This chapter outlines the assembly and annotation of mitochondrial genomes and transcriptomes of kinetoplastids and diplonemids using high-throughput sequencing data. The mitochondrial genomes of these protists are highly atypical, characterized by multipartition and extensive RNA editing. These complexities pose significant challenges for genome assembly, gene prediction, and transcript reconstruction. Here, we describe analytical strategies developed in our laboratories that address these issues.

Department of Biochemistry and Robert Cedergren Centre for Bioinformatics and Genomics Université de Montréal Montréal Canada

Department of Parasitology Faculty of Science Charles University BIOCEV Vestec Czechia

Division of Infectious Diseases Department of Medicine Faculty of Medicine and Dentistry University of Alberta Edmonton Canada

Faculty of Biology Lomonosov Moscow State University Moscow Russia

Institute for Information Transmission Problems Russian Academy of Sciences Moscow Russia

Institute of Parasitology Biology Centre Czech Academy of Sciences České Budějovice Czechia

Life Science Research Centre Faculty of Science University of Ostrava Ostrava Czechia

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