Contrasting genomic epidemiology between sympatric Plasmodium falciparum and Plasmodium vivax populations.

The malaria parasites Plasmodium falciparum and Plasmodium vivax differ in key biological processes and associated clinical effects, but consequences on population-level transmission dynamics are difficult to predict. This co-endemic malaria study from Guyana details important epidemiological contrasts between the species by coupling population genomics (1396 spatiotemporally matched parasite genomes, primarily from 2020-21) with sociodemographic analysis (nationwide patient census from 2019). We describe how P.

Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance.

Background: Artemisinin-based combination therapies are the first line of treatment for Plasmodium falciparum infections worldwide, but artemisinin resistance has risen rapidly in Southeast Asia over the past decade. Mutations in the kelch13 gene have been implicated in this resistance. We used longitudinal genomic surveillance to detect signals in kelch13 and other loci that contribute to artemisinin or partner drug resistance.

Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly.

Background: De novo reference assemblies that are affordable, practical to produce, and of sufficient quality for most downstream applications, remain an unattained goal for many taxa. Insects, which may yield too little DNA from individual specimens for long-read sequencing library construction and often have highly heterozygous genomes, can be particularly hard to assemble using inexpensive short-read sequencing data. The large number of insect species with medical or economic importance makes this a critical problem to address.

COIL: a methodology for evaluating malarial complexity of infection using likelihood from single nucleotide polymorphism data.

Background: Complex malaria infections are defined as those containing more than one genetically distinct lineage of Plasmodium parasite. Complexity of infection (COI) is a useful parameter to estimate from patient blood samples because it is associated with clinical outcome, epidemiology and disease transmission rate. This manuscript describes a method for estimating COI using likelihood, called COIL, from a panel of bi-allelic genotyping assays.

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila.

Genome sequencing sheds light on emerging drug resistance in malaria parasites.

Plasmodium falciparum in Southeast Asia are gradually becoming resistant to artemesinin, a standard first-line treatment for malaria. Whole-genome sequencing offers a chance to better understand and perhaps undermine the parasite's evolutionary response to this drug.

The evolution of the Anopheles 16 genomes project.

We report the imminent completion of a set of reference genome assemblies for 16 species of Anopheles mosquitoes. In addition to providing a generally useful resource for comparative genomic analyses, these genome sequences will greatly facilitate exploration of the capacity exhibited by some Anopheline mosquito species to serve as vectors for malaria parasites. A community analysis project will commence soon to perform a thorough comparative genomic investigation of these newly sequenced genomes.

‘Big data’ from shrinking pathogen populations.

Falling costs for genome sequencing and genotyping mean that population genomic data sets are becoming commonplace for a wide variety of species. Once these data are used for the initial tasks of investigating population structure and demographic history, however, is there reason to go back for more? In this issue of Molecular Ecology, Nkhoma et al. (2013) explore the applications of longitudinal genomic diversity data for detecting changes in the prevalence and transmission of the Plasmodium falciparum malaria parasite in South-East Asia.

'Next-generation' sequencing becomes 'now-generation'.

A report on the Advances in Genome Biology & Technology conference, Marco Island, USA, 2-5 February 2011.

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.

We have sequenced the genomes of 18 isolates of the closely related human pathogenic fungi Coccidioides immitis and Coccidioides posadasii to more clearly elucidate population genomic structure, bringing the total number of sequenced genomes for each species to 10. Our data confirm earlier microsatellite-based findings that these species are genetically differentiated, but our population genomics approach reveals that hybridization and genetic introgression have recently occurred between the two species. The directionality of introgression is primarily from C.