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

Arthan, Watchara; McKain, Michael R.; Traiperm, Paweena; Welker, Cassiano Aimberê Dorneles; Teisher, Jordan K.; Kellogg, Elizabeth A.

doi:10.1600/036364417x696023

Cited by 36 publications

(74 citation statements)

References 78 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The best base pair substitution model was determined to be GTR + gamma + I using the Aikake Information Criterion (AIC) in jModelTest2 v.2.1.5 (42). The total data set had 173 taxa (S1) and included taxa from GenBank, Arthan et al (43), Welker et al (44), and newly sequenced plastomes from this study.…”

Section: Chloroplast Genome Assembly Annotation and Tree Estimationmentioning

confidence: 99%

“…Results were filtered using scripts included with PhyDS to remove instances where outgroups (Dichanthelium, Panicum, or Setaria), Arundinella, Sorghum, Ischaemum, Miscanthus, Saccharum, Themeda, Bothriochloa, Dichanthium, Andropogon, or Schizachyrium were present in the descendants of the ancestral node. These were chosen to be excluded based on known relationships in Andropogoneae (43,44,57) and the chloroplast genome phylogeny presented in this study. Andropogoneae nuclear gene trees are known for extremely short branches potentially due to a rapid diversification (16) which can impede identification of relationships among paralogs and orthologs but can be lessened with the removal of suspect topologies.…”

Section: Identification Of Maize Subgenomesmentioning

confidence: 99%

See 1 more Smart Citation

Ancestry of the two subgenomes of maize

Pasquet

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

Maize (Zea mays ssp. mays) is not only one of the world's most important crops, but it also is a powerful tool for studies of genetics, genomics, and cytology. The genome of maize shows the unmistakable signature of an ancient hybridization event followed by whole genome duplication (allopolyploidy), but the parents of this event have been a mystery for over a century, since studies of maize cytogenetics began. Here we show that the whole genome duplication event preceded the divergence of the entire genus Zea and its sister genus Tripsacum. One genome was donated, in whole or in part, by a plant related to the modern African genera Urelytrum and Vossia, although genomic rearrangement has been extensive. The other genome donor is less well-supported, but may have been related to the modern Rottboellia-Hemarthria clade, which is also African. Thus Zea and Tripsacum together represent a New World radiation derived from African ancestors.

show abstract

Section: Chloroplast Genome Assembly Annotation and Tree Estimationmentioning

confidence: 99%

Section: Identification Of Maize Subgenomesmentioning

confidence: 99%

Ancestry of the two subgenomes of maize

Pasquet

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…The newly generated plastomes were aligned with others publicly available for Andropogoneae and Arundinella Raddi using MAFFT v. 7.123b (Arthan et al 2017;Katoh and Standley 2013). The alignment was manually refined and the inverted repeat region removed.…”

Section: Assembly Alignment and Phylogenetic Inferencementioning

confidence: 99%

“…The highest concentration of species diversity is located in Asia, in particular India (Morales 2014). Despite ongoing phylogenetic work in Andropogoneae (Giussani et al 2001;Mathews et al 2002;Sánchez-Ken and Clark 2010;Arthan et al 2017), the tribe that includes Themeda, detailed analyses of this ecologically important genus are lacking.…”

Section: Introductionmentioning

confidence: 99%

The recent and rapid spread of Themeda triandra

et al. 2017

View full text Add to dashboard Cite

Tropical savannas cover over 20% of land surface. They sustain a high diversity of mammalian herbivores and promote frequent fires, both of which are dependent on the underlying grass composition. These habitats are typically dominated by relatively few taxa, and the evolutionary origins of the dominant grass species are largely unknown. Here, we trace the origins of the genus Themeda, which contains a number of widespread grass species dominating tropical savannas. Complete chloroplast genomes were assembled for seven samples and supplemented with chloroplast and nuclear ITS markers for 71 samples representing 18 of the 27 Themeda species. Phylogenetic analysis supports a South Asian origin for both the genus and the widespread dominant T. triandra. This species emerged ~1.5 Ma from a group that had lived in the savannas of Asia for several million years. It migrated to Australia ~1.3 Ma and to mainland Africa ~0.5 Ma, where it rapidly spread in pre-existing savannas and displaced other species. Themeda quadrivalvis, the second most widespread Themeda species, is nested within T. triandra based on whole chloroplast genomes, and may represent a recent evolution of an annual growth form that is otherwise almost indistinguishable from T. triandra. The recent spread and modernday dominance of T. triandra highlight the dynamism of tropical grassy biomes over millennial time-scales that has not been appreciated, with dramatic shifts in species dominance in recent evolutionary times. The ensuing species replacements likely had profound effects on fire and herbivore regimes across tropical savannas.

show abstract

“…Although plastid sequences are often highly conserved, comparative analyses of large datasets of complete plastomes present enough variation to resolve phylogenetic relationships between taxa, even at low taxonomic levels (Parks & al., ; Steele & al., ; Burke & al., ). This is particularly important for problematic groups resulting from rapid evolutionary radiation, such as the grass tribe Andropogoneae (Estep & al., ; Welker & al., ; Arthan & al., ).…”

Section: Introductionmentioning

confidence: 97%

Plastome phylogenomics of sugarcane and relatives confirms the segregation of the genus Tripidium (Poaceae: Andropogoneae)

Welker

McKain

Vorontsova

et al. 2019

TAXON

Self Cite

View full text Add to dashboard Cite

Sugarcane (Saccharum officinarum) is one of the most important crops in the world and a major source of sugar for human consumption. Despite this immense value, the circumscription of the genus Saccharum is complex, contentious, and largely unresolved. Saccharum is accepted in a broad sense by some authors or split into various genera such as Erianthus and Tripidium by others. A plastome phylogenomic analysis of sugarcane and relatives was performed in order to investigate generic delimitation, with emphasis on Tripidium (= Erianthus sect. Ripidium). Our plastome analysis demonstrates that Saccharum s.l. is polyphyletic and Tripidium (distributed in the Old World) belongs to a distinct lineage from Saccharum s.str. (Old World) and Erianthus s.str. (= Erianthus sect. Erianthus, New World). Therefore, this study confirms the recognition of Tripidium as a genus distinct from Saccharum and Erianthus, which is also supported by morphology and nuclear markers. The circumscription of Erianthus s.str. remains unclear since our results are consistent with either considering it as a distinct genus or including it in Saccharum. Better understanding of the evolutionary relationships of sugarcane and relatives may be useful for the selection of potential taxa for interspecific and intergeneric crosses in the genetic improvement of sugarcane. A taxonomic treatment of the six species of Tripidium is also presented, including descriptions, illustrations, data on geographical distribution, and three new nomenclatural combinations.

show abstract

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

Cited by 36 publications

References 78 publications

Ancestry of the two subgenomes of maize

Ancestry of the two subgenomes of maize

The recent and rapid spread of Themeda triandra

Plastome phylogenomics of sugarcane and relatives confirms the segregation of the genus Tripidium (Poaceae: Andropogoneae)

Contact Info

Product

Resources

About