Complete Genome Assembly, Annotation and Comparative Analysis of Six Leishmaniinae Parasites

Almutairi, Hatim and Gatherer, Derek and Dillon, Roderick (2022) Complete Genome Assembly, Annotation and Comparative Analysis of Six Leishmaniinae Parasites. PhD thesis, Lancaster University.

Text (2022hatimphd)
2022hatimphd.pdf - Published Version
Available under License Creative Commons Attribution.
Download (7MB)

Abstract

Leishmania is a widespread parasite that causes leishmaniasis, a serious but neglected tropical disease reported in nearly 100 countries. Leishmaniasis manifests itself in three main forms: visceral, cutaneous, and mucocutaneous. Leishmania is classified into four subgenera: Leishmania, Sauroleishmania, Viannia, and more recently, Mundinia, the latter of which accommodates the L. enriettii complex as well as other species from a variety of hosts and geographic locations. I detail here sequencing, assembly, and annotation of six Mundinia genomes, including those of the Asian species Leishmania (Mundinia) martiniquensis and L. (M.) orientalis, the American species L. (M.) enriettii and Porcisia hertigi (formerly L. hertigi), and two unnamed African species from Ghana and Namibia, namely L. (M.) sp. Ghana and L. (M.) sp. Namibia. To maintain chromosome structure while maximising the quality of short read sequencing, genomes were sequenced and assembled using both short and long reads platforms, specifically Illumina and Oxford Nanopore Technologies. They were then annotated using ab initio annotation in conjunction with publicly available proteins and transcripts. Each genome contains a complete set of 36 chromosomes and measures between 32.2-35.9 Mega-bases in length with an average N50 of 1,062,685 bases. Each assembly contained an average of 8,126 genes, mRNAs, exons, and protein coding regions. When compared to other Leishmania genomes, all were recognisably related to Mundinia species, except for Porcisia hertigi, which was found to be more closely related to Endotrypanum monterogeii, setting it as an outgroup. Phylogenomic analyses revealed that Mundinia genomes share a common ancestor with the other three Leishmania subgenera, which was estimated to have existed approximately 121 million years ago, during the early Cretaceous period. Selection pressure analysis showed that there are 36 positively selected proteins, four of which may be novel proteins. This work may pave the way for future research on Leishmania biology and evolution.