We annotated the assemblies using the MAKER2 annotation pipeline (version 2.31.10) over two rounds: 1) an evidence-based annotation round using EST, mRNA-seq and protein homology evidence from TriTrypDB (release-47) along with our repeat-masking output. The second round is an ab initio round using AUGUSTUS, with the pre-trained Leishmania tarentolae as the model organism. After completion of all annotation rounds, we assigned functional annotations from the Uniprot and Pfam databases using blast+ and InterProScan.