A worldwide phylogenetic classification of the Poaceae (Gramineae) II: An update and a comparison of two 2015 classifications
01 Jul 2017-Journal of Systematics and Evolution (Wiley Blackwell (Blackwell Publishing))-Vol. 55, Iss: 4, pp 259-290
TL;DR: A new worldwide phylogenetic classification of 11 506 grass species in 768 genera, 12 subfamilies, seven supert tribes, 52 tribes, five supersubtribes, and 90 subtribes is presented and a radial tree illustrating the hierarchical relationships among the subtribes, tribes, and subfam families is included.
Abstract: We present a new worldwide phylogenetic classification of 11506 grass species in 768 genera, 12 subfamilies, seven supertribes, 52 tribes, five supersubtribes, and 90 subtribes; and compare two phylogenetic classifications of the grass family published in 2015 (Soreng et al. and Kellogg). The subfamilies (in descending order based on the number of species) are Pooideae with 3968 species in 202 genera, 15 tribes, and 30 subtribes; Panicoideae with 3241 species in 247 genera, 13 tribes, and 19 subtribes; Bambusoideae with 1670 species in 125 genera, three tribes, and 15 subtribes; Chloridoideae with 1602 species in 124 genera, five tribes, and 26 subtribes; Aristidoideae with 367 species in three genera, and one tribe; Danthonioideae with 292 species in 19 genera, and one tribe; Micrairoideae with 184 species in eight genera, and three tribes; Oryzoideae with 115 species in 19 genera, four tribes, and two subtribes; Arundinoideae with 40 species in 14 genera, two tribes, and two subtribes; Pharoideae with 12 species in three genera, and one tribe; Puelioideae with 11 species in two genera, and two tribes; and the Anomochlooideae with four species in two genera, and two tribes. We also include a radial tree illustrating the hierarchical relationships among the subtribes, tribes, and subfamilies. Newly described taxa include: supertribes Melicodae and Nardodae; supersubtribes Agrostidodinae, Boutelouodinae, Gouiniodinae, Loliodinae, and Poodinae; and subtribes Echinopogoninae and Ventenatinae.
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University of Camerino1, University of Pisa2, University of Pavia3, University of Cagliari4, University of Genoa5, University of Calabria6, University of Turin7, University of Florence8, Sapienza University of Rome9, University of Palermo10, National Museum of Natural History11, University of Trieste12, University of Naples Federico II13, Seconda Università degli Studi di Napoli14, University of Perugia15
TL;DR: An updated inventory of the vascular flora alien to Italy, providing details on the occurrence at regional level, is presented in this paper, which includes 1597 species, subspecies, and hybrids, distributed in 725 genera and 152 families; 2 taxa are lycophytes, 11 ferns and fern allies, 33 gymnosperms and 1551 angiosperms.
Abstract: An updated inventory of the vascular flora alien to Italy, providing details on the occurrence at regional level, is presented. The checklist includes 1597 species, subspecies, and hybrids, distributed in 725 genera and 152 families; 2 taxa are lycophytes, 11 ferns and fern allies, 33 gymnosperms, and 1551 angiosperms. 157 taxa are archaeophytes and 1440 neophytes. The alien taxa currently established in Italy are 791 (570 naturalized and 221 invasive), while 705 taxa are casual aliens, 4 are not assessed, 7 are of unknown regional distribution, 47 have not been confirmed in recent times, 3 are considered extinct or possibly extinct in the country, and 40 are doubtfully occurring in Italy. This checklist allows to establish an up-to-date number (9792) of taxa constituting the whole (native and alien) Italian flora.
492 citations
Cites background from "A worldwide phylogenetic classifica..."
...(soreng et al. 2017); Lolium l. (ardenghi and foggi 2015; Banfi et al. 2018); Triticum l. (Perrino et al. 2014); according to Kellogg (2015) and saarela et al. (2017), Avellinia Parl., Gaudinia P.Beauv., Koeleria Pers. and Rostraria trin. should be included in Trisetaria forssk. as well as Trisetum…...
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...Veldkamp – note: for the nomenclature of this species, see soreng et al. (2017)....
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...– note: the nomenclature follows the phylogenetic classification proposed by soreng et al. (2017)....
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...Anthoxanthum nipponicum honda Anthoxanthum nitens (weber) y.schouten & Veldkamp – note: for the nomenclature of this species, see soreng et al. (2017)....
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TL;DR: Scientific Reports 5: Article number: 984610; published online: April202015; updated: October052015
Abstract: Scientific Reports 5: Article number: 984610.1038/srep09846; published online: April202015; updated: October052015
169 citations
University of Naples Federico II1, Federal University of Paraná2, San Juan de Dios Educational Foundation3, University of Salerno4, University of Helsinki5, University of Córdoba (Spain)6, Nippon Medical School7, Charité8, University of Parma9, Universidad Autónoma de Nuevo León10, University of Paris11
TL;DR: Studies showed that plants exhibit enhanced photosynthesis and reproductive effects and produce more pollen as a response to high atmospheric levels of carbon dioxide (CO2) and Mold proliferation is increased by floods and rainy storms are responsible for severe asthma.
Abstract: The impact of climate change on the environment, biosphere, and biodiversity has become more evident in the recent years Human activities have increased atmospheric concentrations of carbon dioxide (CO2 ) and other greenhouse gases Change in climate and the correlated global warming affects the quantity, intensity, and frequency of precipitation type as well as the frequency of extreme events such as heat waves, droughts, thunderstorms, floods, and hurricanes Respiratory health can be particularly affected by climate change, which contributes to the development of allergic respiratory diseases and asthma Pollen and mold allergens are able to trigger the release of pro-inflammatory and immunomodulatory mediators that accelerate the onset the IgE-mediated sensitization and of allergy Allergy to pollen and pollen season at its beginning, in duration and intensity are altered by climate change Studies showed that plants exhibit enhanced photosynthesis and reproductive effects and produce more pollen as a response to high atmospheric levels of carbon dioxide (CO2 ) Mold proliferation is increased by floods and rainy storms are responsible for severe asthma Pollen and mold allergy is generally used to evaluate the interrelation between air pollution and allergic respiratory diseases, such as rhinitis and asthma Thunderstorms during pollen seasons can cause exacerbation of respiratory allergy and asthma in patients with hay fever A similar phenomenon is observed for molds Measures to reduce greenhouse gas emissions can have positive health benefits
142 citations
TL;DR: resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.
Abstract: The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 287 Mbases of sequence data Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP) Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees Analyses of newly sequenced plastomes were in agreement with current classifications Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies Alternative topologies were recovered in trees from partitions that included alignment gaps This suggests that ambiguities in aligning these uncertain regions might introduce a false signal Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 999% of grass diversity
127 citations
Cites background or result from "A worldwide phylogenetic classifica..."
...Subtribe Boivinellinae includes 18–19 genera (Silva et al., 2017; Soreng et al., 2017)....
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...Subtribe Cenchrinae includes some 24 genera (Soreng et al., 2017) and most aspects of its phylogeny are poorly resolved (Kellogg et al., 2009; Chemisquy et al., 2010; Morrone et al., 2012)....
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...In recent classifications, Streptogyna has been treated as incertae sedis among grasses (Grass Phylogeny Working Group, 2001), as incertae sedis within the BOP clade (Kellogg, 2015) and as a tribe of Oryzoideae (Soreng et al., 2015b, 2017)....
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...…on molecular phylogenetic evidence recognized 12 subfamilies, six supertribes, 52 tribes and 90 subtribes of grasses, with 21 genera unplaced to tribe and 39 unplaced to subtribe (Soreng et al., 2017); this is an update of a classification proposed two years earlier by Soreng et al. (2015b)....
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...…Gouiniodinae comprising subtribes Cteniinae, Farragininae, Gouiniinae, Hubbardochloinae, Perotidinae, Trichoneurinae and Zaqiqahinae, of which only Trichoneurinae is sampled here (Peterson, Romaschenko & Arrieta, 2015; Peterson, Romaschenko & Herrera Arrieta, 2016; Soreng et al., 2017)....
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TL;DR: Two new AVR genes are identified and characterized and it is demonstrated that Pm3 receptors are determinants of host-specificity for grass mildews, demonstrating their involvement in host specificity.
Abstract: The wheat Pm3 resistance gene against the powdery mildew pathogen occurs as an allelic series encoding functionally different immune receptors which induce resistance upon recognition of isolate-specific avirulence (AVR) effectors from the pathogen. Here, we describe the identification of five effector proteins from the mildew pathogens of wheat, rye, and the wild grass Dactylis glomerata, specifically recognized by the PM3B, PM3C and PM3D receptors. Together with the earlier identified AVRPM3A2/F2, the recognized AVRs of PM3B/C, (AVRPM3B2/C2), and PM3D (AVRPM3D3) belong to a large group of proteins with low sequence homology but predicted structural similarities. AvrPm3b2/c2 and AvrPm3d3 are conserved in all tested isolates of wheat and rye mildew, and non-host infection assays demonstrate that Pm3b, Pm3c, and Pm3d are also restricting the growth of rye mildew on wheat. Furthermore, divergent AVR homologues from non-adapted rye and Dactylis mildews are recognized by PM3B, PM3C, or PM3D, demonstrating their involvement in host specificity. The wheat Pm3 immune receptors confer resistance against powdery mildew by recognizing isolate-specific avirulence (AVR) effectors of the pathogen. Here, the authors identify and characterize two new AVR genes and demonstrate that Pm3 receptors are determinants of host-specificity for grass mildews.
91 citations
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"A worldwide phylogenetic classifica..." refers background in this paper
...Table 1 A worldwide phylogenetic classification of the family Poaceae Barnhart [1895] (nom. alt.: Gramineae Juss. [1789])....
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...Table 1 A worldwide phylogenetic classification of the family Poaceae Barnhart [1895] (nom....
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...951; Zwickl, 2006) on a large dataset of 448 grass species using matK and ndhF plastid DNA markers (available upon request). DNA sequences were primarily gathered from GenBank with secondary sources taken from Hilu & Alice (2001), Davis & Soreng (2007), Romaschenko et al. (2008, 2012), Davis & Soreng (2010), GPWG II (2012), Morrone et al....
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...951; Zwickl, 2006) on a large dataset of 448 grass species using matK and ndhF plastid DNA markers (available upon request). DNA sequences were primarily gathered from GenBank with secondary sources taken from Hilu & Alice (2001), Davis & Soreng (2007), Romaschenko et al....
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...As already indicated by Clayton (1981), those proposed by Link (1827) are especially problematical....
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TL;DR: The entire chloroplast genome of the monocot rice (Oryza sativa) has been sequenced and comprises 134525 bp and a model invoking illegitimate recombination between tRNA genes is proposed which accounts simultaneously for the origin of this pseudogene, the large inversion and the creation of repeated sequences near the inversion endpoints.
Abstract: The entire chloroplast genome of the monocot rice (Oryza sativa) has been sequenced and comprises 134525 bp. Predicted genes have been identified along with open reading frames (ORFs) conserved between rice and the previously sequenced chloroplast genomes, a dicot, tobacco (Nicotiana tabacum), and a liverwort (Marchantia polymorpha). The same complement of 30 tRNA and 4 rRNA genes has been conserved between rice and tobacco. Most ORFs extensively conserved betweenN. tabacum andM. polymorpha are also conserved intact in rice. However, several such ORFs are entirely absent in rice, or present only in severely truncated form. Structural changes are also apparent in the genome relative to tobacco. The inverted repeats, characteristic of chloroplast genome structure, have expanded outward to include several genes present only once per genome in tobacco and liverwort and the large single copy region has undergone a series of inversions which predate the divergence of the cereals. A chimeric tRNA pseudogene overlaps an apparent endpoint of the largest inversion, and a model invoking illegitimate recombination between tRNA genes is proposed which accounts simultaneously for the origin of this pseudogene, the large inversion and the creation of repeated sequences near the inversion endpoints.
1,088 citations
"A worldwide phylogenetic classifica..." refers background in this paper
...The rice plastid genome was the first to be completely sequenced in the monocots (Hiratsuka et al., 1989)....
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...The classification largely follows BPG (2012). Tribe Arundinarieae with only the subtribe Arundinariinae contains 621 species in 31 genera that are almost exclusively distributed in Eurasia; only the three species of Arundinaria Michx....
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TL;DR: A large collaborative effort has yiel(led a comprehensive study of the phylogeny and a new suhfanilial classification of the grass family (Poaceae/Graminieae) and 1 new subfamily (Danthonioideae) is proposed.
Abstract: A large collaborative effort has yiel(led a comprehensive study of the phylogeny and a new suhfanilial classification of the grass family (Poaceae/Graminieae). The stu(ly was (con(luc(ted on an integratedl andl representative set of 62 grasses (0.6% of the species and ca. 8% of the genera) plus four outgroup taxa using six molecular sequence (lata sets ({ndhFl, rbcL, rpoC2, phyB, ITS2, and (;BSSI or waxy), chloroplast restriction site (lata, and( morphological idata. A parsimony analysis using 2143 informative characters (the comblined analysis) resulted in a single most parsimonious tree of 8752 steps with an RI of 0.556 and bootstrap support of > 90% for more than half of the internal no(les. Significant relationships that appear consistently in all analyses of all (lata sets and are strongly supported by the combined analysis include the following: Joinvilleaceae are sister to a monophyletic Poaceae; the earliest (liverging lineages of the Poaceae are Anomochlooideae, Pharoideae, and Puelioideae, respectively; and( all remaining grasses form a clade. Multiple monophyletic clades were recovere(, including Bambusoideae s. str., Ehrhartoideae, Pooideae s.l., Aristidoideae, l)anthonioideae, Chloridoideae s. str., Chloridoideae s.l., Panicoideae, Parianeae, Olyreae s. str., Oryzeae, Stipeae, Meliceae, Lygeum + Nardus, and Molinia + Phragmites. 'The PACCAI) Clade is monophyletic, containing Aristidoideae, Danthonioideae, Arundinoideae s. str., Chloridoideae s.l., Centothecoideae, Panicoideae, Eriachne, Micraira, and Gynerium. Based on the phylogeny, a classification of 11 previously published subfamilies (Anomochlooideae, Pharoideae, Puelioideae, Bambusoideae, Ehrhartoideae, Pooideae, Aristidoideae, Arundinoideae, Chloridoideae, Centothecoideae, and Panicoideae) and 1 new subfamily (Danthonioideae) is proposed. Several changes in the circumscription of traditionally recognized subfamilies are included. Previous phylogenetic work and classifications are reviewed in relation to this classification and circumscription, and major characteristics of each subfamily are discussed and described. The matrix, trees, and updated data matrix are available at (http://www.virtualherbarium.org/grass/gpwg/ default.htm).
725 citations