Table 1.
Summary of Ld1S assembly and annotation and comparison with LdBPK282A2.
Fig 1.
Chromosome organization of Ld1S and LdBPK282A1.
(A), (B) and (C) Display a NUCmer plot comparing the Ld1S assembly (y-axis) and the LdBPK282A1 assembly (x-axis) for chromosome 24, 7 and 23 respectively. Axis represents the size of the scaffolds in kb. Each plot represents the similarity between the two genomes (color scale of similarity on the right). Red and blue blocks represent the different Polycistronic Transcription Units (PTUs) on each chromosome: blue blocks represent PTUs on the negative strand and red blocks PTUs on the positive strand. The black box highlights the two translocations displayed in D. (D) Representation of the chromosomal rearrangement of chromosome 7 from Ld1S (at the bottom) and LdBPK282A1 (at the top). Each arrow represents a gene; the ones in blue and red are not inverted or translocated, a vertical bar represents a transcription termination stop, and opposite arrows represent transcription switches between two PTUs. The green and yellow lines illustrate the two translocations (D) The panel shows polycistronic ONT direct RNA sequencing reads (in pink) spanning the rearrangement site.
Fig 2.
Characterization of the 5’ and 3’ UTR lengths in L. donovani.
(A) Distribution of the 5’ UTR (on the left) and 3’ UTR (on the right) lengths. (B) Correlation plot between the 5’ UTR length and the corresponding 3’ UTR length of each transcript. Violin plots showing the distribution of the lengths (in log of bp) of the 5’ (C) and 3’ (D) UTRs in L. donovani (blue), L. major (red) and T. brucei (green). Comparison of the length of the 5’ (E) and 3’ (F) UTRs between L. donovani (x-axis) and L. major (y-axis). Each dot represents one gene.
Fig 3.
rG4 are more frequent in the UTRs of L. donovani and L. major than in coding sequences.
(A) representation of a canonical rG4 and its sequence. (B) Number of predicted rG4 per bp (y-axis) in different genome and transcriptome regions for L. donovani (blue), L. major (red) and T. brucei.
Fig 4.
L. donovani transcript length isoform.
(A) IGS screenshot showing the coverage of direct RNA sequencing reads from Leishmania donovani promastigotes (top panel) and amastigotes (bottom panel). The bottom panel shows the Stringtie transcript prediction as well as the TransDecoder OFR annotation. (B) Schematic representation of the two transcript isoforms: Ld1S.212290.1 is present in both promastigotes and amastigotes and Ld1S.212290.2 is only present in promastigotes.