Genome skimming provides new insight into the relationships in <i>Ludwigia</i> section <i>Macrocarpon</i>, a polyploid complex

Liu, Shih-Hui; Edwards, Christine E.; Hoch, Peter C.; Raven, Peter H.; Barber, Janet C.

doi:10.1002/ajb2.1086

Cited by 8 publications

(8 citation statements)

References 87 publications

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“…Glycine (Doyle et al, 2004), two extinct diploids closely related to Hordeum murinum (Jakob & Blattner, 2010), and at least two extinct diploids in Ludwigia sect. Macrocarpon (Liu et al, 2018). The extinction of the diploid progenitors in the Microcarpium complex might be associated with climate cooling in the Tertiary, which drove extinctions in many other north-temperate plant lineages (Tiffney, 1985;Tiffney & Manchester, 2001;Wen et al, 2016).…”

Section: Evolutionmentioning

confidence: 99%

Disentangling Reticulate Evolution of North Temperate Haplostemonous Ludwigia (Onagraceae)

Liu

Yang

Kono

et al. 2020

annals

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While it is known that whole genome duplication (WGD) and reticulate evolution play important roles in plant evolution, the origins and evolutionary histories of most polyploid and reticulate groups are still poorly known. The North Temperate haplostemonous (NTH) Ludwigia L. (sections Isnardia (L.) W. L. Wagner & Hoch, Ludwigia, Microcarpium Munz, and Miquelia P. H. Raven) group, characterized by having 4-merous and haplostemonous flowers, pluriseriate and free seeds, glabrous and convex nectaries, and a north-temperate distribution, is a polyploid complex (2×, 4×, 6×, and 8×) of 24 species with frequent reports of inter- and intrasectional hybridization. Although earlier biosystematics studies postulated some evolutionary scenarios and recent molecular phylogenetic studies have partially tested these propositions, the full history of their reticulate evolution remains puzzling. In this study, we sequenced four chloroplast regions (rpL16, rpoB-trnC, trnL-trnF, and ycf6-psbM) and conducted extensive molecular cloning of the biparentally inherited single-copy nuclear PgiC gene (376 clones in total), sampling 23 of the 24 NTH Ludwigia species whose chromosome numbers and ploidy levels were confirmed. Both the chloroplast and PgiC trees include strongly supported sister clades of section Ludwigia (four diploid species) and the “Microcarpium complex” (composed of sections Isnardia, Microcarpium, and Miquelia), which together are sister to the rest of Ludwigia. In the PgiC tree, eight clades are identified within the Microcarpium complex, with four clades including no extant diploid species. Neither sections Isnardia nor Microcarpium are monophyletic, while the monospecific section Miquelia has a hybrid origin. By integrating our phylogenetic trees with previous cytological hypotheses, the reticulate evolution of NTH Ludwigia is disentangled and four to eight extinct diploid species are inferred. Ancestral area reconstruction supports a North American origin of L. ovalis whose current East Asian distribution reflects a relict of the Arcto-Tertiary Geoflora. Based on our results, we propose to synonymize sections Microcarpium and Miquelia under the expanded section Isnardia.

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Section: Evolutionmentioning

confidence: 99%

Disentangling Reticulate Evolution of North Temperate Haplostemonous Ludwigia (Onagraceae)

Liu

Yang

Kono

et al. 2020

annals

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“…Recent studies that did such comparisons include determining the origin of wild octoploid species [49], the placement of the Celastrales-Oxalidales-Malpighiales (COM) clade within Rosidae [50], and the origin and evolution of species in Ludwigia sect. Macrocarpon of Onagraceae [51].…”

Section: Introductionmentioning

confidence: 99%

Resolving the Phylogeny of the Olive Family (Oleaceae): Confronting Information from Organellar and Nuclear Genomes

Dupin

Raimondeau

Hong‐Wa

et al. 2020

Genes

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The olive family, Oleaceae, is a group of woody plants comprising 28 genera and ca. 700 species, distributed on all continents (except Antarctica) in both temperate and tropical environments. It includes several genera of major economic and ecological importance such as olives, ash trees, jasmines, forsythias, osmanthuses, privets and lilacs. The natural history of the group is not completely understood yet, but its diversification seems to be associated with polyploidisation events and the evolution of various reproductive and dispersal strategies. In addition, some taxonomical issues still need to be resolved, particularly in the paleopolyploid tribe Oleeae. Reconstructing a robust phylogenetic hypothesis is thus an important step toward a better comprehension of Oleaceae’s diversity. Here, we reconstructed phylogenies of the olive family using 80 plastid coding sequences, 37 mitochondrial genes, the complete nuclear ribosomal cluster and a small multigene family encoding phytochromes (phyB and phyE) of 61 representative species. Tribes and subtribes were strongly supported by all phylogenetic reconstructions, while a few Oleeae genera are still polyphyletic (Chionanthus, Olea, Osmanthus, Nestegis) or paraphyletic (Schrebera, Syringa). Some phylogenetic relationships among tribes remain poorly resolved with conflicts between topologies reconstructed from different genomic regions. The use of nuclear data remains an important challenge especially in a group with ploidy changes (both paleo- and neo-polyploids). This work provides new genomic datasets that will assist the study of the biogeography and taxonomy of the whole Oleaceae.

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“…In addition, comparative analyses of the chloroplast genome and nrDNA may help reveal evidence of hybridization, which may be common in Rosaceae (Robertson et al, ). Genome skimming has been successfully applied to reconstruct the phylogenetic history of various plant lineages (Dillenberger et al, ; Liu et al, ; Mabry & Simpson, ; Thomson et al, ; Wen et al, ).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic analyses of thePhotiniacomplex support the recognition of a new genusPhippsiomelesand the resurrection of a redefinedStranvaesiain Maleae (Rosaceae)

Liu

De‐Yuan

Zhou

et al. 2019

J of Sytematics Evolution

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Photinia and its morphologically similar allies in Maleae (Rosaceae) consist of five currently recognized genera: Aronia, Heteromeles, Photinia, Pourthiaea, and Stranvaesia, and 68 species, distributed in Asia and North and Central America. Despite previous efforts to clarify relationships in this group, the generic delimitations have remained uncertain. Our goals were to reconstruct a robust phylogeny of Photinia and its close allies to test the monophyly of the currently recognized genera, especially Photinia and Stranvaesia, and the hybrid origin hypothesis of Photinia bodinieri. This study employs complete plastomes and the entire nuclear ribosomal DNA (nrDNA) repeats assembled from the genome skimming approach with a broad taxon sampling of 81 species in 30 genera of Rosaceae, especially Maleae. Based on three datasets, including the whole plastome, coding sequence, and nrDNA repeats, the results of maximum likelihood and Bayesian inference analyses showed that the previously circumscribed Stranvaesia and Photinia were each non‐monophyletic. Six clades have been recovered herein within Photinia and its allied genera: Aronia, Heteromeles, Photinia s.s., Pourthiaea, Stranvaesia, and a new genus Phippsiomeles consisting of the Central American species formerly placed in Photinia. The strong conflicts between the plastome and nrDNA phylogenies of Phippsiomeles and Stranvaesia tomentosa suggest the possibility that they may have each originated involving hybridization events, while no incongruence among datasets was detected to support the hybrid origin of Photinia bodinieri. We provide 12 new combinations, to transfer eight taxa of the New World Photinia into Phippsiomeles and clarify the generic placements of several species of Photinia and Stranvaesia.

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Genome skimming provides new insight into the relationships in Ludwigia section Macrocarpon, a polyploid complex

Abstract: Genome skimming provided important insights into the complex evolutionary relationships within sect. Macrocarpon, but additional sampling and data from single-copy nuclear regions are necessary to further elucidate the origins of the polyploids in this section.

Cited by 8 publications

References 87 publications

Disentangling Reticulate Evolution of North Temperate Haplostemonous Ludwigia (Onagraceae)

Disentangling Reticulate Evolution of North Temperate Haplostemonous Ludwigia (Onagraceae)

Resolving the Phylogeny of the Olive Family (Oleaceae): Confronting Information from Organellar and Nuclear Genomes

Phylogenomic analyses of thePhotiniacomplex support the recognition of a new genusPhippsiomelesand the resurrection of a redefinedStranvaesiain Maleae (Rosaceae)

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