Phylogeny and photosynthesis of the grass tribe Paniceae

Washburn, Jacob D.; Schnable, James C.; Davidse, Gerrit; Pires, J. Chris

doi:10.3732/ajb.1500222

Cited by 69 publications

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“…Chloroplast sequences show that it is closely related to the large clade (the MPC clade) that includes groups of species utilizing different C 4 photosynthesis subtypes: Melinidinae (PEPCK), Panicinae (NAD-ME), and Cenchrinae (NADP-ME) [25]. Depending on the sample of taxa and chloroplast sequences, Dichanthelium is either sister to the MPC plus the Australian species Homopholis and Walwhalleya [11] or as part of a larger clade including mostly C 3 species but also the C 4 members of the Australian Neurachninae [25]. In contrast, data from a single nuclear gene sequence place it sister to all Paniceae except Echinochloa [26].…”

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confidence: 99%

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

et al. 2016

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BackgroundComparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C3 and C4 grasses.ResultsWe report the assembly of the nuclear and chloroplast genomes of D. oligosanthes, from high-throughput short read sequencing data and a comparative transcriptomics analysis of the developing leaf of D. oligosanthes, S. viridis, and S. bicolor. Physiological and anatomical characterizations verified that D. oligosanthes utilizes the C3 pathway for carbon fixation and lacks Kranz anatomy. Expression profiles of transcription factors along developing leaves of D. oligosanthes and S. viridis were compared with previously published data from S. bicolor, Zea mays, and Oryza sativa to identify a small suite of transcription factors that likely acquired functions specifically related to C4 photosynthesis.ConclusionsThe phylogenetic location of D. oligosanthes makes it an ideal C3 plant for comparative analysis of C4 evolution in the panicoid grasses. This genome will not only provide a better C3 species for comparisons with C4 panicoid grasses, but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1080-3) contains supplementary material, which is available to authorized users.

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The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

et al. 2016

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“…2009), and modeling photosynthetic types based on their category of C 4 cycle does not improve the inference (Washburn et al. 2015). For traits assumed to evolve via sequential stages, the accepted sequence of changes can be incorporated in the model (e.g., Marazzi et al.…”

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“…2015; Washburn et al. 2015). Overall, nonhomology of key C 4 components among some closely related C 4 groups, including the cells, enzymes, and genes modified to generate the C 4 pathway (Prendergast et al.…”

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Introgression and repeated co-option facilitated the recurrent emergence of C₄photosynthesis among close relatives

et al. 2017

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The origins of novel traits are often studied using species trees and modeling phenotypes as different states of the same character, an approach that cannot always distinguish multiple origins from fewer origins followed by reversals. We address this issue by studying the origins of C4 photosynthesis, an adaptation to warm and dry conditions, in the grass Alloteropsis. We dissect the C4 trait into its components, and show two independent origins of the C4 phenotype via different anatomical modifications, and the use of distinct sets of genes. Further, inference of enzyme adaptation suggests that one of the two groups encompasses two transitions to a full C4 state from a common ancestor with an intermediate phenotype that had some C4 anatomical and biochemical components. Molecular dating of C4 genes confirms the introgression of two key C4 components between species, while the inheritance of all others matches the species tree. The number of origins consequently varies among C4 components, a scenario that could not have been inferred from analyses of the species tree alone. Our results highlight the power of studying individual components of complex traits to reconstruct trajectories toward novel adaptations.

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“…A number of studies have taken advantage of this technology, using either chloroplast protein-coding genes (e.g. Givnish et al 2015;Washburn et al 2015;Barrett et al 2016) or complete chloroplast genomes (e.g. Carbonell-Caballero et al 2015;Cotton et al 2015;Burke et al 2016;McKain et al 2016b) to resolve phylogenetic relationships from as deep as across Viridiplantae (Ruhfel et al 2014) to within a species complex (e.g.…”

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Phylogenomics of Andropogoneae (Panicoideae: Poaceae) of Mainland Southeast Asia

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Phylogeny and photosynthesis of the grass tribe Paniceae

Cited by 69 publications

References 71 publications

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

Introgression and repeated co-option facilitated the recurrent emergence of C₄photosynthesis among close relatives

Phylogenomics of Andropogoneae (Panicoideae: Poaceae) of Mainland Southeast Asia

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Phylogeny and photosynthesis of the grass tribe Paniceae

Cited by 69 publications

References 71 publications

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

Introgression and repeated co-option facilitated the recurrent emergence of C4photosynthesis among close relatives

Phylogenomics of Andropogoneae (Panicoideae: Poaceae) of Mainland Southeast Asia

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Introgression and repeated co-option facilitated the recurrent emergence of C₄photosynthesis among close relatives