Functional genomic tools for emerging model species

Gudmunds, Erik; Wheat, Christopher W.; Khila, Abderrahman; Husby, Arild

doi:10.1016/j.tree.2022.07.004

Cited by 24 publications

(18 citation statements)

References 104 publications

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“…However, existing annotations provide only a hint on how these genes may influence morph development. Our results thus echo recent calls for a broader application of functional validation tools, in order to understand how lineage-specific genes contribute to phenotypic variation in natural populations 52 .…”

Section: Discussionsupporting

confidence: 82%

The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies

Tunström

Nilén

Chikhi

et al. 2023

Preprint

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Sex-limited morphs can provide profound insights into the evolution and genomic architecture of complex phenotypes. Inter-sexual mimicry is one particular type of sex-limited polymorphism in which a novel morph resembles the opposite sex. While inter-sexual mimics are known in both sexes and a diverse range of animals, their evolutionary origin is poorly understood. Here, we investigated the genomic basis of female-limited morphs and male mimicry in the Common Bluetail damselfly. Differential gene expression between morphs has been documented in damselflies, but no causal locus has been previously identified. We found that male-mimicry originated in an ancestrally sexually-dimorphic lineage in association with multiple structural changes, probably driven by TE transposition. These changes resulted in ~900 kb of novel genomic content that is partly shared by male mimics in a close relative, indicating that male mimicry is a trans-species polymorphism. More recently, a third morph originated following the translocation of part of the male-mimicry sequence into a genomic position ~3.5 mb apart. We provide evidence of balancing selection maintaining male-mimicry, in line with previous field population studies. Our results underscore how structural variants affecting a handful of potentially regulatory genes and morph-specific genes, can give rise to novel and complex phenotypic polymorphisms.

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Section: Discussionsupporting

confidence: 82%

The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies

Tunström

Nilén

Chikhi

et al. 2023

Preprint

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“…We did uncover two interesting candidate genes, both involved in flight behaviour in Drosophila melanogaster . Future studies could investigate their expression and methylation profiles across ontogenetic stages and assess their potential functions associated with migratory behaviour using, for example, RNAi or CRISPR‐Cas9 methodologies (Gudmunds et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Environmental stress during larval development induces DNA methylation shifts in the migratory painted lady butterfly (Vanessa cardui)

et al. 2023

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Organisms are forced to adapt to seasonal variation in both abiotic and biotic factors. Butterflies and moths (lepidopterans) have adopted strategies to cope with unfavourable conditions by either entering a state of dormancy and metabolic inactivity (diapause) or by migrating to regions with more favourable conditions, or a combination thereof (Urquhart, 1976;Williams, 1930). While the mechanistic underpinnings of diapause in lepidopterans have been investigated in some detail (e.g.,

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“…We found that methylation proportion at NR1D1 , but not at CLDN22 remained related to infection status, and that recruitment probability of fledged juveniles infected by S. trachea was positively related to methylation levels at NR1D1 . This underscores the importance of performing follow‐up studies on putative candidate genes, and ideally the need for functional studies on methylation levels at candidate genes (Gudmunds et al, 2022 ; Husby, 2020 , 2022 ).…”

Section: Discussionmentioning

confidence: 99%

“…Nonetheless, the limited sample size of our RRBS dataset reduces the power to detect CpG sites with small differences in DNA methylation and the limited sample size could also lead to inflation of effect sizes. For the above reasons, it is important that the DMCs identified here should be regarded as candidate loci until verification or ideally functional studies have been done (Gudmunds et al, 2022 ). Accordingly, the MS‐HRM analyses we used to verify the relationship between methylation proportion and infection status for NR1D1 and CLDN22 serve as a first step toward substantiating the results of the differential methylation analyses in this study.…”

Section: Discussionmentioning

confidence: 99%

Infection by a helminth parasite is associated with changes in DNA methylation in the house sparrow

Lundregan

Mäkinen

Buer

et al. 2022

Ecology and Evolution

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Parasites can exert strong selective pressures on their hosts and influence the evolution of host immunity. While several studies have examined the genetic basis for parasite resistance, the role of epigenetics in the immune response to parasites is less understood. Yet, epigenetic modifications, such as changes in DNA methylation, may allow species to respond rapidly to parasite prevalence or virulence. To test the role of DNA methylation in relation to parasite infection, we examined genome‐wide DNA methylation before and during infection by a parasitic nematode, Syngamus trachea , in a natural population of house sparrows ( Passer domesticus ) using reduced representation bisulfite sequencing (RRBS). We found that DNA methylation levels were slightly lower in infected house sparrows, and we identified candidate genes relating to the initial immune response, activation of innate and adaptive immunity, and mucus membrane functional integrity that were differentially methylated between infected and control birds. Subsequently, we used methylation‐sensitive high‐resolution melting (MS‐HRM) analyses to verify the relationship between methylation proportion and S. trachea infection status at two candidate genes in a larger sample dataset. We found that methylation level at NR1D1 , but not CLDN22 , remained related to infection status and that juvenile recruitment probability was positively related to methylation level at NR1D1 . This underscores the importance of performing follow‐up studies on candidate genes. Our findings demonstrate that plasticity in the immune response to parasites can be epigenetically mediated and highlight the potential for epigenetic studies in natural populations to provide further mechanistic insight into host–parasite interactions.

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Functional genomic tools for emerging model species

Cited by 24 publications

References 104 publications

The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies

The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies

Environmental stress during larval development induces DNA methylation shifts in the migratory painted lady butterfly (Vanessa cardui)

Infection by a helminth parasite is associated with changes in DNA methylation in the house sparrow

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