The Plasmodium vivax genome sequencing project

With the successful completion of the project to sequence the Plasmodium falciparum genome, researchers are now turning their attention to other malaria parasite species. Here, an update on the Plasmodium vivax genome sequencing project is presented, as part of the Trends in Parasitology series of reviews expanding on various aspects of P. vivax research.     

Speculations on the origins of Plasmodium vivax malaria

It is likely that Plasmodium vivax diverged approximately 2 million years ago from a group of malaria parasites which are now endemic in monkeys and apes in southern Asia. In those times, primates were spread throughout most of Eurasia and Africa, indicating an Old World location, but nothing more precise, for the place of divergence of P. vivax. From approximately 1 million years ago, the Ice Ages would have isolated human malaria, including P. vivax, into humid temperate or warm climate refuges around the Mediterranean, in sub-Saharan Africa and in south and east Asia. As there appears to be no record of humans in south and east Asia from 100,000 to 60,000 years ago, they might not have passed on their parasites, including P. vivax, to modern humans entering the region after this time. Today, all P. vivax might be descended from parasites which infected human populations in the Mediterranean region and in sub-Saharan Africa during the last Ice Age, between 100,000 and 20,000 years ago. Evidence for the latter is provided by the presence of very high frequency RBC Duffy negativity in sub-Saharan Africa.     

Whole-genome sequencing of a Plasmodium vivax isolate from the China-Myanmar border area

Currently, there is a trend of an increasing number of Plasmodiumvivaxmalaria cases in China that are imported across its Southeast Asiaborder, especially in the China-Myanmar border area (CMB). To date, little is knownabout the genetic diversity of P. vivax in this region. In thispaper, we report the first genome sequencing of a P. vivaxisolate(CMB-1) from a vivax malaria patient in CMB. The sequencing data were aligned onto96.43% of the P. vivax Salvador I reference strain (Sal I) genomewith 7.84-fold coverage as well as onto 98.32% of 14 Sal I chromosomes. Usingthe de novo assembly approach, we generated 8,541 scaffolds andassembled a total of 27.1 Mb of sequence into CMB-1 scaffolds. Furthermore, weidentified all 295 known virgenes, which is the largest subtelomericmultigene family in malaria parasites. These results provide an important foundationfor further research onP. vivax population genetics.     

The putative mitochondrial genome of Plasmodium falciparum

Intraerythrocytic stages of mammalian malarial parasites employ glycolysis for energy production but some aspects of mitochondrial function appear crucial to their survival since inhibitors of mitochondrial protein synthesis and electron transport have antimalarial effects. Investigations of the putative mitochondrial genome of Plasmodium falciparum have detected organellar rRNAs and tRNAs encoded by a 35 kb circular DNA. Some features of the organization and sequence of the rRNA genes are reminiscent of chloroplast DNAs. The 35 kb DNA also encodes open reading frames for proteins normally found in chloroplast but not mitochondrial genomes. An apparently unrelated 6 kb tandemly repeated element which encodes two mitochondrial protein coding genes and fragments of rRNA genes is also found in malarial parasites. The malarial mitochondrial genome thus appears quite unusual. Further investigations are expected to provide insights into the possible functional relationships between these molecules and perhaps their evolutionary history.     

New insights into the evolutionary history of Plasmodium falciparum from mitochondrial genome sequence analyses of Indian isolates

Estimating genetic diversity and inferring the evolutionary history of Plasmodium falciparum could be helpful in understanding origin and spread of virulent and drug‐resistant forms of the malaria pathogen and therefore contribute to malaria control programme. Genetic diversity of the whole mitochondrial (mt) genome of P. falciparum sampled across the major distribution ranges had been reported, but no Indian P. falciparum isolate had been analysed so far, even though India is highly endemic to P. falciparum malaria. We have sequenced the whole mt genome of 44 Indian field isolates and utilized published data set of 96 genome sequences to present global genetic diversity and to revisit the evolutionary history of P. falciparum. Indian P. falciparum presents high genetic diversity with several characteristics of ancestral populations and shares many of the genetic features with African and to some extent Papua New Guinean (PNG) isolates. Similar to African isolates, Indian P. falciparum populations have maintained high effective population size and undergone rapid expansion in the past with oldest time to the most recent common ancestor (TMRCA). Interestingly, one of the four single nucleotide polymorphisms (SNPs) that differentiates P. falciparum from P. falciparum‐like isolates (infecting non‐human primates in Africa) was found to be segregating in five Indian P. falciparum isolates. This SNP was in tight linkage with other two novel SNPs that were found exclusively in these five Indian isolates. The results on the mt genome sequence analyses of Indian isolates on the whole add to the current understanding on the evolutionary history of P. falciparum.     

The origins of replication of the mitochondrial genome of yeast

Recent investigations have provided information on the origin of replication of the mitochondrial genome of yeast and an explanation for the phenomenon of the suppressivity.     

Assessing the impact of Plasmodium falciparum genome sequencing

With the publication of the complete sequences for chromosomes 2 and 3 and the increasing availability of shotgun sequence covering most of its genome, Plasmodium falciparum biology is entering its post-genomic era. Analysis of the results generated to date has identified higher-order organisation of gene families involved in parasite pathology, provided information regarding the unique biology of this parasite and allowed the identification of potential chemotherapeutic drug targets. Continuing efforts to complete the P. falciparum genome and the availability of sequences from other protozoan parasites will facilitate a broader understanding of their biology, particularly with respect to their pathogenicity.     

Mitochondrial genome sequences support ancient population expansion in Plasmodium vivax

Examination of nucleotide diversity in 106 mitochondrial genomes of the most geographically widespread human malaria parasite, Plasmodium vivax, revealed a level of diversity similar to, but slightly higher than, that seen in the virulent human malaria parasite Plasmodium falciparum. The pairwise distribution of nucleotide differences among mitochondrial genome sequences supported the hypothesis that both these parasites underwent ancient population expansions. We estimated the age of the most recent common ancestor (MRCA) of the mitochondrial genomes of both P. vivax and P. falciparum at around 200,000-300,000 years ago. This is close to the previous estimates of the time of the human mitochondrial MRCA and the origin of modern Homo sapiens, consistent with the hypothesis that both these Plasmodium species were parasites of the hominid lineage before the origin of modern H. sapiens and that their population expansion coincided with the population expansion of their host.     

The complete mitochondrial genome of Fusarium oxysporum: insights into fungal mitochondrial evolution

The complete mitochondrial DNA (mtDNA) sequence was determined for the phytopathogenic fungus Fusarium oxysporum. It is 34,477 bp long, maps circularly, and encodes for 14 protein-coding, 25 tRNA and 2 rRNA genes. The nucleotide and amino acid data sets from its 14 concatenated protein-coding mitochondrial (mt) genes were used along with gene order comparisons for an extensive phylogenetic study of the Subphylum Pezizomycotina. Our results are in agreement with current taxonomic treatments and additionally provide better statistical support for all relationships within Pezizomycotina when compared to analyses based on single or few gene data sets. The gene order of F. oxysporum was consistent with that established in the order Hypocreales (Class: Sordariomycetes) and enhanced previous suppositions on the ancestral state of Sordariomycetes. In comparison with mt genomes of the other orders it added further insights to the evolution of Pezizomycotina.     

线粒体基因组测序策略和方法

本文综述了线粒体基因组测序策略和方法,在传统测序方法中介绍了基于物理分离线粒体DNA的克隆文库测序方法和基于PCR扩增产物的直接测序方法,后者重点介绍了基于长PCR扩增产物的引物步移法和基于总DNA的引物步移法;应用新一代高通量测序方法有基于总DNA样品的方法,包括需要预扩增mtDNA的多物种平行高通量和无需预扩增mtDNA的高通量方法,基于总RNA样品的转录组测序方法等。在实际工作中,选择哪种方法取决于研究规模、样品大小和保存状态、经费情况等。总的来说,基于长PCR扩增产物的引物步移法尤其适合小规模昆虫线粒体基因组研究,而对于大规模线粒体基因组研究来说,NGS技术无疑是省时省力的最佳选择。     

The paroxysm of Plasmodium vivax malaria

The paroxysms of Plasmodium vivax malaria are antiparasite responses that, although distressing to the human host, almost never impart serious acute pathology. Using plasma and blood cells from P. vivax patients, the cellular and noncellular mediators of these events have been studied ex vivo. The host response during a P. vivax paroxysm was found to involve T cells, monocytes and neutrophils, and the activity, among others, of the pyrogenic cytokines tumor necrosis factor alpha and interleukin 2 in addition to granulocyte macrophage-colony stimulating factor. However, interferon gamma activity, associated with serious acute pathogenesis in other studies on malaria, was absent. Induction of the cytokines active during a P. vivax paroxysm depends upon the presence of parasite products, which are released into the plasma before the paroxysm. Chemical identification of these natural parasite products will be important for our understanding of pathogenesis and protection in malaria.     

The Plasmodium vivax rhoptry-associated protein 1

Rhoptries are cellular organelles localized at the apical pole of apicomplexan parasites. Their content is rich in lipids and proteins that are released during target cell invasion. Plasmodium falciparum rhoptry-associated protein 1 (RAP1) has been the most widely studied among this parasite species' rhoptry proteins and is considered to be a good anti-malarial vaccine candidate since it displays little polymorphism and induces antibodies in infected humans. Monoclonal antibodies directed against RAP1 are also able to inhibit target cell invasion in vitro and protection against P. falciparum experimental challenge is induced when non-human primates are immunized with this protein expressed in its recombinant form. This study describes identifying and characterizing RAP1 in Plasmodium vivax, the most widespread parasite species causing malaria in humans, producing more than 80 million infections yearly, mainly in Asia and Latin America. This new protein is encoded by a two-exon gene, is proteolytically processed in a similar manner to its falciparum homologue and, as observed by microscopy, the immunofluorescence pattern displayed is suggestive of its rhoptry localization. Further studies evaluating P. vivax RAP1 protective efficacy in non-human primates should be carried out taking into account the relevance that its P. falciparum homologue has as an anti-malarial vaccine candidate.     

The malaria genome sequencing project: complete sequence of Plasmodium falciparum chromosome 2

An international consortium has been formed to sequence the entire genome of the human malaria parasite Plasmodium falciparum. We sequenced chromosome 2 of clone 3D7 using a shotgun sequencing strategy. Chromosome 2 is 947 kb in length, has a base composition of 80.2% A + T, and contains 210 predicted genes. In comparison to the Saccharomyces cerevisiae genome, chromosome 2 has a lower gene density, a greater proportion of genes containing introns, and nearly twice as many proteins containing predicted non-globular domains. A group of putative surface proteins was identified, rifins, which are encoded by a gene family comprising up to 7% of the protein-encoding gene in the genome. The rifins exhibit considerable sequence diversity and may play an important role in antigenic variation. Sixteen genes encoded on chromosome 2 showed signs of a plastid or mitochondrial origin, including several genes involved in fatty acid biosynthesis. Completion of the chromosome 2 sequence demonstrated that the A + T-rich genome of P. falciparum can be sequenced by the shotgun approach. Within 2-3 years, the sequence of almost all P. falciparum genes will have been determined, paving the way for genetic, biochemical, and immunological research aimed at developing new drugs and vaccines against malaria.     

The genetic diversity of Plasmodium vivax populations

Little is known of the genetic diversity and population structure of Plasmodium vivax, a debilitating and highly prevalent malaria parasite of humans. This article reviews the known polymorphic genetic markers, summarizes current data on the population structure of this parasite and discusses future prospects for using knowledge of the genetic diversity to improve control measures.     

Cultivation of Plasmodium vivax

Establishment of a continuous line of Plasmodium vivax parasite is crucial to understand the parasite's biology; however, this has not yet been achieved. Beginning in the 19th century, there were several efforts to cultivate this malaria parasite but without much success until the late 1980s. In addition, to date, only minor modifications of the methodology have been investigated, which has resulted in extending the cultivation period to around four weeks by supplying reticulocytes obtained from normal blood or rare hemochromatotic blood. However, the use of laboratory-produced erythroblasts to cultivate P. vivax enables maintenance of a continuous line of the parasite stably in the laboratory. Here, we summarize and compare the available methodologies and conditions for the in vitro cultivation of P. vivax.     

The origin and age of Plasmodium vivax

The evolutionary history of Plasmodium vivax has recently been addressed in terms of its origin as a parasite of humans and the age of extant populations. The consensus is that P. vivax originated as a result of a host switch from a non-human primate to hominids and that the extant populations did not originate as recently as previously proposed. Here, we show that, in a comparison of parasite isolates from across the world, Asian populations of P. vivax are the oldest. We discuss how this result, together with the phylogenetic evidence that P. vivax derived from Plasmodium found in Southeast Asian macaques, is most simply explained by assuming an Asian origin of this parasite. Nevertheless, the available data show only the tip of the iceberg. We discuss how sampling might affect time estimates to the most recent common ancestor for P. vivax populations and suggest that spatially explicit estimates are needed to understand the demographic history of this parasite better.     

Clinical utility of whole genome sequencing for the detection of mitochondrial genome mutations

正Genetic mitochondrial disorders are a heterogenous group of multi-system disorders caused by an imbalance in mitochondrial function (Moggio et al.,2014;Wallace,2018).In contrast to the nuclear genome,each cell contains hundreds,or even thousands,of mtDNA molecules (Veltri et al.,1990;Calvo et al., 2006).Thus,a mixture of different mtDNA sequences can co-exist within the same individual,a situation referred to as he terop las my.The level of heteroplasmy in an individual often affects the penetrance and phenotypic severity of the diseases.Consequently,detection of sequence heteroplasmy is essential for the proper clinical interpretation of mitochondrial diseases (Stewart and Chinnery,2015).