Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication

Abstract

Large intergenic spacers and tRNA gene duplications have been reported in several insect groups, although little is known about mitogenomes of mayflies. Here, we determined complete mitogenomes of ten heptageniid species and systemically analyzed their mitogenomic features. Both a conserved intergenic spacer (IGS) and trnM duplication were detected in those mitogenomes. The IGS, which was observed in heptageniids, could be further folded into a stable stem–loop structure. The tRNA gene duplication was found in almost all analyzed mitogenomes, and a unique gene block trnI-trnM-trnQ-trnM-ND2 was also discovered. Our analysis demonstrates that the heptageniid gene arrangement pattern can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on the nucleotide and amino acid sequence data recovered the genus Epeorus as monophyletic with strong support. Our results provide a better understanding of mitogenomic evolution in Heptageniidae, as well as novel molecular markers for species identification of mayflies.

The First Two Complete Mitochondrial Genomes of Neoephemeridae (Ephemeroptera): Comparative Analysis and Phylogenetic Implication for Furcatergalia

“…Both Neoephemeridae species showed a negative AT-skew and positive GC-skew in PCGs, while the third codon position had an A + T content (85.58% and 86.71%) much higher than that of all the positions (73.38% and 72.24%; Table 2 ). All PCGs of both mitogenomes started with the typical initiation codon ATN (ATG, ATT, and ATC), as seen in other mayflies [ 4 , 31 , 32 , 33 , 34 ]. For the stop codons, most PCGs were terminated by the typical TAN codon (TAG and TAA), apart from several genes (COI, COII, ND5, ND4, CYTB, and ND1) which ended with an incomplete codon T. This incomplete stop codon (T) has been reported in other insect mitogenomes, which connects with transfer RNAs at their 3′ ends, and the processing is presumed to be completed through posttranscriptional polyadenylation [ 38 ].…”

“…The AT content and codon usage bias phenomenon could be attributed to the fact that the synonymous codon usage bias in the mitogenomes tends to be from codons ending with A/T to promote transcription [46]. The most variable region was in ND2, while the most conserved fragment was in COI (lowest Pi), as also found in other mayflies [4,35]. Ka (Nonsynonymous substitutions) and Ks (Synonymous substitutions) are used as indicators of the selectivity constraint [47].…”

“…In addition, it is composed of a control region (also called A + T-rich region) which contains the initiation sites for transcription and replication [ 2 , 3 ]. Compared to the nuclear genome, the mitogenome possesses multiple obvious advantages, such as maternal inheritance, absence of introns, conserved gene composition, the relatively rare recombination, and high evolutionary rate [ 4 ]. Given the vast diversity of insects, mitogenome sequences are usually considered to be effective molecular markers for species identification and play an increasingly important role in intraspecific and interspecific genetic differences, phylogenetic implications, molecular evolution, and phylogeographic studies across various taxa [ 5 , 6 , 7 , 8 ].…”

“…However, the mitogenomes of Ephemeroptera have been limitedly studied and approximately only 50 reliable sequences (with exact Latin name of the species) were made public in the NCBI database (National Center for Biotechnology Information). More importantly, most of these available mitogenomes were mainly sequenced and focused on several families (such as Heptageniidae and Ephemerellidae), and no sequence of the vast majority of mayfly families was reported up to now [ 4 , 12 ]. This unbalanced distribution of mitogenomes has limited our comprehensive understanding of the evolutionary and phylogenetic relationships within Ephemeroptera at the mitogenome level.…”

“…Amino acid composition of all the PCGs of 13 Furcatergalia mitogenomes. The nucleotide diversity of the PCGs of Furcatergalia mitogenomes is shown in Figure 7A (Sliding window = 100 bp).The most variable region was in ND2, while the most conserved fragment was in COI (lowest Pi), as also found in other mayflies[4,35]. Ka (Nonsynonymous substitutions) and Ks (Synonymous substitutions) are used as indicators of the selectivity constraint[47].…”