DNA Methylation Patterns in the Social Spider, Stegodyphus dumicola

Liu, Shenglin; Aageaard, Anne; Bechsgaard, Jesper; Bilde, Trine

doi:10.3390/genes10020137

Cited by 50 publications

(62 citation statements)

References 74 publications

(100 reference statements)

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“…Weighted methylation level per gene per caste, averaged across colonies, was binned into four categories, no methylation, low (>0–0.2), medium (0.2–0.7), and high (0.7–1), as in Liu et al. (). The red dot indicates the mean with 95% confidence intervals.…”

Section: Resultsmentioning

confidence: 99%

Methylation and gene expression differences between reproductive and sterile bumblebee workers

2019

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Phenotypic plasticity is the production of multiple phenotypes from a single genome and is notably observed in social insects. Multiple epigenetic mechanisms have been associated with social insect plasticity, with DNA methylation being explored to the greatest extent. DNA methylation is thought to play a role in caste determination in Apis mellifera, and other social insects, but there is limited knowledge on its role in other bee species. In this study, we analyzed whole genome bisulfite sequencing and RNA‐seq data sets from head tissue of reproductive and sterile castes of the eusocial bumblebee Bombus terrestris. We found that genome‐wide methylation in B. terrestris is similar to other holometabolous insects and does not differ between reproductive castes. We did, however, find differentially methylated genes between castes, which are enriched for multiple biological processes including reproduction. However, we found no relationship between differential methylation and differential gene expression or differential exon usage between castes. Our results also indicate high intercolony variation in methylation. These findings suggest that methylation is associated with caste differences but may serve an alternate function, other than direct caste determination in this species. This study provides the first insights into the nature of a bumblebee caste‐specific methylome as well as its interaction with gene expression and caste‐specific alternative splicing, providing greater understanding of the role of methylation in phenotypic plasticity within social bee species. Future experimental work is needed to determine the function of methylation and other epigenetic mechanisms in insects.

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Section: Resultsmentioning

confidence: 99%

Methylation and gene expression differences between reproductive and sterile bumblebee workers

2019

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“…1A, supplementary table S1), including NCBI (https://www.ncbi.nlm.nih.gov/) and HGSC (https://www.hgsc.bcm.edu/). Specifically, we used the genomic data of the social spiders Stegodyphus mimosarum (v1.0, NCBI) (Sanggaard et al 2014) and S. dumicola (Liu et al 2019), and the solitary spiders Parasteatoda tepidariorum (v2.0, NCBI) (Schwager et al 2017), Acanthoscurria geniculata (v1, NCBI) (Sanggaard et al 2014), Nephila clavipes (v1.0, NCBI) (Babb et al 2017), Loxosceles reclusa (v1.0, HGSC) and Latrodectus hesperus (v1.0, HGSC).…”

Section: Data Retrieval and Sequence Analysismentioning

confidence: 99%

“…Adapters and reads with a quality score < 20 were trimmed with Trimmomatic (Bolger et al 2014). We mapped all the clean reads to the S. dumicola genome (Liu et al 2019) using RSEM (Li & Dewey 2011) to obtain expected counts and transcripts per million (TPM). We removed genes with low expression that did not meet one of two criteria: (1) counts per million (TPM) greater than one in at least half the samples, or (2) TPM > 1 in all samples of a given tissue.…”

Section: Expression Profiles Of Rapidly Evolving Genes In Four Tissuementioning

confidence: 99%

“…While sociality has also evolved multiple times independently in spiders (Johannesen et al 2007), the high complexity and large size of spider genomes has constrained the development of genomic resources for spiders (Schwager et al 2017;Babb et al 2017;Sanggaard et al 2014;Liu et al 2019;Garb et al 2018), so that comparative genomic studies of spider sociality have lagged behind other groups such as social insects. Previous comparative genomic studies including spiders have compared newly sequenced spider genomes to available insect genomes (Sanggaard et al 2014;Babb et al 2017), but not across spiders or among other arachnids.…”

Section: Introductionmentioning

confidence: 99%

“…Building on previous comparative genomic work in social insects, we performed one of the first spider comparative genomic studies and focused in particular on identifying putative genomic signatures associated with the evolution of social life in spiders. Specifically, we used recently available genomes from seven spider species (Sanggaard et al 2014;Liu et al 2019;Babb et al 2017;Schwager et al 2017), including two social spiders with independent origins of sociality (Settepani et al 2016;Johannesen et al 2007) from the genus Stegodyphus (Liu et al 2019;Sanggaard et al 2014). We aimed to identify genome content and genome-wide patterns of molecular evolution that differ between social and solitary spiders.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Comparative genomics identifies putative signatures of sociality in spiders

Tong

Najm

Pinter‐Wollman

et al. 2019

Preprint

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Comparative genomics has begun to elucidate the genomic basis of social life in insects but insight into the genomic basis of spider sociality has lagged behind. To begin to characterize genomic signatures associated with the evolution of social life in spiders, we performed one of the first spider comparative genomics studies including five solitary species and two social species, representing two independent origins of sociality in the genus Stegodyphus. We found that the two social spider species had a large expansion of gene families associated with transport and metabolic processes and an elevated genomewide rate of molecular evolution compared with the five solitary spider species. Genes that were rapidly evolving in the two social species relative to the five solitary species were enriched for transport, behavior, and immune functions, while genes that were rapidly evolving in the solitary species were enriched for energy metabolism processes. Most rapidly evolving genes in the social species S. dumicola were broadly expressed across four tissues and enriched for transport functions, but 12 rapidly evolving genes showed brain-specific expression and were enriched for social behavioral processes. Altogether, our study identifies putative genomic signatures and potential candidate genes associated with spider sociality. These results indicate that future spider comparative genomic studies, including broader sampling and additional independent origins of sociality, can further clarify the genomic causes and consequences of social life.

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Epigenetics in Crustaceans

Vogt

2023

Epigenetics in Aquaculture

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DNA Methylation Patterns in the Social Spider, Stegodyphus dumicola

Cited by 50 publications

References 74 publications

Methylation and gene expression differences between reproductive and sterile bumblebee workers

Methylation and gene expression differences between reproductive and sterile bumblebee workers

Comparative genomics identifies putative signatures of sociality in spiders

Epigenetics in Crustaceans

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