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.

Characterization of the complete mitochondrial genome of the snow crane-fly Chionea crassipes gracilistyla (Diptera, Tipuloidea, Limoniidae) with phylogenetic analysis

“…The phylogenetic tree in our study (Figure 1) indicated that the Pediciidae was sister-group to the remaining Tipuloidea, which was accepted by Ribeiro (2008), Petersen et al (2010) and Kang et al (2017). Our phylogenetic analysis also showed a strong support for the sister-group relationship between Cylindrotomidae and Tipulidae.…”

“…( 2010 ) and Kang et al. ( 2017 ). Our phylogenetic analysis also showed a strong support for the sister-group relationship between Cylindrotomidae and Tipulidae.…”

A phylogenomic analysis of Culicomorpha (Diptera) resolves the relationships among the eight constituent families

“…The value of the more than a 100‐fold expansion of gene coverage for entomological phylogenomic studies is evident (e.g. Niehuis et al ., ; Letsch & Simon, ; Misof et al ., ; Kang et al ., ; Bazinet et al ., ; Peters et al ., ). For example, the once controversial monophyly of Polyneoptera and positions therein of Strepsiptera as sister to Coleoptera and Hymenoptera as sister group to ‘Aparaglossata’ have become widely accepted.…”

Biological significance of RNA-seq and single-cell genomic research in woody plants

“…Analyses of RNA-seq data in P. alba have identified a total of 39,000 unique singletons that would potentially contribute to the population-based genome studies in the genera (Torales et al 2013). Kang et al obtained 1709 single-copy orthologs genes from analyzed species through RNA-seq data analyses and four-cluster likelihood mapping was used to study potential incongruent signals (Kang et al 2017).…”