trnT-trnL, trnP-psaJ-rpl33 higher among 48 cp genomes, displaying nucleotide SC regions. Following 1128 pairwise comparisons, ndhB, psbJ, psbZ, ycf2 exhibit zero synonymous substitution, revealing divergence or restriction. Furthermore, out 78 protein-coding we found that accD rpl36 under positive selection: however, at entire-chloroplast protein scale, have gone through purifying selection. Also, new tree rebuilt, believe classification clearer than before. The provided here will aid future studies identification, population genetics, conservation.

Language: Английский

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Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics

Plant Diversity, Journal Year: 2023, Volume and Issue: 46(2), P. 219 - 228

Published: Aug. 3, 2023

Here, we infer the historical biogeography and evolutionary diversification of genus Lilium. For this purpose, used complete plastomes 64 currently accepted species in Lilium (14 were newly sequenced) to recover phylogenetic backbone a time-calibrated framework estimate biogeographical history scenarios rates Our results suggest that ancient climatic changes geological tectonic activities jointly shaped distribution range drove radiation Lilium, including Middle Miocene Climate Optimum (MMCO), late global cooling, as well successive uplift Qinghai-Tibet Plateau (QTP) strengthening monsoon climate East Asia during Pliocene. This case study suggests unique events Neogene Asia, particular QTP enhancement monsoonal climate, may have played an essential role formation uneven plant diversity Northern Hemisphere.

Language: Английский

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Comprehensive analysis of the complete mitochondrial genome of Lilium tsingtauense reveals a novel multichromosome structure

Plant Cell Reports, Journal Year: 2024, Volume and Issue: 43(6)

Published: May 24, 2024

Language: Английский

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Reference genome of Calochortus tolmiei Hook. & Arn. (Liliaceae), a cat’s ear mariposa lily

G3 Genes Genomes Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 20, 2025

Abstract Calochortus tolmiei Hook. & Arn., a bulbous monocot with cat’s ear flowers in the angiosperm family Liliaceae, is perennial herb native to northern California, Oregon, and Washington. exhibits substantial morphological karyotype diversity multiple floral forms haploid chromosome number varying from six 10. Here, we present first high-quality reference assembly Liliaceae for C. tolmiei, scaffolded of 2.9 Gbp N50 296 Mbp. Notably, 92% assembled genome into 10 pseudomolecules, matching documented count tolmiei. The contains 31,049 protein-coding genes, 86.2% being functionally annotated. closest reference-quality Chionographis japonica (Willd.) Maxim. (Melianthiaceae), which diverged approximately 83 MYA, providing valuable genomic resource Liliales, an order lacks resources.

Language: Английский

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Incomplete lineage sorting and introgression among genera and species of Liliaceae tribe Tulipeae: insights from phylogenomics

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: April 28, 2025

Phylogenetic research in Tulipa (Liliaceae), a genus of significant economic and horticultural value, has relied on limited nuclear (mostly ribosomal internal transcribed spacer, nrITS) plastid DNA sequences, resulting low-resolution phylogenetic trees uncertain intrageneric classifications. The genus, noted for its large genome, presents discordant relationships among Amana, Erythronium, Tulipa, likely due to incomplete lineage sorting (ILS) and/or reticulate evolution. Thus, phylogenomic approaches are needed clarify these the conflicting signals within tribe Tulipeae. We newly sequenced 50 transcriptomes 46 species Tulipeae (including multiple accessions all four genera) one outgroup sister Lilieae (Notholirion campanulatum), downloaded 15 previously published supplement sampling. One dataset (74 protein-coding genes, PCGs) (2594 orthologous OGs) were constructed, with latter used tree inference based maximum likelihood (ML) multi-species coalescent (MSC) methods. To investigate causes gene discordance, "site con/discordance factors" (sCF sDF1/sDF2) calculated first, after which nodes displaying high or imbalanced sDF1/2 selected network analyses polytomy tests determine whether ILS evolution best explain incongruence. Key not resolved by this technique, especially those further investigated applying D-statistics QuIBL. failed reconstruct reliable unambiguous evolutionary history pervasive evolution, caused either obscured minority signal differing genomic compartments. However, we confirmed monophyly most subgenera, exception two small subgenus Orithyia, heterophylla was recovered as remainder whereas T. sinkiangensis clustered Tulipa. In contrast, traditional sections found be non-monophyletic.

Language: Английский

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The complete chloroplast genomes and phylogenetic analysis of Lilium leichtlinii var. maximowiczii from Northeast Asia

Mitochondrial DNA Part B, Journal Year: 2025, Volume and Issue: 10(6), P. 474 - 479

Published: May 14, 2025

Lilium leichtlinii var. maximowiczii, native to Northeast Asia, shows morphological differences between Korean and Japanese varieties. This study analyzed chloroplast (cp) genomes of three diploid L. groups: (KR), broad-leaved (JB), narrow-leaved (JN). Genome sizes ranged from 152,053 bp 152,588 with GC contents 37.02-37.06%. All had typical quadripartite structures contained 129 genes. Phylogenetic analysis 48 cp revealed at least distinct Most genomic variation was found in non-coding regions, providing insights into intraspecific diversity leichtlinii.

Language: Английский

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Phylogenetic Analysis of Wild Species and the Maternal Origin of Cultivars in the Genus Lilium Using 114 Plastid Genomes

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

Published: July 22, 2022

Lilies are one of the most important ornamental flowers worldwide with approximately 100 wild species and numerous cultivars, but phylogenetic relationships among their contributions to these cultivars poorly resolved. We collected major Lilium assembled plastome sequences. Our reconstruction using 114 plastid genomes, including 70 representing all sections 42 six hybrid divisions two outgroups, uncovered well-supported genetic within . The were separated into distinct groups (groups A B) associated geographical distribution, which further diversified eight different clades that phylogenetically well supported. Additional support was provided by distributions indels single-nucleotide variants, consistent topology. Archelirion, Sinomartagon III, Leucolirion 6a 6b maternal donors for Oriental hybrids, Asiatic Trumpet Longiflorum respectively. OT hybrids originated from Archelirion 6a, LA derived study provides an basis clarifying infrageneric classification origin in

Language: Английский

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