title: Non-concerted ITS evolution, early origin and phylogenetic utility of ITS pseudogenes in Pyrus.
abstract: Molecular studies of 19 species of the genus Pyrus L. revealed different degrees of intra-individual polymorphism of the internal transcribed spacer (ITS 1, 5.8S rDNA and ITS 2) region due to the existence of putative non-functional copies (pseudogenes), putative recombinants and non-concerted evolution among functional copies. Different types of ITS pseudogenes displaying lower GC content and unstable secondary structure were preferentially amplified under normal PCR conditions. Functional ITS copies were successfully obtained in all investigated accessions under the modified PCR conditions. All pseudogenes were highly divergent from their corresponding functional copies and formed a monophyletic group in the phylogenetic tree based on all paralogs, indicating they were of relatively early origin. Functional ITS copies led to confused and poorly resolved phylogeny as a result of low sequence divergence, existence of unidentified ancient recombinants and a high degree of intra-individual functional ITS polymorphism, while certain types of pseudogenes and some relict pseudogenes offered more credible clues for the evolutionary history of Pyrus species.
authors.affiliation: Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth Development & Biotechnology, Zhejiang University, 268 Kaixuan Road, Hangzhou 310029, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Zheng
authors.forename: Danying
authors.initials: D
authors.lastname: Cai
authors.forename: Lihua
authors.initials: L
authors.lastname: Yao
authors.forename: Yuanwen
authors.initials: Y
authors.lastname: Teng
mesh_terms: D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D021901:DNA, Intergenic; D004275:DNA, Ribosomal / Q000235:genetics*; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011544:Pseudogenes; D031989:Pyrus / Q000235:genetics*; D011994:Recombinant Proteins / Q000737:chemistry; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D021901:DNA, Intergenic; D004275:DNA, Ribosomal; D011994:Recombinant Proteins