Mitogenomes provide insights into the phylogeny of Mycetophilidae (Diptera: Sciaroidea)

The family Mycetophilidae (Diptera: Sciaroidea) consists of more than 4,500 described species distributed worldwide. Among them, dozens of species have been reported to be economically important to cultivated mushrooms and crops. Relationships among subfamilies in Mycetophilidae have been controversial by using morphological characters or gene markers. In this study, five mycetophilid mitogenomes representing four subfamilies were sequenced and analyzed with 15 published sciaroid mitogenomes as ingroup, while another two species representing two closely related families were chosen as outgroup. All of the sequenced mitogenomes contain 37 genes arranged in the ancestral order, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region (CR). Among mycetophilid mitogenomes, Leu, Ile, Phe, and Met are the most frequently encoded amino acids (AA), with TTA (Leu), ATT (Ile), TTT (Phe) and ATA (Met) being the most frequent codons. Meanwhile, the phylogenetic results reconstructed based on PCGs, PCGs + rRNAs and AA sequences respectively show that the clade of Sciaroidea was well separated from outgroup, further confirming its monophyly. The phylogenetic relationships within Mycetophilidae were recovered as (Manotinae + Sciophilinae) + (Mycomyinae + Mycetophilinae). Mapped to the phylogram, the gene rearrangements occur frequently in the crown group, implying extremely rapid evolutionary rates in Sciaridae and Cecidomyiidae, which might be the reason why the two families have such high species diversity.