Phylogenetic relationships in Leymus (Triticeae; Poaceae): Evidence from chloroplast trnH‐psbA and mitochondrial coxII intron sequences

Li, Sha; Fan, Xing; Zhang, Haiqin; Kang, Houyang; Wang, Yi; Wang, Xiaoli; Zhang, Li; Ding, Chunbang; Yang, Ruiwu; Zhou, Yong‐Hong

doi:10.1111/jse.12097

Cited by 14 publications

(25 citation statements)

References 62 publications

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“…Triticinae is derived from within Hordeinae s.l, but no new infratribal classification has been offered (Seberg & Petersen, 2007). The tribe is well known for reticulate evolution and the classification of genera is largely based on genome types and pairings (Barkworth et al, ; Anamthawat‐Jonsson, ; Sha et al, ; Sun ; Wang & Lu, 2014; Zhang et al, ).…”

Section: Discussionmentioning

confidence: 99%

A worldwide phylogenetic classification of the Poaceae (Gramineae)

Soreng

Peterson

Romaschenko

et al. 2015

J of Sytematics Evolution

539

688

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Based on recent molecular and morphological studies we present a modern worldwide phylogenetic classification of the AE 12074 grasses and place the 771 grass genera into 12 subfamilies (Anomochlooideae, Aristidoideae, Arundinoideae, Bambusoideae, Chloridoideae, Danthonioideae, Micraioideae, Oryzoideae, Panicoideae, Pharoideae, Puelioideae, and Pooideae), 6 supertribes (Andropogonodae, Arundinarodae, Bambusodae, Panicodae, Poodae, Triticodae), 51 tribes (Ampelodesmeae, Andropogoneae, Anomochloeae, Aristideae, Arundinarieae, Arundineae, Arundinelleae, Atractocarpeae, Bambuseae, Brachyelytreae, Brachypodieae, Bromeae, Brylkinieae, Centotheceae, Centropodieae, Chasmanthieae, Cynodonteae, Cyperochloeae, Danthonieae, Diarrheneae, Ehrharteae, Eragrostideae, Eriachneae, Guaduellieae, Gynerieae, Hubbardieae, Isachneae, Littledaleeae, Lygeeae, Meliceae, Micraireae, Molinieae, Nardeae, Olyreae, Oryzeae, Paniceae, Paspaleae, Phaenospermateae, Phareae, Phyllorachideae, Poeae, Steyermarkochloeae, Stipeae, Streptochaeteae, Streptogyneae, Thysanolaeneae, Triraphideae, Tristachyideae, Triticeae, Zeugiteae, and Zoysieae), and 80 subtribes (Aeluropodinae, Agrostidinae, Airinae, Ammochloinae, Andropogoninae, Anthephorinae, Anthistiriinae, Anthoxanthinae, Arthraxoninae, Arthropogoninae, Arthrostylidiinae, Arundinariinae, Aveninae, Bambusinae, Boivinellinae, Boutelouinae, Brizinae, Buergersiochloinae, Calothecinae, Cenchrinae, Chionachninae, Chusqueinae, Coicinae, Coleanthinae, Cotteinae, Cteniinae, Cynosurinae, Dactylidinae, Dichantheliinae, Dimeriinae, Duthieinae, Eleusininae, Eragrostidinae, Farragininae, Germainiinae, Gouiniinae, Guaduinae, Gymnopogoninae, Hickeliinae, Hilariinae, Holcinae, Hordeinae, Ischaeminae, Loliinae, Melinidinae, Melocanninae, Miliinae, Monanthochloinae, Muhlenbergiinae, Neurachninae, Olyrinae, Orcuttiinae, Oryzinae, Otachyriinae, Panicinae, Pappophorinae, Parapholiinae, Parianinae, Paspalinae, Perotidinae, Phalaridinae, Poinae, Racemobambosinae, Rottboelliinae, Saccharinae, Scleropogoninae, Scolochloinae, Sesleriinae, Sorghinae, Sporobolinae, Torreyochloinae, Traginae, Trichoneurinae, Triodiinae, Tripogoninae, Tripsacinae, Triticinae, Unioliinae, Zizaniinae, and Zoysiinae). In addition, we include a radial tree illustrating the hierarchical relationships among the subtribes, tribes, and subfamilies. We use the subfamilial name, Oryzoideae, over Ehrhartoideae because the latter was initially published as a misplaced rank, and we circumscribe Molinieae to include 13 Arundinoideae genera. The subtribe Calothecinae is newly described and the tribe Littledaleeae is new at that rank.

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Section: Discussionmentioning

confidence: 99%

A worldwide phylogenetic classification of the Poaceae (Gramineae)

Soreng

Peterson

Romaschenko

et al. 2015

J of Sytematics Evolution

539

688

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“…Mitochondrial and plastome sequences may produce incongruent gene trees due to incomplete lineage sorting, recombination events, or potential elevated rates of substitution in grasses [16, 17]. Mitochondrial sequences were here explored with the goal of increasing maternally inherited character sampling among representative taxa.…”

Section: Introductionmentioning

confidence: 99%

Resolving deep relationships of PACMAD grasses: a phylogenomic approach

et al. 2015

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BackgroundPlastome sequences for 18 species of the PACMAD grasses (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) were analyzed phylogenomically. Next generation sequencing methods were used to provide complete plastome sequences for 12 species. Sanger sequencing was performed to determine the plastome of one species, Hakonechloa macra, to provide a reference for annotation. These analyses were conducted to resolve deep subfamilial relationships within the clade. Divergence estimates were assessed to determine potential factors that led to the rapid radiation of this lineage and its dominance of warmer open habitats.ResultsNew plastomes were completely sequenced and characterized for 13 PACMAD species. An autapomorphic ~1140 bp deletion was found in Hakonechloa macra putatively pseudogenizing rpl14 and eliminating rpl16 from this plastome. Phylogenomic analyses support Panicoideae as the sister group to the ACMAD clade. Complete plastome sequences provide greater support at deep nodes within the PACMAD clade. The initial diversification of PACMAD subfamilies was estimated to occur at 32.4 mya.ConclusionsPhylogenomic analyses of complete plastomes provides resolution for deep relationships of PACMAD grasses. The divergence estimate of 32.4 mya at the crown node of the PACMAD clade coincides with the Eocene-Oligocene Transition (EOT). The Eocene was a period of global cooling and drying, which led to forest fragmentation and the expansion of open habitats now dominated by these grasses. Understanding how these grasses are related and determining a cause for their rapid radiation allows for future predictions of grassland distribution in the face of a changing global climate.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0563-9) contains supplementary material, which is available to authorized users.

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“…Leymus Hochst., a polyploid perennial genus in the wheat tribe (Poaceae: Triticeae), includes about 30 species that distribute from the arctic to the subtropics and tropical alpine regions (Dewey, ; Löve, ; Fan et al, , ; Sha et al, ). As accompanied by geographic dispersal, the natural habitats of Leymus species range from coastal to inland areas, including saline or alkaline lands, dry or semi‐dry areas, as well as shady and moist forests.…”

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confidence: 99%

“…As accompanied by geographic dispersal, the natural habitats of Leymus species range from coastal to inland areas, including saline or alkaline lands, dry or semi‐dry areas, as well as shady and moist forests. Subsequently, Leymus species show large morphological variation in rhizome characteristics, spikelet numbers, leaf types, and glume sizes (Sha et al, , ; Yen et al, ). All the Leymus species are allopolyploids ranging from tetraploids, hexaploids, octoploids, decaploids to dodecaploids (Yen et al, ).…”

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confidence: 99%

Phylogeny and molecular evolution of the DMC1 gene in the polyploid genus Leymus (Triticeae: Poaceae) and its diploid relatives

Fan

Zhang

et al. 2016

J of Sytematics Evolution

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The level and pattern of nucleotide variation in duplicate genes provide important information on the evolutionary history of polyploids and divergent processes between homoeologous loci within lineages. Leymus, a group of allopolyploid species with the NsXm genomes, is a perennial genus with a diverse array of morphology, ecology, and distribution in Triticeae. To estimate the phylogeny and molecular evolution of a single-copy DMC1 gene in Leymus and its diploid relatives, DMC1 homoeologous sequences were isolated from the sampled Leymus species and were analyzed with those from 30 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that: (i) different Leymus species might derive their Ns genome from different Psathyrostachys species; (ii) Pseudoroegneria has contributed to the nuclear genome of some Leymus species, which might result from recurrent hybridization or incomplete lineage sorting; (iii) the Xm genome origin of Leymus could differ among species; (iv) rapid radiation and multiple origin might account for the rich diversity, numbers of species, and wide ecological adaptation of Leymus species; and (v) the DMC1 sequence diversity of the Ns genome in Leymus species was lower than that in the Psathyrostachys diploids, while the level of DMC1 sequence diversity in Leymus was higher than that in diploid Pseudoroegneria. Our results provide new insight on the evolutionary dynamics of duplicate DMC1 genes, polyploid speciation, and the phylogeny of Leymus species.

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Phylogenetic relationships in Leymus (Triticeae; Poaceae): Evidence from chloroplast trnH‐psbA and mitochondrial coxII intron sequences

Cited by 14 publications

References 62 publications

A worldwide phylogenetic classification of the Poaceae (Gramineae)

A worldwide phylogenetic classification of the Poaceae (Gramineae)

Resolving deep relationships of PACMAD grasses: a phylogenomic approach

Phylogeny and molecular evolution of the DMC1 gene in the polyploid genus Leymus (Triticeae: Poaceae) and its diploid relatives

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