# Chromosomal scale assembly and functional annotation of the apicomplexan parasite Eimeria acervulina

## TL;DR

This paper presents a high-quality genome assembly and gene annotation for Eimeria acervulina, a parasite that causes coccidiosis in chickens, to aid in drug and vaccine development.

## Contribution

The study provides a chromosomal-scale genome assembly and functional annotation for Eimeria acervulina using advanced sequencing and bioinformatics methods.

## Key findings

- The genome assembly is 52 Mb with 15 chromosomes and 99% BUSCO completeness.
- 7,621 genes were predicted, with 60.97% having Pfam functions and 25.74% having Gene Ontology terms.
- Stage-specific transcriptome analysis identified 9,761 transcripts.

## Abstract

Apicomplexan parasites are single-celled obligate intracellular eukaryotic organisms that cause significant animal and human disease and pose a substantial health and socioeconomic burden worldwide. Eimeria acervulina is one such parasite of chickens, representative of several Eimeria species causing coccidiosis disease. A complete assembly of the E. acervulina genome may help identify markers of drug-resistance and design recombinant vaccines. We sequenced E. acervulina APU1 strain using Oxford Nanopore Sequencing and Illumina technology in combination with a Hi-C (Omni-C) proximity linkage library and achieved a chromosomal scale assembly using the MaSuRCA assembler. The final assembly was 52 Mb. with 15 chromosomes and 99% BUSCO completeness. A total of 7,621 genes were predicted using a pipeline of BRAKER3, GeneMark-ETP and AUGUSTUS, of which 4,647 (60.97%) have a predicted Pfam function and 1,962 (25.74%) have Gene Ontology (GO) terms matching molecular, biological, and functional classes. Stage-specific transcriptome analysis revealed 9,761 transcripts. This genome assembly and transcriptome analysis provides the foundation for identifying biologically important candidates for anticoccidial drug and vaccine development.