Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants

Huang, Jie; Xu, Wenjing; Zhai, Jun-Wen; Hu, Yi; Guo, Jun; Zhang, Cai-Fei; Zhao, Yiyong; Zhang, Lin; Martine, Christopher T.; Ma, H.; Huang, Chien‐Hsun

doi:10.1016/j.xplc.2023.100595

Cited by 19 publications

(18 citation statements)

References 165 publications

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“…Solanaceae (asterids: Solanales; Figure 9) contains ~2,700 species with many crops and medicinal plants, with four previously recognized subfamilies and 15 tribes (Huang et al, 2023). A Solanaceae phylogenomic analysis using up to 1,699 nuclear genes from 180 species representing all four subfamilies and 14 out of 15 tribes (Huang et al, 2023) revealed three new subfamily‐level clades and suggested that Nolaneae and Solaneae were not monophyletic. The nuclear phylogenetic tree showed significant differences in the relationships among tribes and of the delimitation of subfamilies and tribes from the previous plastid analysis (Särkinen et al, 2013).…”

Section: Angiosperm Phylogenomics Using Nuclear Genesmentioning

confidence: 99%

“…Solanum is one of the largest angiosperm genera and the largest Solanaceae genus with >1,300 species. The nuclear phylogeny of Solanum was analyzed using target‐captured data sets of 39 species (Gagnon et al, 2022) or 1,699 genes from 81 species (Huang et al, 2023) with resolved relationships for many of the previously defined clades. The relationships among 29 Solanum species (potato and relatives) were also investigated using 3,971 nuclear genes obtained from genomic data sets (Tang et al, 2022).…”

Section: Angiosperm Phylogenomics Using Nuclear Genesmentioning

confidence: 99%

“…The diversification of Dipsacales began at ~107 Ma, and the divergence among subfamilies of Caprifoliaceae occurred from 95 to 60 Ma (Lee et al, 2021). The crown age of Solanaceae was estimated as 73.3 Ma, with the first and second clades of the family divergent from others before the K‐Pg boundary (Huang et al, 2023), whereas most Solanaceae tribes emerged within the Paleocene and early Eocene. In addition, the divergence time estimation using nuclear phylogenomic data sets was conducted for other families, such as Juglandaceae (Mu et al, 2020) and Theaceae (Cheng et al, 2022), and subdivisions of families, such as Maleae and Malus s.l.…”

Section: Temporal and Spatial Evolutionary Patterns And Diversificati...mentioning

confidence: 99%

“…More specifically, the floral symmetry has shifted ~200 times during angiosperm history and exhibited strong co‐evolution with the diversification of pollinators (Reyes et al, 2016); floral bilateral symmetry is associated with species‐rich lineages, such as Lamiales (~25,000 species), Asteraceae (~28,000 species), Orchidaceae (~28,000 species), and Fabaceae (~19,500 species). Fruit is the defining characteristic of angiosperms, and the divergence of fruit types was proposed to have contributed to the diversity of some large groups such as Rosaceae (~3,300 species) and Solanaceae (~2,700 species) (Xiang et al, 2017; Huang et al, 2023). In addition, important physiological traits were suggested to be crucial for some angiosperm lineages such as C4 photosynthesis and nitrogen fixation for, respectively, Poales (including Poaceae (~12,000 species) and Cyperaceae (~5,500 species)) and the nitrogen‑fixing clade (~33,500 species, including Fabales, Fagales, Rosales, and Cucurbitales) (Zhao et al, 2021; Huang et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Zhang,

2024

JIPB

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

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Section: Angiosperm Phylogenomics Using Nuclear Genesmentioning

confidence: 99%

Section: Angiosperm Phylogenomics Using Nuclear Genesmentioning

confidence: 99%

Section: Temporal and Spatial Evolutionary Patterns And Diversificati...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Zhang,

2024

JIPB

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“…To delineate the five lineages within the MADS-box gene family, we selected protein sequences from Arabidopsis thaliana and tomato as reference gene markers (Huang et al, 2023). These were the AG, AP1, AP3/PI, SEP, and SOC1/TM3 lineages.…”

Section: Ancestral Character Reconstructionmentioning

confidence: 99%

Angiosperm‐wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits

Xiang,

Zhang,

Zhao

et al. 2024

JIPB

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Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types, yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families. Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny, with resolved relationships for orders and families with previously uncertain placements. Using this phylogeny as a framework, molecular dating supports a Triassic origin of the crown angiosperms, followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution. The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types, revealing a trend of parallel carpel fusions during early diversifications in eudicots, monocots, and magnoliids. Moreover, taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits; such associations of ovary, dry and fleshy fruits define several ovary‐fruit “modules” each found in multiple families. One of the frequent modules has an ovary containing multiple ovules, capsules and berries, and another with an ovary having one or two ovules, achenes (or other single‐seeded dry fruits) and drupes. This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types, such as capsule and berry, that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules (such as achenes and drupes). Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications, supporting a possible role of whole‐genome duplications, in combination with climate changes and animal behaviors, in angiosperm fruit and ovary diversification.

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Evolutionary History and Ecology of Andrena (Foveoandrena) androfovea: A New Nearctic Mining Bee (Hymenoptera, Andrenidae) Species and Subgenus

Bossert,

Hung,

Neff

2024

Ecology and Evolution

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With about 1700 described species, the mining bee genus Andrena is a rapidly diversifying lineage and one of the most species‐rich groups of bees. Recent phylogenomic advances have greatly improved our understanding of the phylogeny of the genus, yet many species still await description, subgeneric assignments that are in line with their evolutionary history, as well as study of their morphology and behavior. Here we provide a comprehensive account of a newly discovered species, Andrena androfovea n. sp. We sequence the genome of the new species and include it in the presently most comprehensive phylogenomic analysis of Andrena using ultraconserved element (UCE) sequence data, comprising 264 samples and 249 species. Given the recovered phylogenetic position of the new species, we establish a new subgenus, Foveoandrena, provide a detailed morphological description, and discuss the antiquity and historical biogeography of the lineage in light of molecular divergence time estimates. Lastly, we study and document the foraging behavior of the new species with photos and video footage, and discuss the species' unusual host plant associations with Chamaesaracha and Quincula, both Solanaceae. Being likely oligolectic on these plants, we present the first documented case of an Andrena species being narrowly associated with members of this plant family. By integrating multiple lines of documentation, our study provides a particularly detailed account of species discovery and description.

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Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants

Cited by 19 publications

References 165 publications

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Angiosperm‐wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits

Evolutionary History and Ecology of Andrena (Foveoandrena) androfovea: A New Nearctic Mining Bee (Hymenoptera, Andrenidae) Species and Subgenus

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