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Genomic divergence during in range expansion in the spider Argiope bruennichi

ABSTRACT: We have sequenced whole genomes and transcriptomes of an expanding spider species to identify signatures of adaptive divergence

PROVIDER: PRJEB6920 | ENA |

REPOSITORIES: ENA

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Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation.

Project description:BackgroundArgiope bruennichi, the European wasp spider, has been investigated intensively as a focal species for studies on sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. Therefore, we assembled a high-quality chromosome-level reference genome of the European wasp spider as a tool for more in-depth future studies.FindingsWe generated, de novo, a 1.67 Gb genome assembly of A. bruennichi using 21.8× Pacific Biosciences sequencing, polished with 19.8× Illumina paired-end sequencing data, and proximity ligation (Hi-C)-based scaffolding. This resulted in an N50 scaffold size of 124 Mb and an N50 contig size of 288 kb. We found 98.4% of the genome to be contained in 13 scaffolds, fitting the expected number of chromosomes (n = 13). Analyses showed the presence of 91.1% of complete arthropod BUSCOs, indicating a high-quality assembly.ConclusionsWe present the first chromosome-level genome assembly in the order Araneae. With this genomic resource, we open the door for more precise and informative studies on evolution and adaptation not only in A. bruennichi but also in arachnids overall, shedding light on questions such as the genomic architecture of traits, whole-genome duplication, and the genomic mechanisms behind silk and venom evolution.

| S-EPMC7788392 | biostudies-literature

RNA-Seq of Wolbachia infected and uninfected spider mites

Project description:Four spider mites strains, 1-3 day old adult females with and without Wolbachia infection (Turt_FI, Turt_Fu),and 1 day old adult males with and without Wolbachia infection (Turt_MI, Turt_MU).The four samples were sequenced on the Illumina HiSeq2000 platform.

2014-12-17 | E-MTAB-2491 | biostudies-arrayexpress

Fine-scale adaptive divergence and plasticity revealed by genetic and phenotypic variation in a marine invertebrate

Project description:The interplay between phenotypic plasticity and adaptive evolution has long been an important topic of evolutionary biology. This process is critical to our understanding of a species evolutionary potential in light of rapid climate changes. Despite recent theoretical work, empirical studies of natural populations, especially in marine invertebrates, are scarce. In this study, we investigated the relationship between adaptive divergence and plasticity by integrating genetic and phenotypic variation in Pacific oysters from its natural range in China. Genome resequencing of 371 oysters revealed unexpected fine-scale genetic structure that is largely consistent with phenotypic divergence in growth, physiology, thermal tolerance and gene expression across environmental gradient. These findings suggest that selection and local adaptation are pervasive and together with limited gene flow shape adaptive divergence. Plasticity in gene expression is positively correlated with evolved divergence, indicating that plasticity is adaptive and likely favored by selection in organisms facing dynamic environments such as oysters. Divergence in heat response and tolerance implies that the evolutionary potential to a warming climate differs among oyster populations. We suggest that trade-offs in energy allocation are important to adaptive divergence with acetylation playing a role in energy depression under thermal stress.

2018-07-27 | PXD008057 | Pride

Small RNA-Seq of Wolbachia infected and uninfected spider mites

Project description:Four spider mites strains, 1-3 day old adult females with and without Wolbachia infection (FI, FU),and 1 day old adult males with and without Wolbachia infection (MI, MU).The four samples were sequenced on the Illumina HiSeq2000 platform.

2015-01-15 | E-MTAB-2606 | biostudies-arrayexpress

spider microbiomes

Project description:spider microbiomes

| PRJNA526944 | ENA

Gene expression profile in response to SDH2 deletion during filament formation in both Spider medium and Spider medium supplemented with 100mM glucose

Project description:Transcriptional profiling of Candida albicans comparing SDH2 deletion mutant cells with the wild-type cells in both Spider medium and Spider medium supplemented with 100mM glucose

2016-08-23 | GSE50155 | GEO

Spirodiclofen resistance in the spider mite Tetranychus urticae

Project description:The goal of our microarray experiments was to compare the gene expression profile of two spirodiclofen resistant spider mite strains (SR-VP and SR-TK) with that of a susceptible spider mite strain (LS-VL)

2013-06-26 | GSE43538 | GEO

Spider mite preliminary feeding experiment with mites reared on bean and two Arabidopsis thaliana accessions

Project description:We sequenced messenger RNA from mixed stages of the two-spotted spider mite (Tetranychus urticae) reared on bean (Phaseolus vulgaris cv California Red Kidney; the laboratory host plant for mites) and two Arabidopsis thaliana accessions which were considered to either be susceptible (Kondara) or resistant (Bla-2) to mite feeding. This pilot experiment was conducted to assess gene expression differences of mites grown on sensitive versus resistant Arabidopsis accessions, as well as differences in mites feeding on different host species. The expression data was used for gene model validation of genes predicted by EuGene in the spider mite genome and to assess gene expression levels. Examination of gene expression of spider mites reared on beans and two Arabidopsis accessions (Kondara and Bla-2).

2011-11-23 | E-GEOD-31525 | biostudies-arrayexpress

Developmental profiling of gene expression in embryos of the spider Parasteatoda tepidariorum

Project description:The common house spider Parasteatoda tepidariorum is a chelicerate model organism for studying developmental mechanisms and their evolution in arthropods. In contrast to the well-studied model insect, Drosophila melanogaster, embryos of the spider undergo patterning in a cellular environment from early stages (at least after the number of the nuclei increase to 16). Use of spider embryos provide new opportunities to understand the evolution of developmental mechanisms underlying arthropod body plans. This analysis aims to generate genome-scale, developmental profiles of gene expression in embryos of the spider P. tepidariorum, which facilitate a wide range of studies using this spider species.

2018-04-05 | GSE112712 | GEO

Spider mite preliminary feeding experiment with mites reared on bean and two Arabidopsis thaliana accessions

2011-11-23 | GSE31525 | GEO

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