The data and code used for the Amoebidium genome project.
Genome assembly and raw genomic reads can be found here: PRJEB68378.
EM-seq and RNA-seq raw data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE249241
This repository includes processed files and is divided into 5 folders:
This folder contains the reference chromosome scale genome for Amoebidium appalachense and all the associated annotation files.
This folder contains the original fasta files used to build the alignments and the resulting IQtree phylogenies in Newick format.
This folder contains the TEcounts outputs for both control and 5-Azacytidine treatments for Amoebidium appalachense and Sphaeroforma arctica.
This folder contains the genomes of the two alternative isolate genomes, an isolate of Amoebidium appalachense (9181) and an isolate of Amoebidium parasiticum (9257).
A collection of scripts that covers the R code used to generate the analysis of the various graphics in the paper.
If you use any of this material, reference the original manuscript:
Sarre LA, Kim IV, Ovchinnikov V, Olivetta M, Suga H, Dudin O, Sebé-Pedrós A, de Mendoza A. DNA methylation enables recurrent endogenisation of giant viruses in an animal relative. 2024. Science Advances. 10, eado6406.DOI:10.1126/sciadv.ado6406