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Title: Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases
Abstract

There is a growing focus on the role of DNA methylation in the ability of marine invertebrates to rapidly respond to changing environmental factors and anthropogenic impacts. However, genome‐wide DNA methylation studies in nonmodel organisms are currently hampered by a limited understanding of methodological biases. Here, we compare three methods for quantifying DNA methylation at single base‐pair resolution—whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and methyl‐CpG binding domain bisulfite sequencing (MBDBS)—using multiple individuals from two reef‐building coral species with contrasting environmental sensitivity. All methods reveal substantially greater methylation inMontipora capitata(11.4%) than the more sensitivePocillopora acuta(2.9%). The majority of CpG methylation in both species occurs in gene bodies and flanking regions. In both species, MBDBS has the greatest capacity for detecting CpGs in coding regions at our sequencing depth, but MBDBS may be influenced by intrasample methylation heterogeneity. RRBS yields robust information for specific loci albeit without enrichment of any particular genome feature and with significantly reduced genome coverage. Relative genome size strongly influences the number and location of CpGs detected by each method when sequencing depth is limited, illuminating nuances in cross‐species comparisons. As genome‐wide methylation differences, supported by data across bisulfite sequencing methods, may contribute to environmental sensitivity phenotypes in critical marine invertebrate taxa, these data provide a genomic resource for investigating the functional role of DNA methylation in environmental tolerance.

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Award ID(s):
1634167 1921465 1756623
NSF-PAR ID:
10446419
Author(s) / Creator(s):
 ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  
Publisher / Repository:
Wiley-Blackwell
Date Published:
Journal Name:
Molecular Ecology Resources
Volume:
22
Issue:
4
ISSN:
1755-098X
Page Range / eLocation ID:
p. 1247-1261
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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