Phylogeny and biogeography of the rice tribe (Oryzeae): Evidence from combined analysis of 20 chloroplast fragments

Tang, Liang; Zou, Xinhui; Achoundong, Gaston; Potgieter, C.J.; Second, Gérard; Zhang, Dayong; Ge, Song

doi:10.1016/j.ympev.2009.08.007

Cited by 90 publications

(124 citation statements)

References 79 publications

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“…PATHd8 smooths substitution rates across branches to transform a tree with branch lengths measured as substitutions per site to an ultrametric tree with relative node ages. To convert the relative ages to absolute ages, the age of the crown group of Oryza (the root of the pruned tree) was fixed using a calibration consistent with several recent studies 14,111,112 (15 million years).…”

Section: Methodsmentioning

confidence: 99%

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

et al. 2018

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Section: Methodsmentioning

confidence: 99%

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

et al. 2018

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“…Previous phylogenetic studies supported the placement of Zizania in Oryzeae (Zhang and Second, 1989;Duvall et al, 1993;Ge et al, 2002;Guo and Ge, 2005;Tang et al, 2010). Zizania is most closely related to the South American genus Rhynchoryza Baill.…”

Section: Introductionmentioning

confidence: 75%

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Gao

Zhang

et al. 2016

Front. Ecol. Evol.

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Zizania latifolia (Griseb.) Turcz. ex Stapf was once utilized as an important grain in ancient China and has been cultivated as an aquatic vegetable. Here, we report the complete Z. latifolia chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads generated by directly purified chloroplast (cp) DNA genome sequencing. The Z. latifolia cp genome is 136,501 bp in length, comprising a pair of 20,878-bp inverted repeat regions (IR) separated by small and large single copy regions (SSC and LSC) of 12,590 and 82,155 bp, respectively. The Z. latifolia cp genome encodes 110 unique genes (77 protein-coding genes, 29 tRNA genes, and 4 rRNA genes), of which 15 encompass introns. Sequence analysis identified a total of 39 direct/inverted repeats and 63 simple sequence repeats (SSR) with an average rate of 0.46 SSRs/kb. Our results revealed that the Z. latifolia cp genome is AT-rich (61.02%) and gene codon usage may be largely affected by a low GC content and codon usage bias for A, T-ending codons. We predicted 33 RNA editing sites in the chloroplast of Z. latifolia, all for C-to-U transitions. Comparative analyses with other available Oryzeae plastid genomes showed that the coding and IR sequences were more conserved than the single-copy and non-coding regions, suggesting that the indels should be cautiously employed in phylogenetic studies. Phylogenetic analysis of 52 complete grass chloroplast genomes including the reported Z. latifolia cp genome in this study yielded an identical tree topology as previous plastid-based trees, providing strong support for a sister relationship between Bambusoideae+Pooideae and Ehrhartoideae in the BEP (Bambusoideae, Ehrhartoideae, Pooideae) clade of the grass family.

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“…Divergence times for Poaceae lineages are then estimated using seven previously published fossils and our new fossils, and this framework is employed to investigate the evolutionary history of seven leaf epidermis and phytolith morphology characters. These characters were also scored for 14 taxa formerly used in phylogenetic analysis of the Ehrhartoideae 10 . Our analysis reveals that Changii indicum and Tateokai deccana most likely were members of the Oryzeae, and that diversification of the rice tribe began before the end of the Cretaceous.…”

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Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae

Prasad¹,

et al. 2011

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Rice and its relatives are a focal point in agricultural and evolutionary science, but a paucity of fossils has obscured their deep-time history. Previously described cuticles with silica bodies (phytoliths) from the Late Cretaceous period (67-65 ma) of India indicate that, by the latest Cretaceous, the grass family (Poaceae) consisted of members of the modern subclades PACmAD (Panicoideae-Aristidoideae-Chloridoideae-micrairoideae-ArundinoideaeDanthonioideae) and BEP (Bambusoideae-Ehrhartoideae-Pooideae), including a taxon with proposed affinities to Ehrhartoideae. Here we describe additional fossils and show that, based on phylogenetic analyses that combine molecular genetic data and epidermal and phytolith features across Poaceae, these can be assigned to the rice tribe, oryzeae, of grass subfamily Ehrhartoideae. The new oryzeae fossils suggest substantial diversification within Ehrhartoideae by the Late Cretaceous, pushing back the time of origin of Poaceae as a whole. These results, therefore, necessitate a re-evaluation of current models for grass evolution and palaeobiogeography.

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Phylogeny and biogeography of the rice tribe (Oryzeae): Evidence from combined analysis of 20 chloroplast fragments

Cited by 90 publications

References 79 publications

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae

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