BackgroundThe small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans.ResultsHere we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates.ConclusionsThe H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.

Plasmodium falciparum, the most virulent agent of human malaria, shares a recent common ancestor with the gorilla parasite P. praefalciparum. Little is known about the other gorilla and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum but none of them are capable of establishing repeated infection and transmission in humans. To elucidate underlying mechanisms and the evolutionary history of this subgenus, we have generated multiple genomes from all known Laverania species. The completeness of our dataset allows us to conclude that interspecific gene transfers as well as convergent evolution were important in the evolution of these species. Striking copy number and structural variations were observed within gene families and one, stevor shows a host specific sequence pattern. The complete genome sequence of the closest ancestor of P. falciparum enables us to estimate the timing of the beginning of speciation to be 40,000-60,000 years ago followed by a population bottleneck around 4,000-6,000 years ago. Our data allow us also to search in detail for the features of P. falciparum that made it the only member of the Laverania able to infect and spread in humans.

Plasmodium falciparum, the most virulent agent of human malaria, shares a recent 25 common ancestor with the gorilla parasite P. praefalciparum. Little is known about the other gorilla 26 and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum but none of 27 them are capable of establishing repeated infection and transmission in humans. To elucidate 28 underlying mechanisms and the evolutionary history of this subgenus, we have generated multiple 29 genomes from all known Laverania species. The completeness of our dataset allows us to conclude 30 that interspecific gene transfers as well as convergent evolution were important in the evolution of 31 these species. Striking copy number and structural variations were observed within gene families 32 and one, stevor shows a host specific sequence pattern. The complete genome sequence of the 33 closest ancestor of P. falciparum enables us to estimate confidently for the first time the timing of 34 the beginning of speciation to be 40,000-60,000 years ago followed by a population bottleneck 35 around 4,000-6,000 years ago. Our data allow us also to search in detail for the features of P. 36 falciparum that made it the only member of the Laverania able to infect and spread in humans. 37 39Main Text: 40The evolutionary history of Plasmodium falciparum, the most common and deadliest human 41 malaria parasite, has been the subject of uncertainty and debate 1,2 . Recently it has become clear that 42 P. falciparum is derived from a group of parasites infecting African Great Apes and known as the 43Laverania subgenus 2 . Until 2009, the only other species known in this subgenus was a parasite of 44 chimpanzees known as P. reichenowi, for which only one isolate was available 3 . It is now clear that 45 there are a total of at least seven species in Great Apes that naturally infect chimpanzees (P. gaboni, 46 P. billcollinsi and P. reichenowi), gorillas (P. praefalciparum, P. blacklocki and P. adleri) 4,5 , or 47 humans (P. falciparum) ( Fig. 1a). Within this group, P. falciparum is the only parasite that has 48 successfully adapted to humans after a transfer from gorillas and subsequently spread all over the 49 world 2 . 50Over time there have been various estimates concerning the evolutionary history of P. 51 falciparum with the speciation event having been estimated to be anywhere between 10,000 to 5.5 52 million years ago, the latter falsely based on the date of the chimpanzee-human split 6,7 . Others 53 report a bottleneck less than 10,000 years ago 8 , but suggest a drop to a single progenitor parasite. 54The latter seems unlikely due to the presence of allelic dimorphisms that predate speciation events 55 and therefore could not have both been transmitted if a new species were founded by a single 56 individual infection. Also, the dating of the speciation cannot be accurately estimated without the 57 genome sequence of P. praefalciparum, the closest living sister species to P. falciparum. 58The absence of in vitro culture or a usable animal mode...

Re-examination, using molecular tools, of the diversity of haemosporidian parasites (among which the agents of human malaria are the best known) has generally led to rearrangements of traditional classifications. In this study, we explored the diversity of haemosporidian parasites infecting vertebrate species (particularly mammals, birds and reptiles) living in the forests of Gabon (Central Africa), by analyzing a collection of 492 bushmeat samples. We found that samples from five mammalian species (four duiker and one pangolin species), one bird and one turtle species were infected by haemosporidian parasites. In duikers (from which most of the infected specimens were obtained), we demonstrated the existence of at least two distinct parasite lineages related to Polychromophilus species (i.e., bat haemosporidian parasites) and to sauropsid Plasmodium (from birds and lizards). Molecular screening of sylvatic mosquitoes captured during a longitudinal survey revealed the presence of these haemosporidian parasite lineages also in several Anopheles species, suggesting a potential role in their transmission. Our results show that, differently from what was previously thought, several independent clades of haemosporidian parasites (family Plasmodiidae) infect mammals and are transmitted by anopheline mosquitoes.