The genomes of seven economic Caesalpinioideae trees provide insights into polyploidization history and secondary metabolite biosynthesis DOI Creative Commons
Rong Chen, Sihan Meng, Anqi Wang

et al.

Plant Communications, Journal Year: 2024, Volume and Issue: 5(9), P. 100944 - 100944

Published: May 10, 2024

The Caesalpinioideae subfamily contains many well-known trees that are important for economic sustainability and human health, but a lack of genomic resources has hindered their breeding utilization. Here, we present chromosome-level reference genomes the two food industrial Gleditsia sinensis (921 Mb) Biancaea sappan (872 Mb), three shade ornamental Albizia julibrissin (705 Delonix regia (580 Acacia confusa (566 pioneer hedgerow Leucaena leucocephala (1338 Mimosa bimucronata (641 Mb). Phylogenetic inference shows mimosoid clade much higher evolutionary rate than other clades Caesalpinioideae. Macrosynteny comparison suggests fusion breakage an unstable chromosome responsible difference in basic number (13 or 14) After ancient whole-genome duplication (WGD) shared by all species (CWGD, ∼72.0 million years ago [MYA]), there were recent successive WGD events, LWGD-1 (16.2-19.5 MYA) LWGD-2 (7.1-9.5 MYA), L. leucocephala. Thereafter, ∼40% gene loss genome-size contraction have occurred during diploidization process To investigate secondary metabolites, identified copies involved mimosine metabolism these found abundance biosynthesis genes largely explains its high production. We also set potential triterpenoid saponin G. sinensis, which is more complete based on previous transcriptome-derived unigenes. Our results will facilitate biological studies promote utilization valuable metabolites.

Language: Английский

Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae DOI Creative Commons
Yiyong Zhao, Rong Zhang,

Kai-Wen Jiang

et al.

Molecular Plant, Journal Year: 2021, Volume and Issue: 14(5), P. 748 - 773

Published: Feb. 23, 2021

Language: Английский

Citations

171

Disintegration of the genus Prosopis L. (Leguminosae, Caesalpinioideae, mimosoid clade) DOI Creative Commons
Colin E. Hughes, Jens J. Ringelberg, Gwilym P. Lewis

et al.

PhytoKeys, Journal Year: 2022, Volume and Issue: 205, P. 147 - 189

Published: Aug. 22, 2022

Robust evidence from phylogenomic analyses of 997 nuclear genes has recently shown, beyond doubt, that the genus

Language: Английский

Citations

73

Precipitation is the main axis of tropical plant phylogenetic turnover across space and time DOI Creative Commons
Jens J. Ringelberg, Erik J. M. Koenen,

Benjamin Sauter

et al.

Science Advances, Journal Year: 2023, Volume and Issue: 9(7)

Published: Feb. 17, 2023

Early natural historians—Comte de Buffon, von Humboldt, and De Candolle—established environment geography as two principal axes determining the distribution of groups organisms, laying foundations for biogeography over subsequent 200 years, yet relative importance these remains unresolved. Leveraging phylogenomic global species data Mimosoid legumes, a pantropical plant clade c. 3500 species, we show that water availability gradient from deserts to rain forests dictates turnover lineages within continents across tropics. We demonstrate 95% speciation occurs precipitation niche, showing profound phylogenetic niche conservatism, lineage boundaries coincide with isohyets precipitation. reveal similar patterns on different continents, implying evolution dispersal follow universal processes.

Language: Английский

Citations

50

Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification DOI Creative Commons
Anne Bruneau, Luciano Paganucci de Queiroz, Jens J. Ringelberg

et al.

PhytoKeys, Journal Year: 2024, Volume and Issue: 240, P. 1 - 552

Published: April 3, 2024

Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It an ecologically economically important group formed mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas shrubs, which has a global distribution, occurring on every continent except Antarctica. Following recent re-circumscription 15 genera as presented in Advances Legume Systematics 14, Part 1, using basis phylogenomic analysis 997 nuclear gene sequences for 420 all but five currently recognised subfamily, we present new higher-level classification subfamily. The comprises eleven tribes, are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 / 223 species), Campsiandreae LPWG (2 5–22), Cassieae Bronn (7 695), Ceratonieae (4 6), Dimorphandreae Benth. 35), Erythrophleeae /13), Gleditsieae Nakai (3 20), Mimoseae (100 3510), Pterogyneae (1 1), Schizolobieae (8 42–43), Sclerolobieae & Hook. f. (5 113). Although many these lineages have been named past, tribes informal generic groups, their circumscriptions varied widely changed over past decades, such described here differ membership those previously recognised. Importantly, approximately 3500 100 former Mimosoideae now placed reinstated, newly circumscribed, tribe Mimoseae. Because size ecological importance tribe, also provide clade-based system includes 17 lower-level clades. Fourteen remain unplaced clades: eight resolved two grades six phylogenetically isolated monogeneric lineages. In addition classification, key genera, morphological descriptions notes diversity growth forms, foliage, flowers fruits illustrated each genus distribution map, based quality-controlled herbarium specimen localities. A glossary specialised terms used legume morphology provided. This provides solid communication framework downstream analyses biogeography, trait evolution diversification, well taxonomic revision still understudied

Language: Английский

Citations

28

Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics DOI Creative Commons
In‐Su Choi, Domingos Cardoso, Luciano Paganucci de Queiroz

et al.

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

Published: Feb. 23, 2022

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one most extraordinarily diverse clades among angiosperms. Papilionoids are a major source food forage, ecologically successful in all biomes, display dramatic variation both floral architecture plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding relationships groups Papilionoideae, yet backbone phylogeny remains unresolved. In this study, we sequenced assembled 39 new plastomes that covering key representing morphological diversity subfamily. From 244 total taxa, produced eight datasets for maximum likelihood (ML) based on entire and/or concatenated sequences 77 protein-coding (CDS) two multispecies coalescent (MSC) individual gene trees. We additionally combined nucleotide dataset comprising CDS plus matK only, which papilionoid were sampled. A ML tree plastome maximally supported deep recent divergences papilionoids (223 out 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, Amburaneae), Cladrastis, Andira, Exostyleae formed grade to remainder concordant with nine MSC Phylogenetic remaining five lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because insufficient support conflicting Our study fully resolved nodes however, some require further exploration. More genome-scale data rigorous needed disentangle lineages.

Language: Английский

Citations

58

Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae) DOI Creative Commons
Jens J. Ringelberg, Erik J. M. Koenen, João Ricardo Vieira Iganci

et al.

PhytoKeys, Journal Year: 2022, Volume and Issue: 205, P. 3 - 58

Published: Aug. 22, 2022

Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically economically important group trees, shrubs lianas a pantropical distribution. Despite major advances last few decades towards aligning clades across Caesalpinioideae, generic delimitation remains state considerable flux, especially mimosoid clade. We test monophyly via phylogenomic analysis 997 nuclear genes sequenced targeted enrichment (Hybseq) for 420 147 currently recognised subfamily. show that 22 are non-monophyletic or nested other non-monophyly concentrated clade where 25% 90 found to be non-monophyletic. suggest two main reasons this pervasive non-monophyly: (i) extensive morphological homoplasy we document here handful traits and, particularly, repeated evolution distinctive fruit types were historically emphasised delimiting (ii) artefact lack taxonomic syntheses sampling previous phylogenies consequent failure identify span Old World New conversely amphi-Atlantic non-monophyletic, both which critical large Finally, discuss taxon era how assessing patterns gene tree conflict can provide additional insights into delimitation. This new framework provides foundations series papers reclassifying presented

Language: Английский

Citations

57

The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes DOI
Sérgio Miana de Faria, Jens J. Ringelberg, Eduardo Gross

et al.

New Phytologist, Journal Year: 2022, Volume and Issue: 235(6), P. 2365 - 2377

Published: July 28, 2022

Nitrogen-fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains focus considerable debate. Recent evidence suggesting a single origin followed by massive parallel losses raises questions about why few lineages N

Language: Английский

Citations

51

Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia DOI
Todd G. B. McLay, Rachael M. Fowler, Patrick S. Fahey

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 187, P. 107869 - 107869

Published: July 8, 2023

Language: Английский

Citations

23

Morphological trait evolution in Solanum (Solanaceae): Evolutionary lability of key taxonomic characters DOI Creative Commons
Rebecca Hilgenhof, Edeline Gagnon, Sandra Knapp

et al.

Taxon, Journal Year: 2023, Volume and Issue: 72(4), P. 811 - 847

Published: July 4, 2023

Abstract Solanum is one of the world's largest and economically most important plant genera, including 1245 currently accepted species several major minor crops (e.g., tomato, potato, brinjal eggplant, scarlet Gboma lulo, pepino). Here we provide an overview evolution 25 key morphological traits for clades this giant genus based on stochastic mapping using a well‐sampled recently published phylogeny . The evolutionarily labile (showing >100 transitions across genus) relate to structure (growth form sympodial unit structure), herbivore defence (glandular trichomes), pollination (corolla shape colour), dispersal (fruit colour). Ten further show evolutionary lability with 50–100 specialised underground organs, trichome structure, leaf type, inflorescence position branching, stamen heteromorphism). Our results reveal number highly convergent in , tubers, rhizomes, simple leaves, yellow corollas, heteromorphic anthers, dioecy, dry fruits, some unexpected pathways trait that could be explored future studies. We informally named can morphologically defined by combinations providing tool identification enabling predictive phylogenetic placement unsampled species.

Language: Английский

Citations

18

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution DOI Creative Commons
Guojin Zhang, Hong Mā

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(3), P. 546 - 578

Published: Jan. 30, 2024

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of angiosperms in fossil record was referred to Darwin as "abominable mystery," hence contributing heightened interest angiosperm evolution. display wide ranges morphological, physiological, and ecological characters, some which have probably influenced their species richness. evolutionary analyses these characteristics help address questions diversification require well resolved phylogeny. Following great successes phylogenetic using plastid sequences, dozens thousands nuclear genes from next-generation sequencing been used phylogenomic analyses, providing phylogenies new insights into evolution angiosperms. In this review we focus on recent large clades, orders, families, subdivisions families provide a summarized Nuclear Phylogenetic Tree Angiosperm Families. newly established relationships highlighted compared previous results. sequenced genomes Amborella, Nymphaea, Chloranthus, Ceratophyllum, monocots, Magnoliids, basal eudicots, facilitated phylogenomics among five major clades. All but one 64 orders were included except placements several orders. Most robust highly supported placements, especially for within important families. Additionally, examine divergence time estimation biogeographic basis frameworks discuss differences analyses. Furthermore, implications ancestral reconstruction characters groups, limitations current studies, taxa that future attention.

Language: Английский

Citations

8