Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids

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Abstract
Background: Rosids are a major clade in the angiosperms containing 13 orders and about one-third of angiosperm species. Recent molecular analyses recognized two major groups (i.e., fabids with seven orders and malvids with three orders). However, phylogenetic relationships within the two groups and among fabids, malvids, and potentially basal rosids including Geraniales, Myrtales, and Crossosomatales remain to be resolved with more data and a broader taxon sampling. In this study, we obtained DNA sequences of the mitochondrialmatRgene from 174 species representing 72 families of putative rosids and examined phylogenetic relationships and phylogenetic utility ofmatRin rosids. We also inferred phylogenetic relationships within the "rosid clade" based on a combined data set of 91 taxa and four genes includingmatR, two plastid genes (rbcL,atpB), and one nuclear gene (18S rDNA).Results: Comparison of mitochondrialmatRand two plastid genes (rbcLandatpB) showed that the synonymous substitution rate inmatRwas approximately four times slower than those ofrbcLandatpB; however, the nonsynonymous substitution rate inmatRwas relatively high, close to its synonymous substitution rate, indicating that thematRhas experienced a relaxed evolutionary history. Analyses of ourmatRsequences supported the monophyly of malvids and most orders of the rosids. However, fabids did not form a clade; instead, the COM clade of fabids (Celastrales, Oxalidales, Malpighiales, and Huaceae) was sister to malvids. Analyses of the four-gene data set suggested that Geraniales and Myrtales were successively sister to other rosids, and that Crossosomatales were sister to malvids.Conclusion: Compared to plastid genes such asrbcLandatpB, slowly evolvingmatRproduced less homoplasious but not less informative substitutions. Thus,matRappears useful in higher-level angiosperm phylogenetics. Analysis ofmatRalone identified a novel deep relationship within rosids, the grouping of the COM clade of fabids and malvids, which was not resolved by any previous molecular analyses but recently suggested by floral structural features. Our four-gene analysis supported the placements of Geraniales, Myrtales at basal nodes of the rosid clade and placed Crossosomatales as sister to malvids. We also suggest that the core part of rosids should include fabids, malvids and Crossosomatales.