Refining the phylogeny of Crambidae with complete sampling of subfamilies (Lepidoptera, Pyraloidea)

Complete Mitochondrial Genome of the Eggplant Fruit and Shoot Borer, Leucinodes orbonalis Guenée (Lepidoptera: Crambidae), and Comparison with Other Pyraloid Moths

The eggplant fruit and shoot borer (EFSB) (Leucinodes orbonalis Guenée) is a devastating lepidopteran pest of eggplant (Solanum melongena L.) in the Philippines. Management of an insect pest like the EFSB requires an understanding of its biology, evolution, and adaptations. Genomic resources provide a starting point for understanding EFSB biology, as the resources can be used for phylogenetics and population structure studies. To date, genomic resources are scarce for EFSB; thus, this study generated its complete mitochondrial genome (mitogenome). The circular mitogenome is 15,244 bp-long. It contains 37 genes, namely 13 protein-coding, 22 tRNA, and 2 rRNA genes, and has conserved noncoding regions, motifs, and gene syntenies characteristic of lepidopteran mitogenomes. Some protein-coding genes start and end with non-canonical codons. The tRNA genes exhibit a conserved cloverleaf structure, with the exception in trnS1. Partitioned phylogenetic analysis using 72 pyraloids generated highly supported maximum likelihood and Bayesian inference trees revealing expected basal splits between Crambidae and Pyralidae, and Spilomelinae and Pyraustinae. Spilomelinae was recovered to be paraphyletic, with the EFSB robustly placed before the split of Spilomelinae and Pyraustinae. Overall, the EFSB mitogenome resource will be useful for delineations within Spilomelinae and population structure analysis.

The genome sequence of the Water Veneer, Acentria ephemerella (Denis & Schiffermüller, 1775)

We present a genome assembly from an individual male Acentria ephemerella (the Water Veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 340.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,748 protein coding genes.

The Complete Mitochondrial Genome of Chilo infuscatellus (Lepidoptera: Pyralidae), and Related Phylogenetic Analysis

The Chilo infuscatellus (Lepidoptera: Pyralidae) is a significant pest of sugarcane in China. The genome-level characteristics of this pest are important genetic resources for identification, phylogenetic analysis, and even management. In the present study, the complete mitogenome of C. infuscatellus was sequenced and characterized. The assembled mitochondrial genome is 15,252 bp in length and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A + T-rich region. Except for the CGA codon for the cox1 gene, the PCGs are initiated with ATN codons (ATG, ATT, and ATA). These PCGs are terminated with TAA or an incomplete termination codon of a single T. Except for the loss of the "DHU" arm for trnS1, the tRNA genes were folded into the typical cloverleaf structure. The A + T-rich region has a high AT content of 96.19% and contains the motifs "ATAGA" and "ATTTA", as well as a 19 bp poly-T stretch and microsatellite regions. The C. infuscatellus mitogenome exhibits a conserved gene order among lepidopteran insects, with a rearrangement of the trnM gene compared to the ancestral insect gene order. Phylogenetic analysis based on the 13 PCGs using Bayesian inference (BI) and maximum likelihood (ML) methods confirmed the monophyly of Pyralidae and Crambidae within Pyraloidea. The relationships between subfamilies in Pyralidae can be described as (Galleriinae + (Phycitinae + (Pyralinae + Epipaschiinae))). The "PS clade" and "non-PS clade" were formed within the family Crambidae. These findings provide valuable genetic resources for the identification, phylogenetic analysis, and management of sugarcane borers, contributing significantly to our understanding of the phylogeny of Pyraloidea insects and their evolution.

Complete mitochondrial genomes of two moths in the tribe Trichaeini (Lepidoptera: Crambidae) and their phylogenetic implications

The complete mitochondrial genomes of two Prophantis species in the tribe Trichaeini (Lepidoptera: Crambidae) were sequenced using high-throughput sequencing technology. They were assembled and annotated: The complete mitogenomes of P. octoguttalis and P. adusta were 15,197 and 15,714 bp, respectively, and contain 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region. Their arrangement was consistent with the first sequenced mitogenome of Bombyx mori (Bombycidae) in Lepidoptera, which had the trnM-trnI-trnQ rearrangement. The nucleotide composition was obviously AT-biased, and all PCGs, except for the cox1 gene (CGA), used ATN as the start codon. Except for trnS1, which lacked the DHU stem, all tRNA genes could fold into the clover-leaf structure. The features of these two mitogenomes were highly consistent with those of other species of Spilomelinae in previous studies. Phylogenetic trees of Crambidae were reconstructed based on mitogenomic data using maximum likelihood and Bayesian inference analysis methods. Results showed that Trichaeini in this study robustly constitute a monophyletic group in Spilomelinae, with the relationships (Trichaeini + Nomophilini) + ((Spilomelini + (Hymeniini + Agroterini)) + Margaroniini). However, the affinities of the six subfamilies Acentropinae, Crambinae, Glaphyriinae, Odontiinae, Schoenobiinae, and Scopariinae within the "non-PS Clade" in Crambidae remained doubtful with unstable topologies or low supports.

Characterization of four mitochondrial genomes of Crambidae (Lepidoptera, Pyraloidea) and phylogenetic implications

Loxostege turbidalis, Loxostege aeruginalis, Pyrausta despicata, and Crambus perlellus belong to Crambidae, Pyraloidea. Their mitochondrial genomes (mitogenomes) were successfully sequenced. The mitogenomes of L. turbidalis, L. aeruginalis, P. despicata, and C. perlellus are 15 240 bp, 15 339 bp, 15 389 bp, and 15 440 bp. The four mitogenomes all have a typical insect mitochondrial gene order, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one A + T rich region (control region). The PCGs are initiated by the typical ATN codons, except CGA for the cox1 gene. Most PCGs terminate with common codon TAA or TAG, the incomplete codon T is found as the stop codon for cox2, nad4, and nad5. Most tRNA genes exhibit typical cloverleaf structure, except trnS1 (AGN) lacking the dihydrouridine (DHU) arm. The secondary structure of rRNA of four mitogenomes were predicted. Poly-T structure and micro-satellite regions are conserved in control regions. The phylogenetic analyses based on 13 PCGs showed the relationships of subfamilies in Pyraloidea. Pyralidae, and Crambidae are monophyletic, respectively. Pyralidae comprises four subfamilies, which form the following topology with high support values: (Galleriinae + ((Pyralinae + Epipaschiinae)+ Phycitinae)). Crambidae includes seven subfamilies and is divided into two lineages. Pyraustinae and Spilomelinae are sister groups of each other, and form the "PS clade." Other five subfamilies (Crambinae, Acentropinae, Scopariinae, Schoenobiinae, and Glaphyriinae) form the "non-PS clade" in the Bayesian inference tree. However, Schoenobiinae is not grouped with the other four subfamilies and located at the base of Crambidae in two maximum likelihood trees.

“Lepidoptera Flies”, but Not Always…Interactions of Caterpillars and Chrysalis with Soil

Lepidoptera, an order of insects traditionally linked to the aerial habitat, are much more diverse in their living environment than the clichéd image we may have of them. The imago stage, which is the most visible in these insects, is not the one that has the most interaction with the environment (usually caterpillars) nor the one that lasts the longest (very often chrysalises). These two stages are often directly related to litter and soil, although only the interaction at the pupal stage seems to follow a phylogenetic logic with two independent evolutionary events for the preference with soil: Use of litter and the upper “O” horizon as protection against predation for the evolutionarily oldest Lepidoptera families, pupation at greater depths (up to 60 centimetres in extreme cases) for the most derived Lepidoptera families; this probably to take advantage of the thermal and moisture buffer provided by the soil. An estimate suggests that about 25% of lepidopteran species worldwide have more or less obligatory interactions with soil.

Decreasing Species Richness with Increase in Elevation and Positive Rapoport Effects of Crambidae (Lepidoptera) on Mount Taibai

Rapoport's rule proposes that a species' range size increases with the increase in a gradient (such as latitude, altitude or water depth). However, altitudinal distributions and Rapoport's rule have rarely been tested for Asian Lepidoptera. Pyraustinae and Spilomelinae (Lepidoptera: Crambidae) are extremely diverse in temperate Asia, including on Mount Taibai, which is considered a hotspot area for studying the vertical distribution patterns of insect species. Based on the investigation of altitudinal distribution data with identification by using both DNA barcoding and the morphological classification of Pyraustinae and Spilomelinae, this paper determines the altitudinal gradient pattern for these two subfamilies on the north slope of Mount Taibai, and provides a test of the universality of Rapoport's rule in Lepidoptera by using four methods, including Stevens' method, Pagel's method, Rohde's method, and the cross-species method. Our results show that the alpha diversity of Pyraustinae and Spilomelinae both decrease with rising altitude. By contrast, the species' ranges increase with rising altitude. Three of the four methods used to test Rapoport's rule yielded positive results, while Rohde's results show a unimodal distribution model and do not support Rapoport's rule. Our findings fill the research gap on the elevational diversity of Lepidoptera in temperate Asia.

Chromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees

The moth Heortia vitessoides Moore (Lepidoptera: Crambidae) is a major pest of ecologically, commercially and culturally important agarwood-producing trees in the genus Aquilaria. In particular, H. vitessoides is one of the most destructive defoliating pests of the incense tree Aquilaria sinesis, which produces a valuable fragrant wood used as incense and in traditional Chinese medicine [33]. Nevertheless, a genomic resource for H. vitessoides is lacking. Here, we present a chromosomal-level assembly for H. vitessoides, consisting of a 517 megabase (Mb) genome assembly with high physical contiguity (scaffold N50 of 18.2 Mb) and high completeness (97.9% complete BUSCO score). To aid gene annotation, 8 messenger RNA transcriptomes from different developmental stages were generated, and a total of 16,421 gene models were predicted. Expansion of gene families involved in xenobiotic metabolism and development were detected, including duplications of cytosolic sulfotransferase (SULT) genes shared among lepidopterans. In addition, small RNA sequencing of 5 developmental stages of H. vitessoides facilitated the identification of 85 lepidopteran conserved microRNAs, 94 lineage-specific microRNAs, as well as several microRNA clusters. A large proportion of the H. vitessoides genome consists of repeats, with a 29.12% total genomic contribution from transposable elements, of which long interspersed nuclear elements (LINEs) are the dominant component (17.41%). A sharp decrease in the genome-wide percentage of LINEs with lower levels of genetic distance to family consensus sequences suggests that LINE activity has peaked in H. vitessoides. In contrast, opposing patterns suggest a substantial recent increase in DNA and LTR element activity. Together with annotations of essential sesquiterpenoid hormonal pathways, neuropeptides, microRNAs and transposable elements, the high-quality genomic and transcriptomic resources we provide for the economically important moth H. vitessoides provide a platform for the development of genomic approaches to pest management, and contribute to addressing fundamental research questions in Lepidoptera.

Insects allocate eggs adaptively according to plant age, stress, disease or damage

Most herbivorous insects can only survive on a small subset of the plant species in its environment. Consequently, adult females have evolved sophisticated sensory recognition systems enabling them to find and lay eggs on plants supporting offspring development. This leads to the preference-performance or 'mother knows best' hypothesis that insects should be attracted to host plants that confer higher offspring survival. Previous work shows insects generally select plant species that are best for larval survival, although this is less likely for crops or exotic host plants. Even within a species, however, individual plants can vary greatly in potential suitability depending on age, access to water or nutrients or attack by pathogens or other herbivores. Here, I systematically review 71 studies on 62 insect species testing the preference-performance hypothesis with sets of plants varying in age, stress, fungal/microbial infection or herbivore damage. Altogether, 77% of insects tested with a native host (N = 43) allocated their eggs to plants best for offspring development, as did 64% (N = 22) of insects tested with an exotic host. Results were similar across plant age, stress, disease and damage categories. These findings show adaptive maternal behaviour in insects occurs for both host species and variation among individual plants.

The genome sequence of the ringed china-mark, Parapoynx stratiotata (Linnaeus, 1758)

We present a genome assembly from an individual male Parapoynx stratiotata (the ringed china-mark; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 478 megabases in span. The majority of the assembly (99.98%) is scaffolded into 30 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome was also assembled and is 15.4 kilobases in length.

Nine Mitochondrial Genomes of the Pyraloidea and Their Phylogenetic Implications (Lepidoptera)

Simple Summary

The Pyraloidea is a large superfamily of Lepidoptera in species composition. To date, the higher-level phylogenetic relationships in this group remain unresolved, and many taxa, with taxonomic positions historically established by morphological characters, need to be confirmed through sequencing of DNA, including mitochondrial genome sequences (mitogenomes). Here, we newly generated nine complete mitogenomes for Pyraloidea that shared identical gene content, and arrangements that are typical of Lepidoptera. The current phylogenetic results confirmed previous multilocus studies, indicating the effectiveness of mitogenomes for inference of Pyraloidea higher-level relationships. Unexpectedly, Orybina Snellen was robustly placed as basal to the remaining Pyralidae taxa, rather than nested in the Pyralinae of Pyralidae as morphologically defined and placed. Our results bring a greater understanding to Pyraloidea phylogeny, and highlight the necessity of sequencing more pyraloid taxa to reevaluate their phylogenetic positions.

Abstract

The Pyraloidea is one of the species-rich superfamilies of Lepidoptera and contains numerous economically important pest species that cause great loss in crop production. Here, we sequenced and annotated nine complete mitogenomes for Pyraloidea, and further performed various phylogenetic analyses, to improve our understanding of mitogenomic evolution and phylogeny of this superfamily. The nine mitogenomes were circular, double-stranded molecules, with the lengths ranging from 15,214 bp to 15,422 bp, which are comparable to other reported pyraloid mitogenomes in size. Gene content and arrangement were highly conserved and are typical of Lepidoptera. Based on the hitherto most extensive mitogenomic sampling, our various resulting trees showed generally congruent topologies among pyraloid subfamilies, which are almost in accordance with previous multilocus studies, indicating the suitability of mitogenomes in inferring high-level relationships of Pyraloidea. However, nodes linking subfamilies in the “non-PS clade” were not completely resolved in terms of unstable topologies or low supports, and future investigations are needed with increased taxon sampling and molecular data. Unexpectedly, Orybina Snellen, represented in a molecular phylogenetic investigation for the first time, was robustly placed as basal to the remaining Pyralidae taxa across our analyses, rather than nested in Pyralinae of Pyralidae as morphologically defined. This novel finding highlights the need to reevaluate Orybina monophyly and its phylogenetic position by incorporating additional molecular and morphological evidence.

First record and DNA barcoding of Donacaulaniloticus (Zeller, 1867) from the Iberian Peninsula (Lepidoptera: Crambidae)

Background

Donacaulaniloticus (Zeller, 1867) is known from south-eastern Europe, Middle East and Turkey to Central Asia, northern India and China and widely distributed in North Africa (Morocco, Algeria, Libya and Egypt).

New information

Donacaulaniloticus (Zeller 1867) is recorded for the first time from the Iberian Peninsula and the first DNA barcode sequence is published and compared with other European and North American Donacaula species.

An annotated checklist of the Crambidae of the region of Murcia (Spain) with new records, distribution and biological data (Lepidoptera: Pyraloidea, Crambidae)

Background

The Murcia Region (osouth-eastern Iberian Peninsula) has a great diversity of Lepidopteran fauna, as a zoogeographical crossroads and biodiversity hotspot with more than 850 butterflies and moth species recorded.

New information

In the present paper, based on an examination of museum specimens, published records and new samples, a comprehensive and critical species list of Crambidae moths (Lepidoptera: Pyraloidea) is synthesised. In total, 8 subfamilies, 50 genera and 106 species have been recorded and these are listed along with their collection, literature references and biological data including chorotype, voltinism and the flight period in the study area. The subfamilies are as follows: Acentropinae, Crambinae, Glaphyriinae, Lathrotelinae, Odontiinae, Pyraustinae, Scopariinae and Spilomelinae. Forty nine species are here newly recorded for the Murcia Region.

The First Mitogenomes of the Subfamily Odontiinae (Lepidoptera, Crambidae) and Phylogenetic Analysis of Pyraloidea

Simple Summary

The Odontiinae is a small group in the Pyraloidea comprised of 388 species in 88 genera, but externally, these moths are diverse, including heterogeneous maculation and a size range from 9 to 50 mm in total wingspan. The monophyly of Pyraloidea and the two families (Pyralidae and Crambidae) is well supported by phylogenetic analyses based on morphology and molecular data of multiple nuclear genes. However, only a few mito-phylogenetic analyses have been conducted and no mitogenome of Odontiinae species has been reported. Three complete mitogenomes of odontiine species were sequenced and analyzed for the first time herein. The results showed that Odontiinae mitogenomes shared similar genomic characters with other Pyraloidea. The phylogenetic analyses based on 13 PCGs of mitogenomes confirmed the monophyly of Odontiinae and its position within Crambidae.

Abstract

The complete mitochondrial genomes of three species of Odontiinae were newly sequenced: Dausara latiterminalis Yoshiyasu, Heortia vitessoides (Moore), and Pseudonoorda nigropunctalis (Hampson). These circular and double-stranded mitogenomes vary from 15,084 bp to 15,237 bp in size, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A + T-rich region. The nucleotide composition indicated a strong A/T bias. Most PCGs are initiated with an ATN codon and terminated by a codon of TAR. All tRNAs could be folded into the clover-leaf structure with the exception of trnS1 (AGN), in which the dihydrouridine (DHU) arm formed a simple loop, and the motif ‘ATAG’ and ‘ATTTA’ in the A + T-rich region was also founded. The phylogenomic analyses covering Odontiinae + 11 subfamilies of Pyraloidea were conducted. Similar topologies were generated from both Bayesian inference (BI) and maximum likelihood (ML) analyses based on the nucleotide and amino acid sequence data. There was some discrepancy in the sister-group relationship of Odontiinae and Glaphyriinae, and the relationships among the subfamilies in the ‘CAMMSS clade’ of the Crambidae. The results of this study suggest that mitogenomic data are useful for resolving the deep-level relationships of Pyraloidea and the topologies generated from amino acid data might be more realistic and reliable. Moreover, more mitogenomic taxon sampling and larger scale analyses with more genes or a combination of mitogenomic and nuclear genes are needed to reconstruct a comprehensive framework of the pyraloid phylogeny.

The Role of Satellite DNAs in Genome Architecture and Sex Chromosome Evolution in Crambidae Moths

Tandem repeats are important parts of eukaryotic genomes being crucial e.g., for centromere and telomere function and chromatin modulation. In Lepidoptera, knowledge of tandem repeats is very limited despite the growing number of sequenced genomes. Here we introduce seven new satellite DNAs (satDNAs), which more than doubles the number of currently known lepidopteran satDNAs. The satDNAs were identified in genomes of three species of Crambidae moths, namely Ostrinia nubilalis, Cydalima perspectalis, and Diatraea postlineella, using graph-based computational pipeline RepeatExplorer. These repeats varied in their abundance and showed high variability within and between species, although some degree of conservation was noted. The satDNAs showed a scattered distribution, often on both autosomes and sex chromosomes, with the exception of both satellites in D. postlineella, in which the satDNAs were located at a single autosomal locus. Three satDNAs were abundant on the W chromosomes of O. nubilalis and C. perspectalis, thus contributing to their differentiation from the Z chromosomes. To provide background for the in situ localization of the satDNAs, we performed a detailed cytogenetic analysis of the karyotypes of all three species. This comparative analysis revealed differences in chromosome number, number and location of rDNA clusters, and molecular differentiation of sex chromosomes.