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The infrageneric phylogeny and temporal divergence of  Sorghum  were explored in the present study. Sequence data of two low-copy nuclear (LCN) genes, phosphoenolpyruvate carboxylase 4 ( Pepc4 ) and granule-bound starch synthase I ( GBSSI ), from 79 accessions of  Sorghum  plus  Cleistachne sorghoides  together with those from outgroups were used for maximum likelihood (ML) and Bayesian inference (BI) analyses. Bayesian dating based on three plastid DNA markers ( ndhA  intron,  rpl32-trnL , and  rps16  intron) was used to estimate the ages of major diversification events in  Sorghum . The monophyly of  Sorghum  plus  Cleistachne sorghoides  (with the latter nested within  Sorghum ) was strongly supported by the  Pepc4  data using BI analysis, and the monophyly of  Sorghum  was strongly supported by  GBSSI  data using both ML and BI analyses.  Sorghum  was divided into three clades in the  Pepc4 ,  GBSSI , and plastid phylograms: the subg.  Sorghum  lineage; the subg.  Parasorghum  and  Stiposorghum  lineage; and the subg.  Chaetosorghum  and  Heterosorghum  lineage. Two LCN homoeologous loci of  Cleistachne sorghoides  were first discovered in the same accession.  Sorghum arundinaceum ,  S. bicolor ,  S.  x  drummondii ,  S. propinquum , and  S. virgatum  were closely related to  S.  x  almum  in the  Pepc4 ,  GBSSI , and plastid phylograms, suggesting that they may be potential genome donors to  S. almum . Multiple LCN and plastid allelic variants have been identified in  S. halepense  of subg.  Sorghum . The crown ages of  Sorghum  plus  Cleistachne sorghoides  and subg.  Sorghum  are estimated to be 12.7 million years ago (Mya) and 8.6 Mya, respectively. Molecular results support the recognition of three distinct subgenera in  Sorghum : subg.  Chaetosorghum  with two sections, each with a single species, subg.  Parasorghum  with 17 species, and subg.  Sorghum  with nine species and we also provide a new nomenclatural combination,  Sorghum sorghoides .

Infrageneric Phylogeny and Temporal Divergence of Sorghum (Andropogoneae, Poaceae) Based on Low-Copy Nuclear and Plastid Sequences