The complete mitochondrial genome of the long-horned caddisfly Triaenodes tardus (Insecta: Trichoptera: Leptoceridae)

Comparative Mitogenomic Analyses of Hydropsychidae Revealing the Novel Rearrangement of Protein-Coding Gene and tRNA (Trichoptera: Annulipalpia)

Gene rearrangement of the mitochondrial genome of insects, especially the rearrangement of protein-coding genes, has long been a hot topic for entomologists. Although mitochondrial gene rearrangement is common within Annulipalpia, protein-coding gene rearrangement is relatively rare. As the largest family in Annulipalpia, the available mitogenomes from Hydropsychidae Curtis, 1835 are scarce, and thus restrict our interpretation of the mitogenome characteristic. In this study, we obtained 19 novel mitogenomes of Hydropsychidae, of which the mitogenomes of the genus Arctopsyche are published for the first time. Coupled with published hydropsychid mitogenome, we analyzed the nucleotide composition evolutionary rates and gene rearrangements of the mitogenomes among subfamilies. As a result, we found two novel gene rearrangement patterns within Hydropsychidae, including rearrangement of protein-coding genes. Meanwhile, our results consider that the protein-coding gene arrangement of Potamyia can be interpreted by the tandem duplication/random loss (TDRL) model. In addition, the phylogenetic relationships within Hydropsychidae constructed by two strategies (Bayesian inference and maximum likelihood) strongly support the monophyly of Arctopscychinae, Diplectroninae, Hydropsychinae, and Macronematinae. Our study provides new insights into the mechanisms and patterns of mitogenome rearrangements in Hydropsychidae.

It's a moth! It's a butterfly! It's the complete mitochondrial genome of the American moth-butterfly Macrosoma conifera (Warren, 1897) (Insecta: Lepidoptera: Hedylidae)!

The taxonomic placement of the moth-butterfly, Macrosoma conifera (Warren 1897) (Lepidoptera: Hedylidae), has been controversial. The 15,344 bp complete M. conifera circular mitogenome, assembled by genome skimming, consists of 81.7% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region in the typical butterfly gene order. Macrosoma conifera COX1 features an atypical CGA start codon while ATP6, COX1, COX2, and ND5 exhibit incomplete stop codons completed by the post-transcriptional addition of 3' A residues. Phylogenetic reconstruction places M. conifera as sister to the skippers (Hesperiidae), which is consistent with several recent phylogenetic analyses.

The complete mitochondrial genome of the giant casemaker caddisfly Phryganea cinerea (Insecta: Trichoptera: Phryganeidae)

The rush sedge caddisfly Phryganea cinerea Walker, 1852 (Phryganeidae, the giant casemakers), is a widespread and adaptable North American caddisfly. Genome skimming by Illumina sequencing permitted the assembly of a complete 15,043 bp circular mitogenome from P. cinerea consisting of 78.2% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region in the ancestral insect gene order. Phryganea cinerea COX1 features an atypical CGA start codon and COX1, NAD1, NAD4, and NAD5 exhibit incomplete stop codons completed by the addition of 3' A residues to the mRNA. Phylogenetic reconstruction reveals a monophyletic Order Trichoptera and Family Phyrganeidae.

Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes

DNA barcodes are very useful for species identification especially when identification by traditional morphological characters is difficult. However, the short mitochondrial and chloroplast barcodes currently in use often fail to distinguish between closely related species, are prone to lateral transfer, and provide inadequate phylogenetic resolution, particularly at deeper nodes. The deficiencies of short barcode identifiers are similar to the deficiencies of the short year identifiers that caused the Y2K problem in computer science. The resolution of the Y2K problem was to increase the size of the year identifiers. The performance of conventional mitochondrial COI barcodes for phylogenetics was compared with the performance of complete mitochondrial genomes and nuclear ribosomal RNA repeats obtained by genome skimming for a set of caddisfly taxa (Insect Order Trichoptera). The analysis focused on Trichoptera Family Hydropsychidae, the net-spinning caddisflies, which demonstrates many of the frustrating limitations of current barcodes. To conduct phylogenetic comparisons, complete mitochondrial genomes (15 kb each) and nuclear ribosomal repeats (9 kb each) from six caddisfly species were sequenced, assembled, and are reported for the first time. These sequences were analyzed in comparison with eight previously published trichopteran mitochondrial genomes and two triochopteran rRNA repeats, plus outgroup sequences from sister clade Lepidoptera (butterflies and moths). COI trees were not well-resolved, had low bootstrap support, and differed in topology from prior phylogenetic analyses of the Trichoptera. Phylogenetic trees based on mitochondrial genomes or rRNA repeats were well-resolved with high bootstrap support and were largely congruent with each other. Because they are easily sequenced by genome skimming, provide robust phylogenetic resolution at various phylogenetic depths, can better distinguish between closely related species, and (in the case of mitochondrial genomes), are backwards compatible with existing mitochondrial barcodes, it is proposed that mitochondrial genomes and rRNA repeats be used as next generation DNA barcodes.