Phylogeny of the Grasses (Poaceae) Revisited

Duvall, Melvin R.; Davis, Jerrold I.; Clark, Lynn G.; Noll, Jeffrey D; Goldman, Douglas H.; Sánchez-Ken, J. Gabriel

doi:10.5642/aliso.20072301.18

Cited by 62 publications

(84 citation statements)

References 23 publications

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“…The grouping of members of Centothecoideae with the monophyletic Panicoideae is consistent with previous studies (Sánchez-Ken & Clark 2001, Bouchenak-Khelladi et al 2008. We therefore prefer to use the acronym PACMAD instead of PACCMAD, following Duvall et al (2007). Micrairoideae, including Eriachneae and Isachneae, were monophyletic with strong support (100 BP, 1.00 PP), a finding consistent with previous studies (Duvall et al 2007).…”

Section: Pacmad Cladesupporting

confidence: 76%

“…We therefore prefer to use the acronym PACMAD instead of PACCMAD, following Duvall et al (2007). Micrairoideae, including Eriachneae and Isachneae, were monophyletic with strong support (100 BP, 1.00 PP), a finding consistent with previous studies (Duvall et al 2007). However, the position of Micrairoideae within the PACMAD clade was not clear.…”

Section: Pacmad Cladesupporting

confidence: 74%

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Phylogenetics of Panicoideae (Poaceae) based on chloroplast and nuclear DNA sequences

Teerawatananon¹,

Jacobs²,

Hodkinson³

2011

Telopea

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Phylogenetic relationships among major subfamilies in Poaceae and among major tribes within Panicoideae were evaluated using parsimony and Bayesian analyses of chloroplast trnL-F and atpβ-rbcL DNA sequences and a nuclear ribosomal DNA sequence, ITS1-ITS2. The PanicoideaeAristidoideae-Chloridoideae-Micrairoideae-Arundinoideae-Danthonioideae (PACMAD) clade was well resolved. A close relationship between Aristidoideae and Chloridoideae was found. The monophyly of Micrairoideae was resolved but the relationships of three tribes (Eriachneae, Isachneae, Micraireae) within Micrairoideae were unclear, only Eriachne and Isachne were monophyletic. Panicoideae sensu stricto were supported as monophyletic and sister to a clade of Danthoniopsis and Tristachya. Within Panicoideae, only a clade of Andropogoneae + Arundinella + Garnotia was supported. None of the analyses supported the monophyletic status of Paniceae. Within Paniceae, the bristle clade (excluding Cenchrus) + Alexfloydia, and the forest shade clade sensu Giussani et al. (2001), were found, but their circumscription remains ambiguous. A sister relationship between the endemic and rare Australian grasses Homopholis and Walwhalleya was also resolved. Arundinelleae were found to be polyphyletic. This study supported the separation of Arundinella and Garnotia from the remaining Arundinelleae and the inclusion of both genera in their own subtribes (Arundinellinae Honda sensu stricto and Garnotiinae Pilger) within the Andropogoneae. Arundinelleae should be abandoned as a taxonomic tribe within the Centothecoid + Panicoid clade. Within Andropogoneae, five out of a total of 11 subtribes (Chionachninae, Coicinae, Dimeriinae, Germainiinae, and Tripsacinae) were monophyletic. This was the first time that Dimeriinae and Germainiinae have been included in a molecular study. † Deceased November 26 2009. Telopea 13(1-2): 2011Teerawatananon, Jacobs and Hodkinson

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Section: Pacmad Cladesupporting

confidence: 76%

Section: Pacmad Cladesupporting

confidence: 74%

Phylogenetics of Panicoideae (Poaceae) based on chloroplast and nuclear DNA sequences

Teerawatananon¹,

Jacobs²,

Hodkinson³

2011

Telopea

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“…Subsequently Bremer (2002), using rbcL and atpB DNA sequence data, identified (Joinvilleaceae, Ecdeiocoleaceae, Poaceae) as a clade (here referred to as the JEP clade, following Hilu 2004). Bremer also concluded that Ecdeiocoleaceae is sister to Poaceae, a position which was also supported by Duvall (2003). Michaelangeli et al (2003), using morphology with atpA and rbcL DNA sequence data, similarly placed Ecdeiocoleaceae as sister to Poaceae, noting that this grouping had low jackknife support but that alternative arrangements among the JEP families had even lower values.…”

Section: Introductionmentioning

confidence: 71%

Ecdeiocoleaceae and Joinvilleaceae, sisters of Poaceae (Poales): evidence from rbcL and matK data

Marchant¹,

Briggs²

2007

Telopea

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Within Poales, the clade (Poaceae, Ecdeiocoleaceae, Joinvilleaceae) has previously received robust support from DNA sequence data from a range of genes. However, the question of which family (or set of families) is the sister group of Poaceae has not been answered with any degree of confidence, to date. Using Ecdeiocolea monostachya as the only representative of its family, other researchers have found the clade to resolve (although mostly with low levels of support) as (Joinvillea (Ecdeiocolea, Poaceae)). We now provide matK and rbcL data for Georgeantha hexandra, the sole species in the other genus of Ecdeiocoleaceae, in addition to further sampling of other closely related Poales families. Analyses of our data support the alternative topology of (Ecdeiocoleaceae, Joinvilleaceae) as sister to Poaceae and also help to resolve the position of Flagellariaceae. Flagellaria groups with (Poaceae, Ecdeiocoleaceae, Joinvilleaceae) in a graminid clade that is sister to the restiid clade (Anarthriaceae, Restionaceae, Centrolepidaceae) in analyses of matK or matK + rbcL data. A high rate of base substitution has previously been noted in Poales; branch lengths in Ecdeiocoleaceae are comparable with those in Poaceae.

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“…It comprises of many economically important cereals in the grass family, such as rice (Oryza sativa), corn (Zea mays), wheat (Triticum aestivum), and sorghum (Sorghum bicolor). An evolutionary framework has been thoroughly established at the family level based on multiple phylogenetic studies (Clark et al, 1995;GPWG, 2001;Duvall et al, 2007;BouchenakKhelladi et al, 2008;Vicentini et al, 2008;Kellogg, 2009). Poaceae has been classified into some basal lineages as well as two main lineages including the PACMAD clade (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae) and the BEP clade (Bambusoideae, Ehrhartoideae, and Pooideae) (GPWG, 2001;Duvall et al, 2007;Bouchenak-Khelladi et al, 2008;Kellogg, 2009).…”

Section: Introductionmentioning

confidence: 99%

“…An evolutionary framework has been thoroughly established at the family level based on multiple phylogenetic studies (Clark et al, 1995;GPWG, 2001;Duvall et al, 2007;BouchenakKhelladi et al, 2008;Vicentini et al, 2008;Kellogg, 2009). Poaceae has been classified into some basal lineages as well as two main lineages including the PACMAD clade (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae) and the BEP clade (Bambusoideae, Ehrhartoideae, and Pooideae) (GPWG, 2001;Duvall et al, 2007;Bouchenak-Khelladi et al, 2008;Kellogg, 2009). Nuclear and chloroplast DNA sequences have been extensively employed to determine phylogenetic relationships at both higher and lower taxonomic levels in the grass family (Doebley et al, 1990;Barker et al, 1995;Clark et al, 1995;Soreng and Davis, 1998;GPWG, 2001;Bouchenak-Khelladi et al, 2008;Kellogg, 2009).…”

Section: Introductionmentioning

confidence: 99%

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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Phylogeny of the Grasses (Poaceae) Revisited

Cited by 62 publications

References 23 publications

Phylogenetics of Panicoideae (Poaceae) based on chloroplast and nuclear DNA sequences

Phylogenetics of Panicoideae (Poaceae) based on chloroplast and nuclear DNA sequences

Ecdeiocoleaceae and Joinvilleaceae, sisters of Poaceae (Poales): evidence from rbcL and matK data

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

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