DOI: 10.5061/dryad.jdfn2z3jn
title: A plant virus differentially alters DNA methylation in two cryptic species of a hemipteran vector

description: This study investigated DNA methylation patterns in two cryptic species (B
 and Q) of the sweet potato whitefly, Bemisia tabaci (Gennadius), following
 the acquisition of the tomato yellow curl virus, a single-stranded DNA
 virus. The methylation levels in genomic features such as promoters, gene
 bodies, and transposable elements in both cryptic species were described
 in this study. While overall trends were found to be similar, specific
 differences in methylation levels were observed. Virus-induced
 differentially methylated regions (DMRs) were associated with different
 genes in each cryptic species and were negatively correlated with
 differential gene expression. These DMRs were analyzed for changes in gene
 expression and alternative splicing, revealing clusters of hyper- and
 hypomethylated genes related to virus-vector interactions, immune
 functions, and detoxification processes. These methylation differences may
 help explain the distinct biological and physiological traits observed
 between the B and Q cryptic species.
description: This dataset was generated from bisulfite-converted sequencing of
 DNA from non-viruliferous and viruliferous whiteflies.
description: # A plant virus differentially alters DNA methylation in two cryptic
 species of a hemipteran vector
 [https://doi.org/10.5061/dryad.jdfn2z3jn](https://doi.org/10.5061/dryad.jdfn2z3jn) ## Description of the data and file structure The deposited dataset includes methylation calling files from whitefly B and Q cryptic species, from non-viruliferous and viruliferous samples. The OmicsBox (.box) file contains gene annotations for Q cryptic species and can be accessed using [OmicsBox](https://www.biobam.com/download-omicsbox/). Methylation reports are formatted as , see [https://felixkrueger.github.io/Bismark/bismark/methylation_extraction/](https://felixkrueger.github.io/Bismark/bismark/methylation_extraction/) for more information. SeqMonk files (.smk) with calls for methylation can be accessed using [SeqMonk](https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Transposable element annotations have been deposited and can be found in the files with "EDTA" in their file names, see [https://github.com/oushujun/EDTA](https://github.com/oushujun/EDTA) for more information. Files "all_data_filtered_promoter.csv.gz" and "all_data_filtered_gene_body.csv.gz" contain the Position, ID, Methylation level (units: percent methylation within a genomic feature), CpGoe, Group, Sequence, and Description for promoters and gene bodies, respectively. ## Code/Software Custom R scripts with comments have been deposited. The scripts are named after their associated figures. All input files can also be found within the supplementary tables or additional files as called in the scripts. Files can be extracted from their compressed format (.gz) using [gunzip](https://linux.die.net/man/1/gunzip). ## Acronyms * **MEAM1 or B**: Middle East Asia Minor 1 (B cryptic species of *Bemisia tabaci*) * **MED or Q**: Mediterranean (Q cryptic species of *Bemisia tabaci*) * **c**: control/non-viruliferous * **v**: viruliferous * **CpG**: Cytosine-phosphate-Guanine (DNA methylation) * **cds**: Coding Sequence * **EDTA**: Extensive de-novo Transposable Element Annotator (a tool for identifying transposable elements) * **TE**: Transposable Element * **LTR**: Long Terminal Repeat * **SINE**: Short Interspersed Nuclear Element * **LINE**: Long Interspersed Nuclear Element * **MITEs**: Miniature Inverted-repeat Transposable Elements * **TIR**: Terminal Inverted Repeat * **DTA**: A superfamily of DNA transposons named after hobo, Ac, and Tam3 elements (*hAT*) * **DTC**: A superfamily of DNA transposons also known as *CACTA* * **DTH**: Transposable elements belonging to the *PIF/Harbinger* superfamily * **DTM**: A superfamily of DNA transposons also known as *Mutator* * **DTT**: A superfamily of transposable elements also known as Tc1/Mariner * **Helitron**: A type of rolling-circle transposable element ## File Types * **gff3**: General Feature Format version 3 (a file format for describing genes and other features of DNA, RNA, and protein sequences) * **fa**: FASTA (a text-based format for nucleotide sequences) * **box**: Contains gene annotations (File format compatible with OmicsBox) * **smk**: Contains methylation data (File format comparable with SeqMonk) * **csv**: Comma-Separated Values * **tsv**: Tab-Separated Values * **gz**: Gzip (a file compression format)