Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent.

Leishmania donovani causes visceral leishmaniasis (VL), the second most deadly vector-borne parasitic disease. A recent epidemic in the Indian subcontinent (ISC) caused up to 80% of global VL and over 30,000 deaths per year. Resistance against antimonial drugs has probably been a contributing factor in the persistence of this epidemic. Here we use whole genome sequences from 204 clinical isolates to track the evolution and epidemiology of L. donovani from the ISC. We identify independent radiations that have emerged since a bottleneck coincident with 1960s DDT spraying campaigns. A genetically distinct population frequently resistant to antimonials has a two base-pair insertion in the aquaglyceroporin gene LdAQP1 that prevents the transport of trivalent antimonials. We find evidence of genetic exchange between ISC populations, and show that the mutation in LdAQP1 has spread by recombination. Our results reveal the complexity of L. donovani evolution in the ISC in response to drug treatment.

(Post-) Genomic approaches to tackle drug resistance in Leishmania.

Leishmaniasis, like other neglected diseases is characterized by a small arsenal of drugs for its control. To safeguard the efficacy of current drugs and guide the development of new ones it is thus of utmost importance to acquire a deep understanding of the phenomenon of drug resistance and its link with treatment outcome. We discuss here how (post-)genomic approaches may contribute to this purpose. We highlight the need for a clear definition of the phenotypes under consideration: innate and acquired resistance versus treatment failure. We provide a recent update of our knowledge on the Leishmania genome structure and dynamics, and compare the contribution of targeted and untargeted methods for the understanding of drug resistance and show their limits. We also present the main assays allowing the experimental validation of the genes putatively involved in drug resistance. The importance of analysing information downstream of the genome is stressed and further illustrated by recent metabolomics findings. Finally, the attention is called onto the challenges for implementing the acquired knowledge to the benefit of the patients and the population at risk.

Adaptive mechanisms in pathogens: universal aneuploidy in Leishmania.

Genomic stability and maintenance of the correct chromosome number are assumed to be essential for normal development in eukaryotes. Aneuploidy is usually associated with severe abnormalities and decrease of cell fitness, but some organisms appear to rely on aneuploidy for rapid adaptation to changing environments. This phenomenon is mostly described in pathogenic fungi and cancer cells. However, recent genome studies highlight the importance of Leishmania as a new model for studies on aneuploidy. Several reports revealed extensive variation in chromosome copy number, indicating that aneuploidy is a constitutive feature of this protozoan parasite genus. Aneuploidy appears to be beneficial in organisms that are primarily asexual, unicellular, and that undergo sporadic epidemic expansions, including common pathogens as well as cancer.

Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans.

BACKGROUND: The posterior genes of the HoxD cluster play a crucial role in the patterning of the tetrapod limb. This region is under the control of a global, long-range enhancer that is present in all vertebrates. Variation in limb types, as is the case in amphibians, can probably not only be attributed to variation in Hox genes, but is likely to be the product of differences in gene regulation. With a collection of vertebrate genome sequences available today, we used a comparative genomics approach to study the posterior HoxD cluster of amphibians. A frog and a caecilian were included in the study to compare coding sequences as well as to determine the gain and loss of putative regulatory sequences. RESULTS: We sequenced the posterior end of the HoxD cluster of a caecilian and performed comparative analyses of this region using HoxD clusters of other vertebrates. We determined the presence of conserved non-coding sequences and traced gains and losses of these footprints during vertebrate evolution, with particular focus on amphibians. We found that the caecilian HoxD cluster is almost three times larger than its mammalian counterpart. This enlargement is accompanied with the loss of one gene and the accumulation of repeats in that area. A similar phenomenon was observed in the coelacanth, where a different gene was lost and expansion of the area where the gene was lost has occurred. At least one phylogenetic footprint present in all vertebrates was lost in amphibians. This conserved region is a known regulatory element and functions as a boundary element in neural tissue to prevent expression of Hoxd genes. CONCLUSION: The posterior part of the HoxD cluster of Typhlonectes natans is among the largest known today. The loss of Hoxd-12 and the expansion of the intergenic region may exert an influence on the limb enhancer, by having to bypass a distance seven times that of regular HoxD clusters. Whether or not there is a correlation with the loss of limbs remains to be investigated. These results, together with data on other vertebrates show that the tetrapod Hox clusters are more variable than previously thought.

A PCR survey for posterior Hox genes in amphibians.

Hox genes encode transcription factors that play a key role in specifying the body plan in metazoans and are therefore essential in explaining patterns of evolutionary diversity. As an ancient tetrapod group with diverse limb types, amphibians are important for understanding the origin and diversification of limbs in land vertebrates. We conducted a PCR survey in two species of each amphibian order to identify Hox-9 to Hox-13, known to function in limb development. Fifteen distinct posterior Hox genes and one retro-pseudogene were identified, and the former confirm the existence of four Hox clusters in each amphibian order. Some genes expected to occur in all tetrapods, based on the posterior Hox complement of mammals, fishes and coelacanth, were not recovered from our survey, and may have been lost. Hoxd-12 is absent in frogs and possibly other amphibians. Considering its function in autopodial development, the loss of this gene may be related to the absence of the fifth finger in frogs and salamanders.

Local endemism within the Western Ghats-sri Lanka biodiversity hotspot.

The apparent biotic affinities between the mainland and the island in the Western Ghats-Sri Lanka biodiversity hotspot have been interpreted as the result of frequent migrations during recent periods of low sea level. We show, using molecular phylogenies of two invertebrate and four vertebrate groups, that biotic interchange between these areas has been much more limited than hitherto assumed. Despite several extended periods of land connection during the past 500,000 years, Sri Lanka has maintained a fauna that is largely distinct from that of the Indian mainland. Future conservation programs for the subcontinent should take into account such patterns of local endemism at the finest scale at which they may occur.