Transgenerational accumulation of methylome changes discovered in commercially reared honey bee (Apis mellifera) queens

Yao, Yi; He, Xingjian; Barron, Andrew B.; Liu, Yi Bo; Wang, Zi Long; Yan, Wei; Zeng, Zhi

doi:10.1016/j.ibmb.2020.103476

Cited by 6 publications

(6 citation statements)

References 62 publications

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“…The left ovaries of the newly emerged samples were dissected under a microscope. Ovaries were then fixed in 4% paraformaldehyde fix solution for 16 h and paraffin sections of the ovary were created using methods described by Yi et al 68 .…”

Section: Paraffin Sectioning Of the Queen Ovarymentioning

confidence: 99%

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The diverging epigenomic landscapes of honeybee queens and workers revealed by multiomic sequencing

Zhang

Barron

et al. 2023

Insect Biochemistry and Molecular Biology

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Section: Paraffin Sectioning Of the Queen Ovarymentioning

confidence: 99%

“…The sections were photographed and overioles counted under the same microscope (40X) according to our previous methods 68 .…”

Section: Paraffin Sectioning Of the Queen Ovarymentioning

confidence: 99%

The diverging epigenomic landscapes of honeybee queens and workers revealed by multiomic sequencing

Zhang

Barron

et al. 2023

Insect Biochemistry and Molecular Biology

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“…This modification has been reported to play an important role in the caste differentiation, brain plasticity, and body development of honey bees [ 16 ]. For instance, differences in queen and worker larval diets induce changes in DNA methylation contributing to queen–worker dimorphism [ 13 , 14 , 15 , 17 , 18 ]. In addition, a genome-wide association has been reported among differential gene expression, splicing, and differential DNA methylation the overlapped GO terms point to nutrition-related activity in primitively eusocial Bombus terrestris.…”

Section: Introductionmentioning

confidence: 99%

Roles of DNA Methylation in Color Alternation of Eastern Honey Bees (Apis cerana) Induced by the Royal Jelly of Western Honey Bees (Apis mellifera)

Abdelmawla,

Li,

Shi

et al. 2024

IJMS

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Honey bees have a very interesting phenomenon where the larval diets of two different honey bee species are exchanged, resulting in altered phenotypes, namely, a honey bee nutritional crossbreed. This is a classical epigenetic process, but its underlying mechanisms remain unclear. This study aims to investigate the contribution of DNA methylation to the phenotypic alternation of a Apis mellifera–Apis cerana nutritional crossbreed. We used a full nutritional crossbreed technique to rear A. cerana queens by feeding their larvae with A. mellifera royal-jelly-based diets in an incubator. Subsequently, we compared genome-wide methylation sequencing, body color, GC ratio, and the DMRs between the nutritional crossbreed, A. cerana queens (NQs), and control, A. cerana queens (CQs). Our results showed that the NQ’s body color shifted to yellow compared to the black control queens. Genome methylation sequencing revealed that NQs had a much higher ratio of mCG than that of CQs. A total of 1020 DMGs were identified, of which 20 DMGs were enriched into key pathways for melanin synthesis, including tryptophan, tyrosine, dopamine, and phenylalanine KEGG pathways. Three key differentially methylated genes [OGDH, ALDH(NAD+) and ALDH7] showed a clear, altered DNA methylation in multiple CpG islands in NQs compared to CQs. Consequently, these findings revealed that DNA methylation participates in A. cerana–A. mellifera nutritional crossbreeding as an important epigenetic modification. This study serves as a model of cross-kingdom epigenetic mechanisms in insect body color induced by environmental factors.

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“…In insect species where DNA methylation is present, DNA methylation is largely confined to genic regions and elevated in coding regions (Bonasio et al, 2012;Feng et al, 2010;Lyko et al, 2010;Suzuki & Bird, 2008;Zemach et al, 2010). Gene body methylation has been suggested to affect gene expression and function via alternative splicing (Bonasio et al, 2012;Flores et al, 2012;Foret et al, 2012;Libbrecht et al, 2016;Li-Byarlay et al, 2013;Lyko et al, 2010), nucleosome stability (Hunt et al, 2013) or regulation of transcription elongation (Bird, 2002;Lorincz et al, 2004;Luco et al, 2010;Maunakea et al, 2010;Zilberman & Henikoff, 2007).…”

Section: Introductionmentioning

confidence: 99%

“…DNA methylation has been largely studied by whole-genome bisulphite sequencing (BS-seq) for different samples, probing a wide variety of developmental and environmental conditions (Cingolani et al, 2013;Drewell et al, 2014;Feng et al, 2010;Foret et al, 2012;Galbraith et al, 2015;Harris et al, 2019;He et al, 2017;Herb et al, 2012Herb et al, , 2018Li et al, 2017;Li-Byarlay et al, 2013;Lyko et al, 2010;Remnant et al, 2016;Xu et al, 2019;Yagound et al, 2019Yagound et al, , 2020Yao Yi et al, 2020;Zemach et al, 2010). Although all studies have reported low levels of DNA methylation, restricted almost exclusively to cytosines in CpG context, it has been difficult to compare studies even on the same species due to several factors: (1) potential differences in data quality control; (2) use of different computational methods and detection thresholds; and (3) mapping of BS-seq reads to different genome assemblies and annotation versions (Elsik et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Tools and applications for integrative analysis of DNA methylation in social insects

Morandin

Brendel

2021

Molecular Ecology Resources

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DNA methylation is a common epigenetic signalling tool and an important biological process which is widely studied in a large array of species. The presence, level and function of DNA methylation vary greatly across species. In some insects, DNA methylation systems are minimal, and overall methylation rates tend to be low in all studied insect species. Low methylation levels probed by whole‐genome bisulphite sequencing require great care with respect to data quality control and interpretation. Here, we introduce BWASP/R, a complete workflow that allows efficient, scalable and entirely reproducible analyses of raw DNA methylation sequencing data. Consistent application of quality control filters and analysis parameters provides fair comparisons among different studies and an integrated view of all experiments on one species. We describe the capabilities of the BWASP/R workflow by re‐analysing several publicly available social insect WGBS data sets, comprising 70 samples and cumulatively 147 replicates from four different species. We show that the CpG methylome comprises only about 1.5% of CpG sites in the honeybee genome and that the cumulative data are consistent with genetic signatures of site accessibility and physiological control of methylation levels.

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Transgenerational accumulation of methylome changes discovered in commercially reared honey bee (Apis mellifera) queens

Cited by 6 publications

References 62 publications

The diverging epigenomic landscapes of honeybee queens and workers revealed by multiomic sequencing

The diverging epigenomic landscapes of honeybee queens and workers revealed by multiomic sequencing

Roles of DNA Methylation in Color Alternation of Eastern Honey Bees (Apis cerana) Induced by the Royal Jelly of Western Honey Bees (Apis mellifera)

Tools and applications for integrative analysis of DNA methylation in social insects

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