title: Secondary structure of expansion segment D1 in LSU rDNA from Arachnida and its phylogenetic application in Eriophyoid mites and in Acari.
abstract: An increasing number of researchers have applied secondary-structure based multiple alignments of rDNA genes in phylogeny. These studies mostly depended on a few valuable divergent domains in LSU and SSU rDNA. Yet other divergent domains, e.g. D1, were poorly investigated and rarely used. However, these domains might contain additional evolutionary data and play a vital role in DNA-based phylogenetic study. Here, we investigated all available D1 sequences of Arachnida taxa and predicted corresponding secondary structures to help identify homologous positions in the D1 region. Long insertions were found exclusive to Eriophyoidea and folded into three newly proposed helices. Non-Acari taxa were all GC rich. In Acari, most Trombidiformes and all Mesostigmata (Parasitiformes) taxa were AT rich and Ixodida (Parasitiformes) GC rich; however there was no consistent base bias in Sarcoptiformes sequences. For Eriophyoid mites, genera Cecidophyopsis and Aceria were both well supported in MP, NJ, ME and ML tress based on D1 sequences, and clusters of Cecidophyopsis species were identical with former study. This demonstrated that the D1 region could act as a valuable molecular marker in phylogenetic reconstruction of Eriophyoidea. Additionally, D1 has been proven suitable in phylogenetic analysis at the family and genus level in Acari, but not in Opiliones.
authors.affiliation: Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China; Peking University Health Science Center, Beijing, 100191, China.
authors.forename: Zheng-Hang
authors.initials: ZH
authors.lastname: Wang
authors.affiliation: Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China. Electronic address: zhaoyae@mail.xjtu.edu.cn.
authors.forename: Ya-E
authors.initials: YE
authors.lastname: Zhao
authors.affiliation: Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China; Department of Orthodontics, State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China.
authors.forename: Li
authors.initials: L
authors.lastname: Hu
authors.affiliation: Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China.
authors.forename: Yi-Meng
authors.initials: YM
authors.lastname: Chen
mesh_terms: D000053:Acari / Q000145:classification / Q000235:genetics; D000818:Animals; D001097:Arachnida / Q000145:classification* / Q000235:genetics*; D004275:DNA, Ribosomal / Q000737:chemistry* / Q000235:genetics; D005819:Genetic Markers; D008925:Mites / Q000145:classification / Q000235:genetics; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D016415:Sequence Alignment
chemical_list: D004275:DNA, Ribosomal; D005819:Genetic Markers
keywords: Acari; D1 sequence; Eriophyoidea; GC content; Phylogeny; Secondary structure