The macronuclear genome of anaerobic ciliate Entodinium caudatum reveals its biological features adapted to the distinct rumen environment

Entodinium caudatum is an anaerobic binucleated ciliate representing the most dominant protozoal species in the rumen. However, its biological features are largely unknown due to the inability to establish an axenic culture. In this study, we primally sequenced its macronucleus (MAC) genome to aid the understanding of its metabolism, physiology, ecology. We isolated the MAC of E. caudatum strain MZG-1 and sequenced the MAC genome using Illumina MiSeq, MinION, and PacBio RSII systems. De novo assembly of the MiSeq sequence reads followed with subsequent scaffolding with MinION and PacBio reads resulted in a draft MAC genome about 117 Mbp. A large number of carbohydrate-active enzymes were likely acquired through horizontal gene transfer. About 8.74% of the E. caudatum predicted proteome was predicted as proteases. The MAC genome of E. caudatum will help better understand its important roles in rumen carbohydrate metabolism, and interaction with other members of the rumen microbiome. •E. caudatum possibly has nanochromosomes, and its new telomeric repeats can be used to complete the E. caudatum chromosomes.•Numerous peptidases found in the E. caudatum genome corroborates its high bacterivory and proteolysis.•Many carbohydrate-active enzymes were likely acquired by E. caudatum via horizontal gene transfer from other rumen microbes.•This is the first MAC genome from rumen ciliates, thus helping genomic and transcriptomic studies of other rumen ciliates.