The complete mitochondrial genome of the wood tiger moth (Arctia plantaginis) and phylogenetic analyses within Arctiinae.
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ABSTRACT:
SUBMITTER: Galarza JA
PROVIDER: S-EPMC8259826 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. FINDINGS:We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ?1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. CONCLUSIONS:We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.
| S-EPMC7433188 | biostudies-literature
Project description:In this paper we report the public availability of transcriptome resources for the aposematic wood tiger moth (Parasemia plantaginis). A comprehensive assembly methods, quality statistics, and annotation are provided. This reference transcriptome may serve as a useful resource for investigating functional gene activity in aposematic Lepidopteran species. All data is freely available at the European Nucleotide Archive (http://www.ebi.ac.uk/ena) under study accession number: PRJEB14172.
| S-EPMC5374854 | biostudies-literature
Project description:Insect metamorphosis is one of the most recognized processes delimiting transitions between phenotypes. It has been traditionally postulated as an adaptive process decoupling traits between life stages, allowing evolutionary independence of pre- and post-metamorphic phenotypes. However, the degree of autonomy between these life stages varies depending on the species and has not been studied in detail over multiple traits simultaneously. Here, we reared full-sib larvae of the warningly coloured wood tiger moth (Arctia plantaginis) in different temperatures and examined their responses for phenotypic (melanization change, number of moults), gene expression (RNA-seq and qPCR of candidate genes for melanization and flight performance) and life-histories traits (pupal weight, and larval and pupal ages). In the emerging adults, we examined their phenotypes (melanization and size) and compared them at three condition proxies: heat absorption (ability to engage flight), flight metabolism (ability to sustain flight) and overall flight performance. We found that some larval responses, as evidenced by gene expression and change in melanization, did not have an effect on the adult (i.e. size and wing melanization), whereas other adult traits such as heat absorption, body melanization and flight performance were found to be impacted by rearing temperature. Adults reared at high temperature showed higher resting metabolic rate, lower body melanization, faster heating rate, lower body temperature at take-off and inferior flight performance than cold-reared adults. Thus, our results did not unambiguously support the environment-matching hypothesis. Our results illustrate the importance of assessing multiple traits across life stages as these may only be partly decoupled by metamorphosis. This article is part of the theme issue 'The evolution of complete metamorphosis'.
| S-EPMC6711291 | biostudies-literature
Project description:BackgroundAcoustic signals are used by many animals to transmit information. Variation in the acoustic characteristics of these signals often covaries with morphology and can relay information about an individual’s fitness, sex, species, and/or other characteristics important for both mating and defense. Tiger moths (Lepidoptera: Erebidae: Arctiinae) use modified cuticular plates called “tymbal organs” to produce ultrasonic clicks which can aposematically signal their toxicity, mimic the signals of other species, or, in some cases, disrupt bat echolocation. The morphology of the tymbal organs and the sounds they produce vary greatly between species, but it is unclear how the variation in morphology gives rise to the variation in acoustic characteristics. This is the first study to determine how the morphological features of tymbals can predict the acoustic characteristics of the signals they produce.ResultsWe show that the number of striations on the tymbal surface (historically known as “microtymbals”) and, to a lesser extent, the ratio of the projected surface area of the tymbal to that of the thorax have a strong, positive correlation with the number of clicks a moth produces per unit time. We also found that some clades have significantly different regression coefficients, and thus the relationship between microtymbals and click rate is also dependent on the shared ancestry of different species.ConclusionsOur predictive model allows the click rates of moths to be estimated using preserved material (e.g., from museums) in cases where live specimens are unavailable. This has the potential to greatly accelerate our understanding of the distribution of sound production and acoustic anti-bat strategies employed by tiger moths. Such knowledge will generate new insights into the evolutionary history of tiger moth anti-predator defenses on a global scale.
| S-EPMC6902478 | biostudies-literature
Project description:Mitochondrial genomes have proved to be a powerful tool in resolving phylogenetic relationship. In order to understand the mitogenome characteristics and phylogenetic position of the genus Dosinia, we sequenced the complete mitochondrial genomes of Dosinia altior and Dosinia troscheli (Bivalvia: Veneridae), compared them with that of Dosinia japonica and established a phylogenetic tree for Veneridae. The mitogenomes of D. altior (17,536 bp) and D. troscheli (17,229 bp) are the two smallest in Veneridae, which include 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. The mitogenomes of the Dosinia species are similar in size, gene content, AT content, AT- and GC- skews, and gene arrangement. The phylogenetic relationships of family Veneridae were established based on 12 concatenated protein-coding genes using maximum likelihood and Bayesian analyses, which supported that Dosininae and Meretricinae have a closer relationship, with Tapetinae being the sister taxon. The information obtained in this study will contribute to further understanding of the molecular features of bivalve mitogenomes and the evolutionary history of the genus Dosinia.
| S-EPMC5931646 | biostudies-other
Project description:Warning (aposematic) and cryptic colorations appear to be mutually incompatible because the primary function of the former is to increase detectability, whereas the function of the latter is to decrease it. Disruptive coloration is a type of crypsis in which the color pattern breaks up the outline of the prey, thus hindering its detection. This delusion can work even when the prey's pattern elements are highly contrasting; thus, it is possible for an animal's coloration to combine both warning and disruptive functions. The coloration of the wood tiger moth (Parasemia plantaginis) is such that the moth is conspicuous when it rests on vegetation, but when it feigns death and drops to the grass- and litter-covered ground, it is hard to detect. This death-feigning behavior therefore immediately switches the function of its coloration from signaling to camouflage. We experimentally tested whether the forewing patterning of wood tiger moths could function as disruptive coloration against certain backgrounds. Using actual forewing patterns of wood tiger moths, we crafted artificial paper moths and placed them on a background image resembling a natural litter and grass background. We manipulated the disruptiveness of the wing pattern so that all (marginal pattern) or none (nonmarginal pattern) of the markings extended to the edge of the wing. Paper moths, each with a hidden palatable food item, were offered to great tits (Parus major) in a large aviary where the birds could search for and attack the "moths" according to their detectability. The results showed that prey items with the disruptive marginal pattern were attacked less often than prey without it. However, the disruptive function was apparent only when the prey was brighter than the background. These results suggest that warning coloration and disruptive coloration can work in concert and that the moth, by feigning death, can switch the function of its coloration from warning to disruptive.
| S-EPMC4662304 | biostudies-other
Project description:The focus of this study was to reconstruct a phylogenetic hypothesis for the moth subfamily Arctiinae (tiger moths, woolly bears) to investigate the evolution of larval and adult pharmacophagy of pyrrolizidine alkaloids (PAs) and the pathway to PA chemical specialization in Arctiinae. Pharmacophagy, collection of chemicals for non-nutritive purposes, is well documented in many species, including the model species Utetheisa ornatrix L. A total of 86 exemplar ingroup species representing tiger moth tribes and subtribes (68 genera) and nine outgroup species were selected. Ingroup species included the most species-rich generic groups to represent the diversity of host-plant associations and pharmacophagous behaviors found throughout Arctiinae. Up to nine genetic markers were sequenced: one mitochondrial (COI barcode region), one nuclear rRNA (D2 region, 28S rRNA), and seven nuclear protein-coding gene fragments: elongation factor 1-? protein, wingless, ribosomal protein subunit S5, carbamoylphosphate synthase domain regions, glyceraldehyde-3-phosphate dehydrogenase, isocitrate dehydrogenase and cytosolic malate dehydrogenase. A total of 6984 bp was obtained for most species. These data were analyzed using model-based phylogenetic methods: maximum likelihood (ML) and Bayesian inference (BI). Ancestral pharmacophagous behaviors and obligate PA associations were reconstructed using the resulting Bayes topology and Reconstructing Ancestral States in Phylogenies (RASP) software. Our results corroborate earlier studies on the evolution of adult pharmacophagous behaviors, suggesting that this behavior arose multiple times and is concentrated in the phaegopterine-euchromiine-ctenuchine clade (PEC). Our results suggest that PA specialization may have arisen early in the phylogeny of the subfamily and that facultative larval pharmacophagous behaviors are the derived condition.
| S-EPMC4103773 | biostudies-literature
Project description:Indigenous chicken breeds have both cultural significance and economic value since they possess unique genetic characteristics that enable them to adapt to the local environment and contribute to biodiversity, food security, and sustainable agriculture in Vietnam. To (Tò in Vietnamese) chicken, a Vietnamese indigenous chicken breed, is popularly raised in Thai Binh province; however, little known is about the genetic diversity of this breed. In this study, we sequenced the complete mitochondrial genome of To chicken for a better understanding of the diversity and origin of the breed. The results of sequencing showed that the mitochondrial genome of To chicken spans a total length of 16,784 base pairs and comprises one non-coding control region (known as the displacement-loop (D-loop) region), two ribosomal RNA genes, 13 protein-coding genes, and 22 transfer RNA genes. The phylogenetic tree analyses and estimated genetic distances based on 31 complete mitochondrial genome sequences indicated that To chicken has a close genetic distance with the Laotian native chicken breed, Lv'erwu breed in China, and Nicobari black and Kadaknath breeds in India. The result of the current study might be important for conservation, breeding, and further genetic studies of To chicken.
| S-EPMC10218117 | biostudies-literature
Project description:BACKGROUND: Phylogenetic relationships between Lagomorpha, Rodentia and Primates and their allies (Euarchontoglires) have long been debated. While it is now generally agreed that Rodentia constitutes a monophyletic sister-group of Lagomorpha and that this clade (Glires) is sister to Primates and Dermoptera, higher-level relationships within Rodentia remain contentious. RESULTS: We have sequenced and performed extensive evolutionary analyses on the mitochondrial genome of the scaly-tailed flying squirrel Anomalurus sp., an enigmatic rodent whose phylogenetic affinities have been obscure and extensively debated. Our phylogenetic analyses of the coding regions of available complete mitochondrial genome sequences from Euarchontoglires suggest that Anomalurus is a sister taxon to the Hystricognathi, and that this clade represents the most basal divergence among sampled Rodentia. Bayesian dating methods incorporating a relaxed molecular clock provide divergence-time estimates which are consistently in agreement with the fossil record and which indicate a rapid radiation within Glires around 60 million years ago. CONCLUSION: Taken together, the data presented provide a working hypothesis as to the phylogenetic placement of Anomalurus, underline the utility of mitochondrial sequences in the resolution of even relatively deep divergences and go some way to explaining the difficulty of conclusively resolving higher-level relationships within Glires with available data and methodologies.
| S-EPMC1802082 | biostudies-other
Project description:Melanin production is often considered costly, yet beneficial for thermoregulation. Studies of variation in melanization and the opposing selective forces that underlie its variability contribute greatly to understanding natural selection. We investigated whether melanization benefits are traded off with predation risk to promote observed local and geographical variation in the warning signal of adult male wood tiger moths (Parasemia plantaginis). Warning signal variation is predicted to reduce survival in aposematic species. However, in P. plantaginis, male hindwings are either yellow or white in Europe, and show continuous variation in melanized markings that cover 20 to 90 per cent of the hindwing. We found that the amount of melanization increased from 40 to 59 per cent between Estonia (58° N) and north Finland (67° N), suggesting melanization carries thermoregulatory benefits. Our thermal measurements showed that more melanic individuals warmed up more quickly on average than less melanic individuals, which probably benefits flight in cold temperatures. With extensive field experiments in central Finland and the Alpine region, we found that more melanic individuals suffered increased predation. Together, our data suggest that warning signal efficiency is constrained by thermoregulatory benefits. Differences in relative costs and benefits of melanin probably help to maintain the geographical warning signal differences.
| S-EPMC3574392 | biostudies-literature