Arthropod phylotranscriptomics with a special focus on the basal phylogeny of the Myriapoda

Arthropoda are the most diverse animal phylum, but the phylogenetic relationships of arthropods are difficult to determine because many arthropod lineages diverged in a short period of time. In order to solve the controversial problems in the deep phylogeny of arthropods with a focus on Myriapoda, we conducted phylogenetic analyses based on ten supermatrices, which contain 751-1,233 orthologous genes from transcriptome data of 64 representative arthropod species, of which 28 transcriptomes are newly generated in this study. The results unambiguously support monophyly of the higher arthropod taxa, Chelicerata, Mandibulata, Myriapoda, Pancrustacea, and Hexapoda. The Crustacea are paraphyletic, with the class Remipedia supported as the lineage most closely related to hexapods. Within Hexapoda, our results basically support the phylogenetic relationships among the deep hexapod lineages proposed to date, except that the Paraneoptera (Hemiptera, Thysanoptera, and Psocodea) was recovered as a monophyletic lineage in some analyses. The results also strongly support the recently proposed phylogenetic framework of the four myriapod classes, in which the Symphyla and Pauropoda, and the Chilopoda and Diplopoda are sister relationship, respectively. These findings provide important insights into understanding the phylogeny and evolution of arthropods.

Methods
A total of 64 species representing all arthropod classes (three chelicerate classes: Pycnogonida, Merostomata, and Arachnida; four myriapod classes: Chilopoda, Diplopoda, Pauropoda, and Symphyla; six crustacean classes: Ostracoda, Hexanauplia, Malacostraca, Branchiopoda, Cephalocarida, and Remipedia; two hexapod classes: Entognatha and Ectognatha) were analyzed in this study. Of which 28 species (10 crustaceans, 13 myriapods, and 5 chelecerates), which were collected from the Ryukyu Islands and the Kansai region of Japan, were used for transcriptome sequencing. The transcriptome sequences of other arthropod species and five outgroup species were retrieved from NCBI (National Center for Biotechnology Information) sequence database. For construction of the datasets, tree files, etc., refer to the paper.