Susanne U. Franssen

Wellcome Sanger Institute · Pathogen Genetics Programme

Leishmaniasis is an infectious disease caused by protozoan parasites belonging to the genus Leishmania for which there are no approved human vaccines. Infections localise to different tissues in a species-specific manner with the visceral form of the disease caused by Leishmania donovani and L. infantum being the most deadly in humans. Although Lei...

Visceral leishmaniasis (VL) is a fatal disease and a growing public health problem in East Africa, where Ethiopia has one of the highest VL burdens. The largest focus of VL in Ethiopia is driven by high prevalence in migrant agricultural workers and associated with a high rate of coinfection with HIV. This coinfection makes VL more difficult to tre...

Visceral leishmaniasis (VL) is a fatal disease and a growing public health problem in East Africa, where Ethiopia has one of the highest VL burdens. The largest focus of VL in Ethiopia is driven by high prevalence in migrant agricultural workers and associated with a high rate of co-infection with HIV. This co-infection makes VL more difficult to t...

Genetic exchange between Leishmania parasites was demonstrated in sandflies over 10 years ago. Louradour et al. have shown in vitro hybridization of two Leishmania tropica isolates, with the potential to remove a major roadblock to using forward genetics in Leishmania, understanding Leishmania reproductive biology, and analyzing gene flow in natura...

Parasites of the genus Leishmania (Kinetoplastida: Trypanosomatidae) cause widespread and devastating human diseases. Visceral leishmaniasis due to Leishmania donovani is endemic in Ethiopia where it has also been responsible for major epidemics. The presence of hybrid genotypes has been widely reported in surveys of natural populations, genetic va...

Protozoan parasites of the Leishmania donovani complex – L. donovani and L. infantum – cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide...

Protozoan parasites of the Leishmania donovani complex – L. donovani and L. infantum – cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide...

Protozoan parasites of the Leishmania donovani complex – L. donovani and L. infantum – cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide...

Protozoan parasites of the Leishmania donovani complex, L. donovani and L. infantum, cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide w...

Parasites of the genus Leishmania (Kinetoplastida: Trypanosomatidae) cause widespread and devastating human diseases, ranging from self-healing but disfiguring cutaneous lesions to destructive mucocutaneous presentations or usually fatal visceral disease. Visceral leishmaniasis due to Leishmania donovani is endemic in Ethiopia where it has also bee...

The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (PoolSeq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpr...

The genetic architecture of adaptation in natural populations has not yet been resolved: it is not clear to what extent the spread of beneficial mutations (selective sweeps) or the response of many quantitative trait loci drive adaptation to environmental changes. Although much attention has been given to the genomic footprint of selective sweeps,...

Populations distributed across a broad thermal cline are instrumental in addressing adap-tation to increasing temperatures under global warming. Using a space-for-time substi-tution design, we tested for parallel adaptation to warm-temperatures along two inde-pendent thermal clines in Zostera marina, the most widely distributed seagrass in the temp...

Short read sequencing of diploid individuals does not permit the direct inference of the sequence on each of the two chromosomes. Although various phasing software packages exist, they were primarily tailored for and tested on human data, which differ from other species in factors that influence phasing, such as SNP density, amounts of linkage dise...

Whole genome re-sequencing of experimental populations evolving under a specific selection regime has become a popular approach to determine genotype-phenotype maps and understand adaptation to new environments. Despite its conceptual appeal and success in identifying some causative genes, it has become apparent that many studies suffer from an exc...

Evolve and resequence (E&R) is a new approach to investigate the genomic responses to selection during experimental evolution. By using whole genome sequencing of pools of individuals (Pool-Seq), this method can identify selected variants in controlled and replicable experimental settings. Reviewing the current state of the field, we show that E&R...

Genome-wide transcription analysis between related species occurring in overlapping ranges can provide insights into the molecular basis underlying different ecological niches. The co-occurring seagrass species, Zostera marina and Nanozostera noltii, are found in marine coastal environments throughout the northern hemisphere. Z. marina is often dom...

It is generally accepted that gene regulation serves an important role in determining the phenotype. To shed light on the evolutionary forces operating on gene regulation, previous studies mainly focused on the expression differences between species and their inter-specific hybrids. Here, we use RNA-Seq to study the intra-specific distribution of c...

Experimental evolution in combination with whole genome sequencing (evolve and resequence, E&R) is a promising approach to define the genotype-phenotype map and to understand adaptation in evolving populations. Many previous studies have identified a large number of putative selected sites (i.e. candidate loci), but it remains unclear to what exten...

Estimating differences in gene expression among alleles is of high interest for many areas in biology and medicine. Here, we present a user-friendly software tool, Allim, to estimate allele-specific gene expression. Because mapping bias is a major problem for reliable estimates of allele-specific gene expression using RNA-seq, Allim combines two di...

The contribution of metabolism to heat stress may play a significant role in defining robustness and recovery of systems; either by providing the energy and metabolites required for cellular homeostasis, or through the generation of protective osmolytes. However, the mechanisms by which heat stress attenuation could be adapted through metabolic pro...

Large-scale transcription profiling via direct cDNA sequencing provides important insights as to how foundation species cope with increasing climatic extremes predicted under global warming. Species distributed along a thermal cline, such as the ecologically important seagrass Zostera marina, provide an opportunity to assess temperature effects on...

The garden pea, Pisum sativum, is among the best-investigated legume plants and of significant agro-commercial relevance. Pisum sativum has a large and complex genome and accordingly few comprehensive genomic resources exist. We analyzed the pea transcriptome at the highest possible amount of accuracy by current technology. We used next generation...

The alignments used to generate Table 3; data can be loaded into tablet [52]for visualization.

The fasta file of sequences used to generate Table 3; data can be loaded into tablet [45]for visualization.

Proteome coverage of 3' vs. 5' ends; Different sets of query sequences were blasted against the complete Arabidopsis proteome, TAIR9 pep (black) and only 5', 3' ends (100 end standing amino acids) of all peptides, (red, green, respectively) and the number of significant hits (BlastX, e-value ≤ 10-4) was recorded. The sets of query sequences were al...

Fasta file of the unigene database for the the second pass TGICL/CAP3 assembly using the MIRA unigenes of the first pass assembly; The fasta file contains the Mira unigenes annotated with their best BlastX hit (e-value ≤ 10-4) against the proteome of A. thaliana, M. truncatula, Glycine max and the nr database of NCBI (with only the best hit against...

Mapping of the cleaned reads, the first pass assembly and the second pass assembly results against A. thaliana, M. truncatula and G. max to approximate the proportion of chimeric genes in the assembly.

Enriched categories of GO terms for libraries of etiolated seedlings and etiolated seedlings after light treatment; enrichment analysis was performed with topGO [64].

Contribution of retrotransposon-like sequences to the contig databases.

Correlation between reads mapping to a reference and unigenes mapping to the same reference.

Rarefaction analysis of gene representation in different libraries; analysis was performed as described in Figure 3(A) Reads were randomly sampled from the COT library, (B) Reads were randomly sampled from the FLO library, (C) Reads were randomly sampled from the HYP library, (D) Reads were randomly sampled from the EPI library, (E) Reads were rand...