Burke Sean V, Wysocki William P, Zuloaga Fernando O, Craine Joseph M, Pires J Chris, Edger Patrick P, Mayfield-Jones Dustin, Clark Lynn G, Kelchner Scot A, Duvall Melvin R
Department of Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL, 60115-2861, USA.
Instituto de Botánica Darwinion, Labardén 200, Casilla de Correo 22, B1642HYD, San Isidro, Buenos Aires, Argentina.
BMC Plant Biol. 2016 Jun 18;16(1):140. doi: 10.1186/s12870-016-0823-3.
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.
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.
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.
黍亚科是禾本科中第二大亚科，有212个属，约3316个物种。先前的研究已开始揭示该亚科内的关系，但在很大程度上缺乏对某些族和亚族类群的分辨率和/或有力支持。本研究旨在解决这些关系，并对一个谱系中假定的线粒体插入片段进行特征描述。
在一项系统发育基因组学研究中，将35个新测序的黍亚科质体基因组与其他37个物种相结合：15个黍亚科物种和22个外类群物种。获得了一个与先前研究基本一致的稳健的黍亚科拓扑结构，但与先前报道的亚族关系存在一些不一致。在雀稗谱系中发现了线粒体DNA（mtDNA）向质体DNA（ptDNA）的转移。
系统发育基因组学分析得出的拓扑结构在很大程度上支持先前的研究。在拓扑结构上，五个先前认可的亚族似乎不是单系的。此外，在条纹雀稗和宽叶雀稗中均发现了mtDNA向ptDNA转移的证据，这表明在一个共同祖先中发生了一次罕见事件。最后，本研究构建的框架可指导更大规模的全质体基因组采样，以厘清莎稗族、斯氏稗族、吉氏禾族以及其他支持度弱或未解决的地位不确定类群之间的关系。
