title: Transcriptomes of three species of Tipuloidea (Diptera, Tipulomorpha) and implications for phylogeny of Tipulomorpha.
abstract: Tipulomorpha has long been a problematic taxon in terms of familial composition, phylogenetic relationships among families and position relative to other 'lower' Diptera. Whole-transcriptome shotgun sequencing provides a powerful basis for phylogenetic studies. We performed de novo transcriptome sequencing to produce the first transcriptome datasets representing the families Pediciidae, Limoniidae and Cylindrotomidae using high-throughput sequencing technologies. We assembled cDNA libraries for Pedicia vetusta (Alexander) (Pediciidae), Rhipidia sejuga Zhang, Li and Yang (Limoniidae) and Liogma simplicicornis Alexander (Cylindrotomidae). Using the Illumina RNA-Seq method, we obtained 28,252, 44,152 and 44,281 unigenes, from the three respective species. Based on sequence similarity searches, 12,475 (44.16%), 20,334 (46.05%) and 17,478 (39.47%) genes were identified. Analysis of genes highly conserved at the amino acid sequence level revealed there were 1,709 single-copy orthologs genes across the analyzed species. Phylogenetic trees constructed using maximum likelihood (ML) based on the 1,709 single-copy orthologs genes indicated that the relationship between the four major infraorders of lower Diptera was: Culicomorpha + (Tipulomorpha + (Psychodomorpha + (Bibionomorpha + Brachycera))). Trichoceridae belongs within Tipulomorpha as the sister-group of Tipuloidea. Highly supported relationships within the Tipuloidea are Pediciidae + (Limoniidae + (Cylindrotomidae + Tipulidae)). Four-cluster likelihood mapping was used to study potential incongruent signals supporting other topologies, however, results were congruent with the ML tree.
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.
authors.forename: Zehui
authors.initials: Z
authors.lastname: Kang
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.
authors.forename: Shuangmei
authors.initials: S
authors.lastname: Ding
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.
authors.forename: Chufei
authors.initials: C
authors.lastname: Tang
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.
authors.forename: Yuyu
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Naturalis Biodiversity Center, Darwinweg, CR Leiden, the Netherlands.
authors.forename: Herman de
authors.initials: H
authors.lastname: Jong
authors.affiliation: Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America.
authors.forename: Stephen L
authors.initials: SL
authors.lastname: Cameron
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.|Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Mengqing
authors.initials: M
authors.lastname: Wang
authors.affiliation: Department of Entomology, China Agricultural University, Beijing, China.
authors.forename: Ding
authors.initials: D
authors.lastname: Yang
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004175:Diptera / Q000145:classification* / Q000235:genetics*; D020869:Gene Expression Profiling; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D059467:Transcriptome