Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae

Abstract

We provide the raw and processed data produced during the genome sequencing of isolates from six species of parasites from the sub-family Leishmaniinae: Leishmania martiniquensis (Thailand), Leishmania orientalis (Thailand), Leishmania enriettii (Brazil), Leishmania sp. Ghana, Leishmania sp. Namibia and Porcisia hertigi (Panama). De novo assembly was performed using Nanopore long reads to construct chromosome backbone scaffolds. We then corrected erroneous base calling by mapping short Illumina paired-end reads onto the initial assembly. Data has been deposited at NCBI as follows: raw sequencing output in the Sequence Read Archive, finished genomes in GenBank, and ancillary data in BioSample and BioProject. Derived data such as quality scoring, SAM files, genome annotations and repeat sequence lists have been deposited in Lancaster University’s electronic data archive with DOIs provided for each item. Our coding workflow has been deposited in GitHub and Zenodo repositories. This data constitutes a resource for the comparative genomics of parasites and for further applications in general and clinical parasitology.

Comparative Draft Genomes of Leishmania orientalis Isolate PCM2 (Formerly Named Leishmania siamensis) and Leishmania martiniquensis Isolate PCM3 from the Southern Province of Thailand

“…Generally, Leishmania genomes range from 29 to 33 Mb in size (approximately 8300 genes) and are organized into 34 to 36 chromosomes, with aneuploidy observed in some species. Recently, the genomes of L. orientalis isolate LSCM4 and L. martiniquensis isolate LSCM1 from the northern province of Thailand have been sequenced by using several Illumina and Nanopore sequencing platforms [20]. This Leishmania genomic information provides an understanding and basis for the parasite genetics and pathogenesis.…”

TriTrypDB: An integrated functional genomics resource for kinetoplastida

“…Of these 83 genomes, 31 are from Leishmania and 43 are from Trypanosoma genera. TriTrypDB also has genomes of other parasitic kinetoplastids including, Angomonas deanei [ 11 ] , Blechomonas ayalai , Crithidia fasciculata [ 12 ] , Endotrypanum monterogeii [ 12 ] , Leptomonas pyrrhocoris [ 13 ] , Leptomonas seymouri [ 14 ] , Paratrypanosoma confusum [ 15 ], and Porcisia hertigi [ 16 , 17 ] and free-living nonparasitic kinetoplastid Bodo saltans . Gene annotations are available for 66 of these sequences, while the remaining 17 are genome assemblies without annotations ( Table 1 ).…”

“…Below are a few recent examples of how TriTrypDB data and tools have been utilized by the research community to conduct their own research. TriTrypDB genomes and annotations have been used to characterize individual genes [69][70][71][72][73] or gene families [74,75], identify orthologs across species [55,70,76], conduct genome-wide analyses to study genetic variations such as SNPs, CNVs and hybridization events [77][78][79], perform comparative genomic [80][81][82] and phylogenetic/ phylogenomic [82,83] analyses, and as reference genomes for the assembly and/or annotation of newly generated genomes [16,84]. Similarly, the genome assemblies and annotations have also been utilized for the analysis of differential gene expression [19,72,85], protein expression [85][86][87], the identification of post-translational modifications [72] and potential new genes missing in the official gene sets [88].…”

Making the Most of Its Short Reads: A Bioinformatics Workflow for Analysing the Short-Read-Only Data of Leishmania orientalis (Formerly Named Leishmania siamensis) Isolate PCM2 in Thailand

“…Despite concerns about the genetic variation of L. orientalis and their public health impacts, genomic information of multiple L. orientalis isolates has gained attention. To date, three major genome sequencing platforms (Illumina, PacBio, and Oxford Nanopore) have been used to create the complete genomic data of several Leishmania species, including the genome of L. major strain Friedlin [ 31 , 42 , 43 , 44 ], L. infantum strain JPCM5 [ 33 , 42 ], L. martiniquensis strain LSCM1 [ 45 , 46 , 47 ], and a recent L. orientalis strain LSCM4 isolated from the northern province of Thailand [ 46 , 47 , 48 ], in exchange for considerable cost invested in the genome project. Questions have arisen on whether the new Leishmania species shall have their whole genomes decoded using all techniques at first glance.…”