Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) enriettii, Isolate CUR178, Strain LV7

Leishmania (Mundinia) enriettii is a parasitic kinetoplastid first isolated from a guinea pig in Brazil in 1946. We present the complete genome sequence of L. (M.) enriettii, isolate CUR178, strain LV763, sequenced using combined short-read and long-read technologies. This will facilitate a greater understanding of the genome diversity within L. (M.) enriettii. L eishmania enriettii was first isolated from a guinea pig (Cavia porcellus) in Brazil in 1946 and formally described 2 years later (1). The group of related species previously known as the L. enriettii complex is now referred to as the subgenusMundinia (2, 3). A previous genome sequence of L. (M.) enriettii, isolate LEM3045 (MCAV/BR/1995/CUR3), was assembled but with a large number of unplaced contigs, higher gap content, and relatively lower N50 value compared to other Leishmania genomes (2). Additional L. (M.) enriettii isolates have been associated with leishmaniasis lesions in guinea pigs in the Curitiba Metropolitan Region of southern Brazil, 50 years after the first case (4, 5). We report here the complete genome assembly and annotation of L. (M.) enriettii, isolate CUR178, strain LV763 (WHO code MCAV/BR/2001/CUR178; LV763). This will contribute to our understanding of the biology of L. (M.) enriettii and the genomic diversity existing in this species. We obtained intracellular amastigote parasites from six naturally infected guinea pigs from the rural area of Mandirituba (state of Paraná, Brazil). The parasites were grown using an in vitro culture system previously developed for Leishmania (Mundinia) orientalis axenic amastigotes (6) in Schneider’s insect medium at 26°C as promastigotes, then in M199 medium supplemented with 10% fetal calf serum (FCS), 2% stable human urine, 1% basal medium Eagle vitamins, and 25 mg/ml gentamicin sulfate, with subpassage to fresh medium every 4 days to sustain the parasite growth and viability. DNA was extracted and purified using a Qiagen DNeasy blood and tissue kit using the spin column protocol, according to the manufacturer’s instructions. The extracted DNA concentration was assessed using a Qubit fluorometer, microplate reader, and agarose gel electrophoresis. All sequencing libraries were based on the same extracted DNA sample to avoid any inconsistency. Short-read library construction and sequencing were contracted to (i) BGI (Shenzhen, China) for DNBSEQ libraries, producing paired-end reads (270 bp and 500 bp) using the Illumina HiSeq platform, and (ii) Aberystwyth University (Aberystwyth, UK) for TruSeq Nano DNA libraries, producing paired-end reads (300 bp) using the Illumina MiSeq platform. We performed long-read library preparation and sequencing according to the Nanopore protocol (SQK-LSK109) on R9 flow cells (FLO-MIN106). The read quality was assessed using MultiQC (7). We assembled the long reads using Flye (8), with default parameters, to generate chromosome-scale scaffolds. Then, using Minimap2 (9) and SAMtools (10), we mapped the short reads onto the assembled scaffolds to correct erroneous bases within long reads and create consensus sequences. After polishing the assembly with Pilon (11), another round of Citation Almutairi H, Urbaniak MD, Bates MD, Thomaz-Soccol V, Al-Salem WS, Dillon RJ, Bates PA, Gatherer D. 2021. Chromosome-scale assembly of the complete genome sequence of Leishmania (Mundinia) enriettii, isolate CUR178, strain LV763. Microbiol Resour Announc 10:e00575-21. https://doi.org/10 .1128/MRA.00575-21. Editor Antonis Rokas, Vanderbilt University Copyright © 2021 Almutairi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Derek Gatherer, d.gatherer@lancaster.ac.uk. Received 3 June 2021 Accepted 16 August 2021 Published 9 September 2021 Volume 10 Issue 36 e00575-21 mra.asm.org 1 GENOME SEQUENCES