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A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

ABSTRACT: A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

PROVIDER: PRJEB36595 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	ERR3890310_1.fastq.gz	Fastqsanger.gz
	ERR3890310_2.fastq.gz	Fastqsanger.gz
	ERR3890320_1.fastq.gz	Fastqsanger.gz
	ERR3890320_2.fastq.gz	Fastqsanger.gz

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A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning.

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

The complete mitochondrial genome of the wood tiger moth (<i>Arctia plantaginis</i>) and phylogenetic analyses within Arctiinae.

Project description:We report the assembly and annotation of the complete mitochondrial genome of the warningly-coloured wood tiger moth (Arctia plantaginis) and investigate its phylogenetic position within Arctiinae. The A.plantaginis mitogenome is 15,479 bp long with 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNA genes, and an A + T-rich region (D-loop). The phylogenetic analyses based on 13 protein-coding genes showed A.plantaginis clustering within a clade of species with white wings and yellow or red bodies. This result can be useful in understanding the evolution of coloration in Arctiid moths.

| S-EPMC8259826 | biostudies-literature

Evaluating responses to temperature during pre-metamorphosis and carry-over effects at post-metamorphosis in the wood tiger moth (Arctia plantaginis).

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'.

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Defense against predators incurs high reproductive costs for the aposematic moth <i>Arctia plantaginis</i>.

Project description:To understand how variation in warning displays evolves and is maintained, we need to understand not only how perceivers of these traits select color and toxicity but also the sources of the genetic and phenotypic variation exposed to selection by them. We studied these aspects in the wood tiger moth Arctia plantaginis, which has two locally co-occurring male color morphs in Europe: yellow and white. When threatened, both morphs produce defensive secretions from their abdomen and from thoracic glands. Abdominal fluid has shown to be more important against invertebrate predators than avian predators, and the defensive secretion of the yellow morph is more effective against ants. Here, we focused on the morph-linked reproductive costs of secretion of the abdominal fluid and quantified the proportion of phenotypic and genetic variation in it. We hypothesized that, if yellow males pay higher reproductive costs for their more effective aposematic display, the subsequent higher mating success of white males could offer one explanation for the maintenance of the polymorphism. We first found that the heritable variation in the quantity of abdominal secretion was very low (h 2 = 0.006) and the quantity of defensive secretion was not dependent on the male morph. Second, deploying the abdominal defensive secretion decreased the reproductive output of both color morphs equally. This suggests that potential costs of pigment production and chemical defense against invertebrates are not linked in A. plantaginis. Furthermore, our results indicate that environmentally induced variation in chemical defense can alter an individual's fitness significantly.

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Parasemia plantaginis transcriptome

Project description:De novo assembled transcriptome of the aposematic wood tiger moth (Parasemia plantaginis)

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