title: Phylogenetic comparison of local length plasticity of the small subunit of nuclear rDNAs among all Hexapoda orders and the impact of hyper-length-variation on alignment.
abstract: The SSU nrDNA (18S), is one of the most frequently sequenced molecular markers in phylogenetic studies. However, the length-hyper-variation at multiple positions of this gene can affect the accuracy of alignment greatly and this length variation makes alignment across arthropod orders a serious problem. The analyses of Hexapoda phylogeny is such a case. A more clear recognition of the distribution of the length-variable-regions is needed. In this study, the secondary structure of some length-variable-regions in the SSU nrRNA of Arthropoda was adjusted by the principle of co-variation. It is found that the extent of plasticity of some length-variable-region can extraordinarily be higher than 600 bases in hexapods. And the numbers of hyper length-variable-regions are largest in Strepsiptera and Sternorrhyncha (Hemiptera). Our study shows that some length-variable-regions can serve as synapomorphies for some groups. The phylogenetic comparison also suggested that the expansion of a lateral bulge could be the origin of a helix.
authors.affiliation: Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Xie
authors.forename: Xiaoxuan
authors.initials: X
authors.lastname: Tian
authors.forename: Yan
authors.initials: Y
authors.lastname: Qin
authors.forename: Wenjun
authors.initials: W
authors.lastname: Bu
mesh_terms: D000818:Animals; D001181:Arthropods / Q000145:classification / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics*; D014644:Genetic Variation; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D016415:Sequence Alignment
chemical_list: D004275:DNA, Ribosomal