title: Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids.
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 mitochondrial matR gene from 174 species representing 72 families of putative rosids and examined phylogenetic relationships and phylogenetic utility of matR in rosids. We also inferred phylogenetic relationships within the "rosid clade" based on a combined data set of 91 taxa and four genes including matR, two plastid genes (rbcL, atpB), and one nuclear gene (18S rDNA).
  
  
  RESULTS
  Comparison of mitochondrial matR and two plastid genes (rbcL and atpB) showed that the synonymous substitution rate in matR was approximately four times slower than those of rbcL and atpB; however, the nonsynonymous substitution rate in matR was relatively high, close to its synonymous substitution rate, indicating that the matR has experienced a relaxed evolutionary history. Analyses of our matR sequences 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.
  
  
  CONCLUSIONS
  Compared to plastid genes such as rbcL and atpB, slowly evolving matR produced less homoplasious but not less informative substitutions. Thus, matR appears useful in higher-level angiosperm phylogenetics. Analysis of matR alone 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.
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China. zhu_xinyu@ibcas.ac.cn
authors.forename: Xin-Yu
authors.initials: XY
authors.lastname: Zhu
authors.forename: Mark W
authors.initials: MW
authors.lastname: Chase
authors.forename: Yin-Long
authors.initials: YL
authors.lastname: Qiu
authors.forename: Hong-Zhi
authors.initials: HZ
authors.lastname: Kong
authors.forename: David L
authors.initials: DL
authors.lastname: Dilcher
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Li
authors.forename: Zhi-Duan
authors.initials: ZD
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D004722:Endoribonucleases / Q000235:genetics*; D019143:Evolution, Molecular; D017343:Genes, Plant; D014644:Genetic Variation; D016013:Likelihood Functions; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D009713:Nucleotidyltransferases / Q000235:genetics*; D010802:Phylogeny; D018087:Plastids; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial; D018744:DNA, Plant; D009713:Nucleotidyltransferases; C034038:mRNA maturase; D004722:Endoribonucleases; D012273:Ribulose-Bisphosphate Carboxylase