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.

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.

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 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.

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)