Abdi, A. I. | Search bioRxiv

bioRxiv2022

Plasmodium falciparum adapts its investment into replication versus transmission according to the host environment

The malaria parasite life cycle includes asexual replication in human blood, with a proportion of parasites differentiating to gametocytes required for transmission to mosquitoes. Commitment to differentiate into gametocytes, which is marked by activation of the parasite transcription factor ap2-g, is known to be influenced by host factors but a comprehensive model remains uncertain. Here we analyze data from 828 children in Kilifi, Kenya with severe, uncomplicated, and asymptomatic malaria infection over 18 years of falling malaria transmission. We examine markers of host immunity and metabolism, and markers of parasite growth and transmission investment. We find that inflammatory responses and reduced plasma lysophosphatidylcholine levels are associated with markers of increased investment in parasite sexual reproduction (i.e., transmission investment) and reduced growth (i.e., asexual replication). This association becomes stronger with falling transmission and suggests that parasites can rapidly respond to the within-host environment, which in turn is subject to changing transmission.

microbiology↗

bioRxiv2021

From contigs to chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Although there is a promise of long read technologies to obtain "perfect genomes", the number of contigs often exceeds the number of chromosomes by far, containing many insertion and deletion errors around homopolymer tracks. To overcome these issues, we implemented the ILRA pipeline to correct long read-based assemblies, so contigs are reordered, renamed, merged, circularized, or filtered if erroneous or contaminated, and Illumina reads are used to correct homopolymer errors. We successfully tested our approach by improving the genomes of Trypanosoma brucei and Leptosphaeria spp, and generated four novel Plasmodium falciparum assemblies from field samples. We found that correcting homopolymer tracks reduced the number of genes incorrectly annotated as pseudogenes, but an iterative correction seems to be required to correct larger numbers of sequencing errors. In summary, we described and compared the performance of our new tool, which improved the quality of novel long read assemblies of genomes up to 1Gbp. AvailabilityThe tool is available at GitHub: https://github.com/ThomasDOtto/ILRA.

bioinformatics↗