The Gnetales: Recent insights on their morphology, reproductive biology, chromosome numbers, biogeography, and divergence times

Ickert‐Bond, Stefanie M.; Renner, Susanne S.

doi:10.1111/jse.12190

Cited by 71 publications

(72 citation statements)

References 145 publications

(234 reference statements)

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“…Prior studies using fast-evolving chloroplast genes (Magall on & Sanderson, 2002;Rydin et al, 2002) showed the same relationships that we recovered with more slowly evolving genes that were more easily aligned for the group (i.e., atpB, rbcL, and matK). In contrast, other previous studies using single or multiple genes from the chloroplast, mitochondrial, and nuclear genomes have supported Gnetales as sister to Pinaceae (Goremykin et al, 1996;Winter et al, 1999;Bowe et al, 2000;Chaw et al, 2000;Frohlich & Parker, 2000;Gugerli et al, 2001;Burleigh & Mathews, 2004;Qiu et al, 2007) or to conifers Burleigh & Mathews, 2004;Ran et al, 2010; also see review by Ickert-Bond & Renner, 2016). Recently, protein-coding sequence data from the plastid genome for 78 genes from 360 green plant taxa recovered Gnetales as sister to non-Pinaceae conifers, placing Gnetales as sister to a clade of Araucariales þ Cupressales, and the Gne-Arau-Cup clade is then sister to Pinales (Ruhfel et al, 2014).…”

Section: Discussionmentioning

confidence: 92%

Tree of life for the genera of Chinese vascular plants

Chen

Yang

et al. 2016

J of Sytematics Evolution

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We reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We produced a matrix comprising 6098 species and including 13 695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 families of Chinese vascular plants, covering more than 93% of all genera known from China. The comprehensive large phylogeny supports most relationships among and within families recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafamilial relationships of several large families and monophyly of some large genera are well supported by our dense taxonomic sampling. Our results showed that two species of Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except Sarcosperma. We have made our phylogeny of Chinese vascular plants publically available for the creation of subtrees via SoTree (http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.

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Section: Discussionmentioning

confidence: 92%

Tree of life for the genera of Chinese vascular plants

Chen

Yang

et al. 2016

J of Sytematics Evolution

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“…Extant species of Gnetum are unusual among gymnosperms in being restricted to warm, mesic habitats 41 ; this contrasts to conifers that are adapted to cold and water-stressed environments. An analysis of genes involved in water and cold stress revealed some substantial differences between conifers and Gnetum.…”

Section: Water Stressmentioning

confidence: 99%

A genome for gnetophytes and early evolution of seed plants

et al. 2018

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Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes. Comparative analysis of the G. montanum genome with other gymnosperm genomes unveiled some remarkable and distinctive genomic features, such as a diverse assemblage of retrotransposons with evidence for elevated frequencies of elimination rather than accumulation, considerable differences in intron architecture, including both length distribution and proportions of (retro) transposon elements, and distinctive patterns of proliferation of functional protein domains. Furthermore, a few gene families showed Gnetum-specific copy number expansions (for example, cellulose synthase) or contractions (for example, Late Embryogenesis Abundant protein), which could be connected with Gnetum's distinctive morphological innovations associated with their adaptation to warm, mesic environments. Overall, the G. montanum genome enables a better resolution of ancestral genomic features within seed plants, and the identification of genomic characters that distinguish Gnetum from other gymnosperms. NATuRe PLANTS ArticlesNATurE PLANTs phylogenetic position of gnetophytes, with topologies differing depending on the type of sequence data (for example, plastid versus nuclear genes, nucleotide versus amino acid data) and analytical approach used (for example, maximum parsimony, maximum likelihood, Bayesian, multispecies coalescent based methods) [6][7][8] . Consequently, several possible hypotheses have been put forward that place gnetophytes as sister to (1) Pinaceae ('Gnepine' hypothesis); (2) cupressophytes ('Gnecup' hypothesis); (3) all conifers ('Gnetifer' hypothesis); (4) all other gymnosperms; or (5) all seed plants 9 . Currently, the emerging consensus, based on both older and more recent studies, and recently released data from the 1KP initiative (see https://sites.google.com/a/ualberta.ca/onekp/, and Wickett et al. 8 ), indicates that gnetophytes are sister to, or within, the conifers.So far, the availability of whole genome sequences for gymnosperms has been limited to conifers (specifically to Pinaceae) [10][11][12][13] and G. biloba 14 , with no whole genome assemblies available for the two remaining major seed plant lineages-cycads and gnetophytes. This deficiency, together with the conflicting phylogenetic evidence for relationships among these groups, is impeding our understanding of genome evolution across all seed plants. Here, we present a high-quality draft genome of Gnetum ...

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“…Ephedra L. (Gnetales) is another arid‐adapted genus and contains about 56 species distributed evenly between the deserts of the Old and New World (Stapf, ; Ickert‐Bond, ; Ickert‐Bond & Renner, ). Phylogenetic relationships based on nrDNA and cpDNA show six Mediterranean species form a grade at the base of the phylogeny, while the remaining 50 species from a well‐supported clade.…”

Section: Relicts Of Madrean‐tethyan Elementsmentioning

confidence: 99%

Intercontinental disjunctions between eastern Asia and western North America in vascular plants highlight the biogeographic importance of the Bering land bridge from late Cretaceous to Neogene

Wen

Nie

Ickert‐Bond

2016

J of Sytematics Evolution

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193

161

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This review shows a close biogeographic connection between eastern Asia and western North America from the late Cretaceous to the late Neogene in major lineages of vascular plants (flowering plants, gymnosperms, ferns and lycophytes). Of the eastern Asian-North American disjuncts, conifers exhibit a high proportion of disjuncts between eastern Asia and western North America. Several lineages of ferns also show a recent disjunct pattern in the two areas. In flowering plants, the pattern is commonly shown in temperate elements between northeastern Asia and northwestern North America, as well as elements of the relict boreotropical and Neogene mesophytic and coniferous floras. The many cases of intercontinental biogeographic disjunctions between eastern Asia and western North America in plants supported by recent phylogenetic analyses highlight the importance of the Bering land bridge and/or the plant migrations across the Beringian region from the late Cretaceous to the late Neogene, especially during the Miocene. The Beringian region has permitted the filtering and migration of certain plant taxa since the Pliocene after the opening of the Bering Strait, as many conspecific taxa or closely related species occur on both sides of Beringia.

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The Gnetales: Recent insights on their morphology, reproductive biology, chromosome numbers, biogeography, and divergence times

Cited by 71 publications

References 145 publications

Tree of life for the genera of Chinese vascular plants

Tree of life for the genera of Chinese vascular plants

A genome for gnetophytes and early evolution of seed plants

Intercontinental disjunctions between eastern Asia and western North America in vascular plants highlight the biogeographic importance of the Bering land bridge from late Cretaceous to Neogene

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