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. 2016 Jun 18;16(1):140.
doi: 10.1186/s12870-016-0823-3.

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae)

Sean V Burke  1 , William P Wysocki  2 , Fernando O Zuloaga  3 , Joseph M Craine  4 , J Chris Pires  5 , Patrick P Edger  6 , Dustin Mayfield-Jones  7 , Lynn G Clark  8 , Scot A Kelchner  9 , Melvin R Duvall  2
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Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae)

Sean V Burke et al. BMC Plant Biol. .

Abstract

Background: Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage.

Results: 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage.

Conclusions: The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.

Keywords: Grasses; Next generation sequencing; Panicoideae; Paspalum; Phylogenomics; Plastome; Poaceae; Subtribal systematics; mtDNA; ptDNA.

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Figures

Fig. 1
Fig. 1
Plastome maps illustrating the mtDNA inserts in the trnI - trnL intergenic spacer in Paspalum fimbriatum, P. dilatatum and their probable progenitor, as well as Panicum capillare, which has a large deletion in this region, and L. madagascariensis, which illustrates a typical grass plastome. The colors correspond to the similarity of DNA determined by BLAST results: red is mitochondrial-like, purple is smut-like, and green is sequence that did not return high similarity scores with any banked sequences. The ptDNA regions A and B correspond to regions of DNA with high pairwise identity, and is present in most species of Panicoideae
Fig. 2
Fig. 2
Cladogram of the 50 Panicoideae (species names in bold indicate that they are newly sequenced in this study) with outgroup species. All nodes are supported at bootstrap values (BV) of 100 and posterior probabilities (PP) of 1.0 except where noted (MPBV | MLBV | PP). Bootstrap analysis did not support branches marked “--”. Subtribal names with disagreements to monophyly are color coded. Tribes and higher taxonomic groupings are indicated
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