| Molecular systematics is widely used to determine organismal relationships. After twenty years researching, angiosperm phylogeny has been developed much rapidly employed organellar genes, but the relationship haven’t been solved thoroughly. In APG Ⅲ, the scientists couldn’t determine which species is the first ancestor among the angiosperm. They also couldn’t resolve the relationship among monocots, eudicots, rosids and asterids. Organellar genes are generally inherited uniparentally, only partially reflecting the evolutionary history. In addition, chloroplast and mitochondrial genes are highly conserved, with limited numbers of phylogenetically informative characters. Therefore, such genes couldn’t resolve the phylogeny of angiosperm thoroughly.Advanced in the molecular systematic, the low-copy nuclear genes became an efficient method to study this field. Nuclear genes are inherited biparentally and have relatively large numbers of informative sites. The low-copy genes are only separated by speciation events and have not been duplicated since the most recent common ancestor can be considered. In this work, sequences of five low-copy nuclear genes (MCM5, MLH1, AT3G54630, AT3G26730and AT2G47990) were obtained in17species from Brassicaceae and used for phylogenetic analyses with the Maximum-Parsimony, Maximum-Likelihood and Bayesian method. Meanwhile, we also downloaded the data of3genes, which have been used in previous study, to reconstruct the relationship of these17species. In this way, we could compare the high efficiency of phylogeny with low-copy nuclear genes to that with3genes.In our results, the nuclear gene, MCM5, with gene long of704bp, could supply139Parsimony-informative characters (PIC), the ratio of which is19.7%. MLH1, with gene long of1695bp, could provide213PIC, the ratio of which is12.7%.AT3G26730, with gene long is1227bp, could supply179PIC, the ratio of which is21.3%. AT2G47990, with gene long of717bp, could provide206PIC, the ratio of which is28.7%. AT3G54630, with gene long of1227, has724PIC, the ratio of which is36.3%. The matrix of5nuclear genes is4585bp long, which could supply1201PIC, and ratio is26.2%. Among3used genes, ITS could supply158PIC of621bp long, the ratio of which is25.4%. The chloroplast gene, MatK could provide100PIC of1527bp long, the ratio of which is only6.5%. The chloroplast gene, rbcL has sequence of1447bp, but only supply42PIC, the ratio of which is3%. The matrix of3used genes is3624bp long, which could supply314PIC, and ratio is only8.7%. In comparison, these five nuclear genes could supply more data for phylogenetical analyzing than3genes did.At the beginning of researching, we reconstructed the single nuclear gene trees with some clone sequences of one species. All clone sequences of one species could get together in one branch among all five single nuclear gene trees, the supports of all nodes, with three statistics, are nearly to max. In result, we took the different sites among clone sequences of one species into degenerate sites.To analyze the phylogenetic tree of five low-copy nuclear genes, Highly similar topologies were obtained; in addition, compared with organellar genes, the nuclear genes had more phylogenetically informative sites and provide stronger supports. Specifically, the supporting values of all the nodes were100%in MP trees using five nuclear genes, In clade I, Lepidium apetalum and Coronopus didymus are sister group. Cardamine hirsute and Rorippa indica are sister group, which is also sister group with Capsella bursa-pastoris. The supports of above are all max. In clade II, four species of Brassiceae get together in one branch, the relationship among these four are sister group in correct order, and the supports of all nodes, with three statistics, are nearly to max. Therefore, these five genes are excellent candidate marker genes for plant taxonomists who aim to resolve the relationships among low-level taxonomic hierarchies and might also be useful for DNA barcoding.
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