NDLI: Whole genome sequencing and methylome analysis of the wild guinea pig

Content Provider	Springer Nature : BioMed Central
Author	Weyrich, Alexandra Schüllermann, Tino Heeger, Felix Jeschek, Marie Mazzoni, Camila J Chen, Wei Schumann, Kathrin Fickel, Joerns
Abstract	Background DNA methylation is a heritable mechanism that acts in response to environmental changes, lifestyle and diseases by influencing gene expression in eukaryotes. Epigenetic studies of wild organisms are mandatory to understand their role in e.g. adaptational processes in the great variety of ecological niches. However, strategies to address those questions on a methylome scale are widely missing. In this study we present such a strategy and describe a whole genome sequence and methylome analysis of the wild guinea pig. Results We generated a full Wild guinea pig (Cavia aperea) genome sequence with enhanced coverage of methylated regions, benefiting from the available sequence of the domesticated relative Cavia porcellus. This new genome sequence was then used as reference to map the sequence reads of bisulfite treated Wild guinea pig sequencing libraries to investigate DNA-methylation patterns at nucleotide-specific level, by using our here described method, named ‘DNA-enrichment-bisulfite-sequencing’ (MEBS). The results achieved using MEBS matched those of standard methods in other mammalian model species. The technique is cost efficient, and incorporates both methylation enrichment results and a nucleotide-specific resolution even without a whole genome sequence available. Thus MEBS can be easily applied to extend methylation enrichment studies to a nucleotide-specific level. Conclusions The approach is suited to study methylomes of not yet sequenced mammals at single nucleotide resolution. The strategy is transferable to other mammalian species by applying the nuclear genome sequence of a close relative. It is therefore of interest for studies on a variety of wild species trying to answer evolutionary, adaptational, ecological or medical questions by epigenetic mechanisms.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-15-1036.pdf
Ending Page	12
Page Count	12
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/1471-2164-15-1036
Journal	BMC Genomics
Issue Number	1
Volume Number	15
Language	English
Publisher	BioMed Central
Publisher Date	2014-11-28
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Methylated DNA-enrichment-bisulfite-sequencing (MEBS) Immunoprecipitation Methyl-binding domain protein (MBD) Bisulfite Next-generation-sequencing Reference sequence Cavia
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

An integrative approach for efficient analysis of whole genome bisulfite sequencing data

A pipeline for sample tagging of whole genome bisulfite sequencing data using genotypes of whole genome sequencing

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing

Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array

Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

Whole genome sequencing of Borrelia miyamotoi isolate Izh-4: reference for a complex bacterial genome

Whole genome sequencing and methylome analysis of the wild guinea pig

Similar Documents

An integrative approach for efficient analysis of whole genome bisulfite sequencing data

A pipeline for sample tagging of whole genome bisulfite sequencing data using genotypes of whole genome sequencing

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing

Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array

Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

Whole genome sequencing of Borrelia miyamotoi isolate Izh-4: reference for a complex bacterial genome

Whole genome sequencing and methylome analysis of the wild guinea pig