The complete mitochondrial genome of Ideopsis similis (Lepidoptera: Nymphalidae: Danainae)

Mitogenomic phylogeny of nymphalid subfamilies confirms the basal clade position of Danainae (Insecta: Lepidoptera: Nymphalidae)

The phylogenetic relationships among the nymphalid subfamilies have largely been resolved using both morphological and molecular datasets, with the exception of a conflicting basal clade position for Libytheinae or Danainae that remains contentious between morphological and molecular studies. Several phylogenomic analyses have found that the danaine clade is sister to other nymphalid subfamilies; however, it largely depends on utilizing different molecular datasets, analysis methods, and taxon sampling. This study aimed to resolve the basal clade position and relationships among subfamilies and tribes of Nymphalinae by combining the most comprehensive available mitogenomic datasets with various analyses methods by incorporating a new Symbrenthia lilaea Hewitson sequence data. Phylogenetic relationships among 11 nymphalid subfamilies and the tribes of Nymphalinae were inferred by combining new and available mitogenomic sequence data from 80 ingroup and six outgroup species. The phylogenetic trees were reconstructed using maximum-likelihood (ML) and Bayesian inference (BI) methods based on five concatenated datasets: amino acid sequences and nucleotides from different combinations of protein-coding genes (PCGs), ribosomal RNA (rRNAs), and transfer RNA (tRNAs). Danainae is well-supported as the basal clade and sister to the remaining nymphalid subfamilies, except for the paraphyletic Libytheinae. Libytheinae was either recovered as a sister to the danaine clade followed by the satyrine clade or sister to the nymphaline + heliconiine clades, and is consistent with recent phylogenetic studies on Nymphalidae. The monophyletic Nymphalinae has been recovered in all analyses and resolves tribal-level relationships with high support values in both BI and ML analyses. We supported the monophyletic Nymphalini as a sister clade to Victorini, Melitaeini, and Kallimini + Junoniini with high supporting values in BI and ML analyses, which is consistent with previously published morphological and molecular studies.

Characterization of complete mitochondrial genome of the common tiger, Danaus genutia (Lepidoptera: Nymphalidae: Danainae) and phylogenetic implications within the subfamily Danainae

Nymphalidae is the most diverse butterfly family worldwide, with more than 6000 species, whereas the mitogenomic data of nymphalid species, especially the subfamily Danainae, is still lacking for more comprehensive systematic studies. To this contribution, the complete mitogenome of Danaus genutia (Lepidoptera: Nymphalidae: Danainae) was determined via sequencing and annotating. The mitogenome in total consists of 15,255 base pairs (bp), containing 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a 440-bp noncoding A+T-rich region. Furthermore, phylogeny of the subfamily Danainae was reconstructed applying maximum likelihood and Bayesian inference on the basis of the mitogenomic data sets. Combined with our analysis and previous studies, the genus-level phylogenetic relationships within the subfamily Danainae are ((Tirumala + Danaus) + ((Idea + Euploea) + (Ideopsis + Parantica))). This study offers molecular information and provides a new perspective for phylogenetic research within the subfamily Danainae.

The complete mitochondrial genome of Parantica sita sita (Lepidoptera: Nymphalidae: Danainae) revealing substantial genetic divergence from its sibling subspecies P. s. niphonica

Currently, there are two subspecies of the chestnut tiger butterfly (Parantica sita) recognized in China. P. s. sita is widely distributed in southwest China and P. s. niphonica in Taiwan. Periodically, Taiwan Island and the Chinese mainland have been connected and separated because of sea level changes caused by Pleistocene glaciations, most likely influencing the genetic structure among P. sita populations on both sides of the Taiwan Strait. Also, P. s. niphonica's well-documented long-distance migration may have influenced genetic differentiation within this species as well. So, investigation of the genetic differentiation of these two subspecies is well warranted. In this study, we sequenced the complete mitogenome (15,156 bp in length) of P. s. sita and its general characteristics agreed with general butterfly mitogenomic characteristics. However, when compared genetically with P. s. niphonica, P. s. sita diverged substantially. First, there were 4.1% variable sites between these two subspecies, with 5.3% at COI and 3.8% at COII, differences much greater than those expected of general interspecific divergences in butterflies. Second, there was a 59 bp fragment deletion in the A + T rich region of P. s. sita and, third, the relationships of these two subspecies and P. luzonensis could not be distinguished using Bayesian inference and P. s. niphonica first clustered with P. luzonensis, rather than P. s. sita, using maximum likelihood. Based on these results, we propose that P. s. sita and P. s. niphonica are independent species instead of subspecies. This proposal should be clarified through further research.

The complete mitochondrial genome of Damora sagana and phylogenetic analyses of the family Nymphalidae

The monotypic genus Damora (Nymphalidae, Heliconiinae) contains a single species, Damora sagana, which is widely distributed across southern China. Herein, its complete mitogenome was sequenced to further understand lepidopteran mitogenome characteristics, reconstruct the nymphalid family phylogeny, and infer the subdivision of Heliconiinae species. The circular mitogenome was 15,151 bp long, abundant in A and T, and comprised of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and one control region with a gene arrangement typical of lepidopteran mitogenomes. ATN codons initiated all PCGs, except cytochrome c oxidase subunit 1 (COX1), which was initiated by a CGA sequence as has been observed in other lepidopterans. Three PCGs (COX1, COX2 and ND4) employed a single T termination signal, whereas others had the typical complete termination codon (TAA). All tRNA genes were folded into the typical cloverleaf structure except for tRNA-Ser (AGN). The A+T-rich region included the conserved motif 'ATAGA' followed by a 17 bp poly-T stretch, which was also observed in tribe Argynnini mitogenomes. A phylogenetic tree was constructed via multiple methods using the 13 PCGs data of D. sagana and other available mitogenomes of nymphalid species. All three phylogenetic trees yielded the same topology. These results were consistent with those from previous studies of most major nymphalid groups, except those regarding tribe subdivision in certain subfamilies such as Argynnini + (Acraeini + Heliconiini) for Heliconiine. Furthermore, our analyses identified that the genus Cethosia was grouped with the genus Acraea composing the tribe Acraeini with strong support.

The complete mitochondrial genome of Papilio glaucus and its phylogenetic implications

Due to the intriguing morphology, lifecycle, and diversity of butterflies and moths, Lepidoptera are emerging as model organisms for the study of genetics, evolution and speciation. The progress of these studies relies on decoding Lepidoptera genomes, both nuclear and mitochondrial. Here we describe a protocol to obtain mitogenomes from Next Generation Sequencing reads performed for whole-genome sequencing and report the complete mitogenome of Papilio (Pterourus) glaucus. The circular mitogenome is 15,306 bp in length and rich in A and T. It contains 13 protein-coding genes (PCGs), 22 transfer-RNA-coding genes (tRNA), and 2 ribosomal-RNA-coding genes (rRNA), with a gene order typical for mitogenomes of Lepidoptera. We performed phylogenetic analyses based on PCG and RNA-coding genes or protein sequences using Bayesian Inference and Maximum Likelihood methods. The phylogenetic trees consistently show that among species with available mitogenomes Papilio glaucus is the closest to Papilio (Agehana) maraho from Asia.

The complete mitochondrial genome of the Orange Hairstreak Japonica lutea (Lepidoptera: Lycaenidae: Theclinae)

The complete mitochondrial genome of Japonica lutea is 15,225 bp in length, containing 37 typical insect genes: 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and a non-coding AT-rich region. All the 13 PCGs are initiated with ATN, except for COI gene which is started by CGA. Nine PCGs use the complete termination codon (TAN), whereas the COI, COII, ND4 and ND5 genes end with single nucleotide T. In total, 131 bp intergenic spacers and 31 bp overlapping sequences are interspersed throughout the whole genome. The two rRNA genes (lrRNA and srRNA) are 1327 bp and 770 bp in size, with their AT contents of 87.8% and 85.5%, respectively. All tRNAs display typical secondary cloverleaf structures except for tRNA^Ser(AGN) which loses the DHU arm. The 401 bp long AT-rich region contains several features characteristic of the lepidopterans, such as the ATAGA motif followed by a 19 bp poly-T stretch, a microsatellite-like (AT)₇ element preceded by the ATTTA motif and a 9 bp poly-A stretch.