Genome Analysis of Endotrypanum and Porcisia spp., Closest Phylogenetic Relatives of Leishmania, Highlights the Role of Amastins in Shaping Pathogenicity

Abstract

While numerous genomes of Leishmania spp. have been sequenced and analyzed, an understanding of the evolutionary history of these organisms remains limited due to the unavailability of the sequence data for their closest known relatives, Endotrypanum and Porcisia spp., infecting sloths and porcupines. We have sequenced and analyzed genomes of three members of this clade in order to fill this gap. Their comparative analyses revealed only minute differences from Leishmaniamajor genome in terms of metabolic capacities. We also documented that the number of genes under positive selection on the Endotrypanum/Porcisia branch is rather small, with the flagellum-related group of genes being over-represented. Most significantly, the analysis of gene family evolution revealed a substantially reduced repertoire of surface proteins, such as amastins and biopterin transporters BT1 in the Endotrypanum/Porcisia species when compared to amastigote-dwelling Leishmania. This reduction was especially pronounced for δ-amastins, a subfamily of cell surface proteins crucial in the propagation of Leishmania amastigotes inside vertebrate macrophages and, apparently, dispensable for Endotrypanum/Porcisia, which do not infect such cells.

Keywords: gene gain; gene loss; genome analysis; leishmaniinae.

Figure 1

Phylogenomic tree based on 410 proteins encoded by single-copy genes from 44 trypanosomatids and the eubodonid Bodo saltans, Posterior probabilities and bootstrap supports are shown (in black) only if the latter is <100%. The scale bar represents substitutions per site. The numbers of orthologous groups (OG) gained/lost/expanded/contracted at certain nodes and leaves (species) are depicted using bar plots placed at the nodes and on the right of the tree, respectively (see Table S8 for exact counts; node numbers indicated in blue correspond to those in the Table S8). The Endotrypanum/Porcisia node (node 20) and the isolates sequenced in this study are marked with red and blue circles, respectively. The length of B. saltans and P. confusum branches was reduced four- and two-fold, respectively, for visualization purposes.

Figure 2

Maximum-likelihood phylogenetic tree of 188 kinetoplastid amastins. Only bootstrap supports over 50% are shown. The sequences obtained in this study are shown in red with the respective OG IDs. The five classes of amastins are highlighted in different colors. Most analyzed proteins have four transmembrane domains (TMDs), with a few exceptions indicated in the tree and Table S12. Numbers of sequences within collapsed clades are shown in brackets.