Complete mitochondrial genomes of Epeorus carinatus and E. dayongensis (Ephemeroptera: Heptageniidae): Genomic comparison and phylogenetic inference

(1) Background: Gene rearrangement of mitochondrial genome, especially those with phylogenetic signals, has long fascinated evolutionary biologists. The synapomorphic gene rearrangements have been identified across multiple orders and at many different taxonomic levels, supporting the monophyletic or systematic relationships of related lineages. However, mitochondrial gene rearrangement has never been observed in the non-biting midges (Diptera: Chironomidae); (2) methods: in this study, the complete mitogenomes of seven Stenochironomus species were sequenced and analyzed for the first time; (3) results: each mitogenome of Stenochironomus contains 37 typical genes and a control region. The whole mitogenomes of Stenochironomus species exhibit a higher A+T bias than other published chironomid species. The gene order rearranges from trnI-trnQ-trnM to trnI-trnM-trnQ in all the seven mitogenomes of Stenochironomus, which might be act as a synapomorphy of the genus, supporting the monophyletic of Stenochironomus species. In addition, another derived gene cluster: trnA-trnG-ND3-trnR exists in Stenochironomus tobaduodecimus. The derived gene orders described above are the first case of mitochondrial gene rearrangement in Chironomidae. Coupled with published data, phylogenetic relationships were reconstructed within Chironominae, and strongly supported the monophyly of Stenochironomus; (4) conclusions: our study provides new insights into the mitochondrial gene order of Chironomidae, and provides a valuable resource for understanding the synapomorphic gene rearrangements.

Section: Introductionmentioning

confidence: 99%

First Report on Mitochondrial Gene Rearrangement in Non-Biting Midges, Revealing a Synapomorphy in Stenochironomus Kieffer (Diptera: Chironomidae)

Zheng

Liu

Zhao

et al. 2022

“…Both maximum likelihood and Bayesian phylogenetic trees showed that Vietnamellidae was closely related to Ephemerellidae and had a distant relationship with Teloganellidae, which was consistent with the results of Cai et al [ 12 ], Gao et al [ 45 ], and Rutschmann et al [ 90 ]. Over the last few years, many scholars did not include sequences of Teloganodidae when constructing the phylogenetic tree within Ephemeroptera, so the sister clade of Vietnamellidae and Ephemerellidae were still supported [ 41 , 42 , 43 , 44 ].…”

Section: Discussionmentioning

confidence: 99%

“…In 2009, Ogden et al combined the molecular data ( sRNA , IrRNA , 18S rDNA , 28S rDNA , and H 3 genes) and morphological data suggesting that Vietnamellidae, Teloganodidae, and Ephemerellidae were in a parallel relationship, and the phylogenetic relationships among them had not been effectively analyzed [ 29 ]. In recent years, Li et al [ 41 , 42 , 43 ], Zhang et al [ 44 ], Cai et al [ 12 ], and Gao et al [ 45 ] reconstructed the phylogeny of Ephemeroptera based on mt genomes, all of which supported the formation of sister groups between Ephemerellidae and Vietnamellidae.…”

Section: Introductionmentioning

confidence: 99%

Cryptic Species Exist in Vietnamella sinensis Hsu, 1936 (Insecta: Ephemeroptera) from Studies of Complete Mitochondrial Genomes

Tong

Ayivi

et al. 2022

Ephemeroptera (Insecta: Pterygota) are widely distributed all over the world with more than 3500 species. During the last decade, the phylogenetic relationships within Ephemeroptera have been a hot topic of research, especially regarding the phylogenetic relationships among Vietnamellidae. In this study, three mitochondrial genomes from three populations of Vienamella sinensis collected from Tonglu (V. sinensis TL), Chun’an (V. sinensis CN), and Qingyuan (V. sinensis QY) in Zhejiang Province, China were compared to discuss the potential existence of cryptic species. We also established their phylogenetic relationship by combining the mt genomes of 69 Ephemeroptera downloaded from NCBI. The mt genomes of V. sinensis TL, V. sinensis CN, and V. sinensis QY showed the same gene arrangement with lengths of 15,674 bp, 15,674 bp, and 15,610 bp, respectively. Comprehensive analyses of these three mt genomes revealed significant differences in mt genome organization, genetic distance, and divergence time. Our results showed that the specimens collected from Chun’an and Tonglu in Zhejiang Province, China belonged to V. sinensis, and the specimens collected from Qingyuan, Zhejiang Province, China were a cryptic species of V. sinensis. In maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees, the monophyly of the family Vietnamellidae was supported and Vietnamellidae has a close relationship with Ephemerellidae.

“…The studies on the mitochondrial genomes of Ephemeroptera and Heptageniidae have increased in recent years [ 18 , 19 , 21 , 22 , 23 ]. The duplication of trnM has been observed in all reported mitochondrial genomes of Rhithrogeninae and Ecdyonurinae species (except Paegniodes cupulatus ), and the genes were arranged as CR -trnI-trnM-trnQ-trnM-ND2 , and another rearrangement (CR -trnI-trnM-trnQ- NCR -ND2 ) was reported in the Heptageniinae species [ 18 , 19 , 24 , 25 , 26 ]. In addition, a conserved intergenic spacer (IGS) between trnA and trnR was also observed in all heptageniid species [ 18 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative Mitogenome Analyses of Subgenera and Species Groups in Epeorus (Ephemeroptera: Heptageniidae)

Zhu

et al. 2022

Self Cite

Epeorus Eaton, 1881 is a diverse mayfly genus in Heptageniidae comprising more than 100 species which are further divided into nine subgenera and several species groups. However, the classification and the phylogenetic relationships among them are still uncertain. Here, 15 complete mitochondrial genomes of Epeorus were sequenced and compared together with six available ones of same genus in the NCBI database. Based on morphological classification, the 21 mitogenomes were classified into six subgenera (Proepeorus, Epeorus s.str., Belovius, Iron, Caucasiron and Siniron) and four species groups (G1, G2, montanus and longimanus). Among all analyzed mitogenomes, the gene rearrangement of trnI-trnM-trnQ-NCR-ND2 was first found occurring in three species of group G1, whereas the gene block trnI-trnM-trnQ-trnM-ND2 was observed in all other mitogenomes of Epeorus. Furthermore, the genetic composition and codon usage of species in group G1 were also significantly different from all other Epeorus species, except group longimanus. The intergenic spacer between trnA and trnR, which has the stem-loop secondary structure, occurred in all 21 mitogenomes, and the sequences of stems and loops were conserved within species groups. Furthermore, the phylogenetic analyses strongly support the monophyly of all species groups, although three of six recognized subgenera Proepeorus, Belovius, and Iron, were shown as the non-monophyletic groups.