Mitogenomes of Giant-Skipper Butterflies reveal an ancient split between deep and shallow root feeders

Comparative mitochondrial genome analysis and phylogenetic relationship among lepidopteran species

Lepidoptera has rich species including many agricultural pests and economical insects around the world. The mitochondrial genomes (mitogenomes) were utilized to explore the phylogenetic relationships between difference taxonomic levels in Lepidoptera. However, the knowledge of mitogenomic characteristics and phylogenetic position about superfamily-level in this order is unresolved. In this study, we integrated 794 mitogenomes consisting of 37 genes and a noncoding control region, which covered 26 lepidopteran superfamilies from newly sequenced and publicly available genomes for comparative genomic and phylogenetic analysis. In primitive taxon, putative start codon of cox1 gene was ATA or ATT instead of CGA, but stop codon of that showed four types, namely TAA, TAG, TA and T. The 7-bp overlap between atp8 and atp6 presented as "ATGATAA". Moreover, the most frequently utilized amino acids were leucine (UUA) in 13 PCGs. Phylogenetic analysis showed that the main backbone relationship in Lepidoptera was (Hepialoidea + (Nepticuloidea + (Adeloidea + (Tischerioidea + (Tineoidea + (Yponomeutoidea + (Gracillarioidea + (Papilionoidea + ((Zygaenoidea + Tortricoidea) + (Gelechioidea + (Pyraloidea + ((Geometroidea + Noctuoidea) + (Lasiocampoidea + Bombycoidea))))))))))))).

Macrostructural Evolution of the Mitogenome of Butterflies (Lepidoptera, Papilionoidea)

Simple Summary

Papilionoidea is a superfamily of Lepidoptera encompassing about 19,000 species. In the present work, we study the evolution of the structure of the mitogenome of these lepidopterans. The mechanisms generating the eight arrangements known for Papilionoidea were investigated analysing the movements of different mitochondrial genes. Five newly sequenced/assembled mitogenomes were included in our analysis involving more than 600 genomes. We provide new findings that help to understand the evolution of the gene orders MIQGO, IMQGO, 2S1GO, ES1GO and S1NGO in different butterflies. We demonstrate that the evolution of the 2S1GO in Lycaenidae followed a complicated pathway with multiple events of duplication and loss of trnS1 and changes in anticodon. We describe two new gene orders 2FFGO and 4QGO for Ampittia subvittatus (Hesperiidae) and Bhutanitis thaidina (Papilionidae).

Abstract

The mitogenome of the species belonging to the Papilionodea (Lepidoptera) is a double stranded circular molecule containing the 37 genes shared by Metazoa. Eight mitochondrial gene orders are known in the Papilionoidea. MIQGO is the plesiomorphic gene order for this superfamily, while other mitochondrial arrangements have a very limited distribution. 2S1GO gene order is an exception and is present in several Lycaenidae and one species of Hesperiidae. We studied the macrostructural changes generating the gene orders of butterflies by analysing a large data set (611 taxa) containing 5 new mitochondrial sequences/assemblies and 87 de novo annotated mitogenomes. Our analysis supports a possible origin of the intergenic spacer trnQ-nad2, characterising MIQGO, from trnM. We showed that the homoplasious gene order IMQGO, shared by butterflies, species of ants, beetles and aphids, evolved through different transformational pathways. We identify a complicated evolutionary scenario for 2S1GO in Lycaenidae, characterised by multiple events of duplication/loss and change in anticodon of trnS1. We show that the gene orders ES1GO and S1NGO originated through a tandem duplication random loss mechanism. We describe two novel gene orders. Ampittia subvittatus (Hesperiidae) exhibits the gene order 2FFGO, characterised by two copies of trnF, one located in the canonical position and a second placed in the opposite strand between trnR and trnN. Bhutanitis thaidina (Papilionidae) exhibits the gene order 4QGO, characterised by the quadruplication of trnQ.

Mitogenomes of Nine Asian Skipper Genera and Their Phylogenetic Position (Lepidoptera: Hesperiidae: Pyrginae)

In this study, complete mitochondrial genomes of nine species representing three tribes in the subfamily Pyrginae sensu lato were newly sequenced. The mitogenomes are closed double-stranded circular molecules, with the length ranging from 15,232 bp to 15,559 bp, which all encode 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. The orientation and gene order of these nine mitogenomes are identical to the inferred ancestral arrangement of insects. All PCGs exhibit the typical start codon ATN except for cox1 (using CGA) and cox2 (using TTG) in Mooreana trichoneura. Most of the PCGs terminate with a TAA stop codon, while cox1, cox2, nad4, and nad5 end with the incomplete codon single T. For the different datasets, we found that the one comprising all 37 genes of the mitogenome produced the highest nodal support, indicating that the inclusion of RNAs improves the phylogenetic signal. This study re-confirmed the status of Capila, Pseudocoladenia, and Sarangesa; namely, Capila belongs to the tribe Tagiadini, and Pseudocoladenia and Sarangesa to the tribe Celaenorrhini. Diagnostic characters distinguishing the two tribes, the length of the forewing cell and labial palpi, are no longer significant. Two populations of Pseudocoladenia dan fabia from China and Myanmar and P. dan dhyana from Thailand are confirmed as conspecific.

Comparative Mitogenomic Analysis of Five Awl Skippers (Lepidoptera: Hesperiidae: Coeliadinae) and Their Phylogenetic Implications

Simple Summary

The subfamily Coeliadinae (Lepidoptera: Hesperiidae) is a unique group of over 70 species in the butterfly family, and its mitochondrial genome data still needs to be supplemented. This study sequenced and analyzed five additional complete mitochondrial genomes of the Coeliadinae species (Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis) and compared them in detail with those of the other known skipper mitogenomes. All five of these mitogenomes have the typical lepidopteran mitogenome characteristics of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding region. Our results indicate that their structure, nucleotide composition, codon usage, secondary structure of tRNAs, and so on, are highly conserved. Expanded sampling and gene data from the GenBank, phylogenetic analyses using maximum likelihood, and Bayesian inference methods indicate that Coeliadinae is monophyletic. These results contribute toward refining the phylogeny.

Abstract

To determine the significance of mitochondrial genome characteristics in revealing phylogenetic relationships and to shed light on the molecular evolution of the Coeliadinae species, the complete mitochondrial genomes (mitogenomes) of five Coeliadinae species were newly sequenced and analyzed, including Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis. The results show that all five mitogenomes are double-strand circular DNA molecules, with lengths of 15,340 bp, 15,295 bp, 15,304 bp, 15,295 bp, and 15,289 bp, respectively, and contain the typical 37 genes and a control region. Most protein-coding genes (PCGs) begin with ATN, with 3 types of stop codons including TAA, TAG, and an incomplete codon T-; most of the genes terminate with TAA. All of the transfer RNA genes (tRNAs) present the typical cloverleaf secondary structure except for the trnS1. Several conserved structural elements are found in the AT-rich region. Phylogenetic analyses based on three datasets (PCGs, PRT, and 12PRT) and using maximum likelihood (ML) and Bayesian inference (BI) methods show strong support for the monophyly of Coeliadinae, and the relationships of the five species are (B. exclamationis + ((B. harisa + (B. oedipodea + B. miracula)) + H. schoenherr)).

Complete mitochondrial genomes of three skippers in the tribe Aeromachini (Lepidoptera: Hesperiidae: Hesperiinae) and their phylogenetic implications

The mitochondrial genome is now widely used in the study of phylogenetics and molecular evolution due to its maternal inheritance, fast evolutionary rate, and highly conserved gene content. To explore the phylogenetic relationships of the tribe Aeromachini within the subfamily Hesperiinae at the mitochondrial genomic level, we sequenced and annotated the complete mitogenomes of 3 skippers: Ampittia virgata, Halpe nephele, and Onryza maga (new mitogenomes for 2 genera) with a total length of 15,333 bp, 15,291 bp, and 15,381 bp, respectively. The mitogenomes all contain 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a noncoding A + T-rich region and are consistent with other lepidopterans in gene order and type. In addition, we reconstructed the phylogenetic trees of Hesperiinae using maximum likelihood (ML) and Bayesian inference (BI) methods based on mitogenomic data. Results show that the tribe Aeromachini in this study robustly constitute a monophyletic group in the subfamily Hesperiinae, with the relationships Coeliadinae + (Euschemoninae + (Pyrginae + ((Eudaminae + Tagiadinae) + (Heteropterinae + ((Trapezitinae + Barcinae) + Hesperiinae))))). Moreover, our study supports the view that Apostictopterus fuliginosus and Barca bicolor should be placed out of the subfamily Hesperiinae.

Unique Duplication of trnN in Odontoptilum angulatum (Lepidoptera: Pyrginae) and Phylogeny within Hesperiidae

To explore the variation and relationship between gene rearrangement and phylogenetic effectiveness of mitogenomes among lineages of the diversification of the tribe Tagiadini in the subfamily Pyrginae, we sequenced the complete mitogenome of Odontoptilum angulatum. The genome is 15,361 bp with the typical 37 genes, a large AT-rich region and an additional trnN (trnN2), which is completely identical to trnN (sequence similarity: 100%). The gene order differs from the typical Lepidoptera-specific arrangement and is unique to Hesperiidae. The presence of a "pseudo-trnS1" in the non-coding region between trnN1 and trnN2 supports the hypothesis that the presence of an extra trnN can be explained by the tandem duplication-random loss (TDRL) model. Regarding the phylogenetic analyses, we found that the dataset comprising all 37 genes produced the highest node support, as well as a monophyly of Pyrginae, indicating that the inclusion of RNAs improves the phylogenetic signal. Relationships among the subfamilies in Hesperiidae were also in general agreement with the results of previous studies. The monophyly of Tagiadini is strongly supported. Our study provides a new orientation for application of compositional and mutational biases of mitogenomes in phylogenetic analysis of Tagiadini and even all Hesperiidae based on larger taxon sampling in the future.

The mitogenome of a Malagasy butterfly Malaza fastuosus (Mabille, 1884) recovered from the holotype collected over 140 years ago adds support for a new subfamily of Hesperiidae (Lepidoptera)

Malaza fastuosus is a lavishly patterned skipper butterfly from a genus that has three described species, all endemic to the mainland of Madagascar. To our knowledge, M. fastuosus has not been collected for nearly 50 years. To evaluate the power of our techniques to recover DNA, we used a single foreleg of an at least 140-year-old holotype specimen from the collection of the Natural History Museum London with no destruction of external morphology to extract DNA and assemble a complete mitogenome from next generation sequencing reads. The resulting 15 540 bp mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A+T rich region, similarly to other Lepidoptera mitogenomes. Here we provide the first mitogenome also for Trapezitinae (Rachelia extrusus). Phylogenetic analysis of available skipper mitogenomes places Malaza outside of Trapezitinae and Barcinae + Hesperiinae, with a possible sister relationship to Heteropterinae. Of these, at least Heteropterinae, Trapezitinae, and almost all Hesperiinae have monocot-feeding caterpillars. Malaza appears to be an evolutionarily highly distinct ancient lineage, morphologically with several unusual hesperiid features. The monotypic subfamily Malazinae Lees & Grishin subfam. nov. (type genus Malaza) is proposed to reflect this morphological and molecular evidence.

Complete mitochondrial genome of the silver stripped skipper, Leptalina unicolor (Lepidoptera: Hesperiidae)

The silver stripped skipper, Leptalina unicolor Bremer and Grey, 1853 (Lepidoptera: Hesperiidae), is listed as endangered insect in South Korea. We sequenced the whole genome (15,854 bp) of L. unicolor species using Next-Generation Sequencing method and the subsequent gap-filling method. This genome included a set of typical genes and one major non-coding A + T-rich region, with an arrangement identical to that observed in most lepidopteran genomes. Twelve protein-coding genes (PCGs) had the typical ATN start codon, whereas COI had the atypical CGA codon that is frequently found in the start region of the lepidopteran COI. The 757-bp long A + T-rich region was the second largest among completely sequenced Hesperiidae, which ranged from 234 to 793 bp. Phylogenetic reconstruction was performed by maximum-likelihood method using the concatenated sequences of 13 PCGs and two rRNAs of available species of Hesperiidae, including that of L. unicolor (a total of 28 species). The resulting phylogeny provided strong support for monophyletic Heteropterinae in which L. unicolor belongs, with the highest nodal support and a sister relationship between current L. unicolor and co-subfamilial species Carterocephalus silvicola with a bootstrap value of 91%.

The mitochondrial genomes of three skippers: Insights into the evolution of the family Hesperiidae (Lepidoptera)

We sequenced the mitogenomes of Astictopterus jama, Isoteinon lamprospilus and Notocrypta curvifascia to obtain further insight into the mitogenomic architecture evolution and performed phylogenetic reconstruction using 29 Hesperiidae mitogenome sequences. The complete mitogenome sequences of A. jama, I. lamprospilus and N. curvifascia are 15,430, 15,430 and 15,546 bp in size, respectively. All contain 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and an A + T-rich region. Nucleotide composition is A + T biased, and the majority of the protein-coding genes exhibit a negative AT-skew, which is reflected in the nucleotide composition, codon, and amino acid usage. The A + T-rich region is comprised of nonrepetitive sequences, including the motif ATAGA followed by a poly-T stretch, a microsatellite-like element next to the ATTTA motif, and a poly-A adjacent to tRNAs. Although most genes evolve under a strong purifying selection, the entire nad gene family (especially nad6) exhibits somewhat relaxed purifying selection, and atp8, evolving under a highly relaxed selection, is an outlier in the family Hesperiidae. Several different approaches relatively consistently indicated that nad6, atp8 and nad4 are comparatively fast-evolving genes in this family, which may have implications for future phylogenetic, population genetics and species diagnostics studies. For phylogenetic analyses of Hesperiidae, we tested a few datasets, and found that the one comprising all 37 genes produced the highest node support, indicating that the inclusion of RNAs improves the phylogenetic signal. Results indicate that subfamilies Euschemoninae, Heteropterinae, and Coeliadinae are monophyletic with strong nodal support, but Pyrginae and Eudaminae are paraphyletic. Finally, we confirm that A. jama and I. lamprospilus are close relatives.

The complete mitochondrial genomes of two skipper genera (Lepidoptera: Hesperiidae) and their associated phylogenetic analysis

The systematic positions of two hesperiid genera, Apostictopterus and Barca (Lepidoptera: Hesperiidae), remain ambiguous. We sequenced and annotated the two mitogenomes of Apostictopterus fuliginosus and Barca bicolor and inferred the phylogenetic positions of the two genera within the Hesperiidae based on the available mitogenomes. The lengths of the two circular mitogenomes of A. fuliginosus and B. bicolor are 15,417 and 15,574 base pairs (bp), respectively. These two mitogenomes show similar AT skew, GC skew, codon usage and nucleotide bias of AT: the GC skew of the two species is negative, and the AT skew of A. fuliginosus is negative, while the AT skew of B. bicolor is slightly positive. The largest intergenic spacer is located at the same position between trnQ and ND2 in A. fuliginosus (73 bp) and B. bicolor (72 bp). Thirteen protein-coding genes (PCGs) start with ATN codons except for COI, which starts with CGA. The control regions of both mitogenomes possess a long tandem repeat, which is 30 bp long in A. fuliginosus, and 18 bp in B. bicolor. Bayesian inference and maximum likelihood methods were employed to infer the phylogenetic relationships, which suggested that A. fuliginosus and B. bicolor belong in the subfamily Hesperiinae.

The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca roots

Giant-Skippers (Megathymini) are unusual thick-bodied, moth-like butterflies whose caterpillars feed inside Yucca roots and Agave leaves. Giant-Skippers are attributed to the subfamily Hesperiinae and they are endemic to southern and mostly desert regions of the North American continent. To shed light on the genotypic determinants of their unusual phenotypic traits, we sequenced and annotated a draft genome of the largest Giant-Skipper species, the Bear (Megathymus ursus violae). The Bear skipper genome is the least heterozygous among sequenced Lepidoptera genomes, possibly due to much smaller population size and extensive inbreeding. Their lower heterozygosity helped us to obtain a high-quality genome with an N50 of 4.2 Mbp. The ~ 430 Mb genome encodes about 14000 proteins. Phylogenetic analysis supports placement of Giant-Skippers with Grass-Skippers (Hesperiinae). We find that proteins involved in odorant and taste sensing as well as in oxidative reactions have diverged significantly in Megathymus as compared to Lerema, another Grass-Skipper. In addition, the Giant-Skipper has lost several odorant and gustatory receptors and possesses many fewer (1/3-1/2 of other skippers) anti-oxidative enzymes. Such differences may be related to the unusual life style of Giant-Skippers: they do not feed as adults, and their caterpillars feed inside Yuccas and Agaves, which provide a source of antioxidants such as polyphenols.

Anchored phylogenomics illuminates the skipper butterfly tree of life

BACKGROUND

Butterflies (Papilionoidea) are perhaps the most charismatic insect lineage, yet phylogenetic relationships among them remain incompletely studied and controversial. This is especially true for skippers (Hesperiidae), one of the most species-rich and poorly studied butterfly families.

METHODS

To infer a robust phylogenomic hypothesis for Hesperiidae, we sequenced nearly 400 loci using Anchored Hybrid Enrichment and sampled all tribes and more than 120 genera of skippers. Molecular datasets were analyzed using maximum-likelihood, parsimony and coalescent multi-species phylogenetic methods.

RESULTS

All analyses converged on a novel, robust phylogenetic hypothesis for skippers. Different optimality criteria and methodologies recovered almost identical phylogenetic trees with strong nodal support at nearly all nodes and all taxonomic levels. Our results support Coeliadinae as the sister group to the remaining skippers, the monotypic Euschemoninae as the sister group to all other subfamilies but Coeliadinae, and the monophyly of Eudaminae plus Pyrginae. Within Pyrginae, Celaenorrhinini and Tagiadini are sister groups, the Neotropical firetips, Pyrrhopygini, are sister to all other tribes but Celaenorrhinini and Tagiadini. Achlyodini is recovered as the sister group to Carcharodini, and Erynnini as sister group to Pyrgini. Within the grass skippers (Hesperiinae), there is strong support for the monophyly of Aeromachini plus remaining Hesperiinae. The giant skippers (Agathymus and Megathymus) once classified as a subfamily, are recovered as monophyletic with strong support, but are deeply nested within Hesperiinae.

CONCLUSIONS

Anchored Hybrid Enrichment sequencing resulted in a large amount of data that built the foundation for a new, robust evolutionary tree of skippers. The newly inferred phylogenetic tree resolves long-standing systematic issues and changes our understanding of the skipper tree of life. These resultsenhance understanding of the evolution of one of the most species-rich butterfly families.