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Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria

https://doi.org/10.1101/095679
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Effective/census population size ratio estimation: a compendium and appraisal
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From Sequence Mapping to Genome Assemblies
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Allelic dimorphism in a surface antigen gene of the malaria parasite Plasmodium falciparum
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STEVOR Is a Plasmodium falciparum Erythrocyte Binding Protein that Mediates Merozoite Invasion and Rosetting
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Genetic diversity of VAR2CSA ID1-DBL2Xb in worldwide Plasmodium falciparum populations: Impact on vaccine design for placental malaria
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The Plasmodium gaboni genome illuminates allelic dimorphism of immunologically important surface antigens in P. falciparum
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A family affair: var genes, PfEMP1 binding, and malaria disease
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Duplication, gene conversion, and genetic diversity in the species-specific acyl-CoA synthetase gene family of Plasmodium falciparum
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The pir multigene family of Plasmodium: Antigenic variation and beyond
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An EBA175 homologue which is transcribed but not translated in erythrocytic stages of Plasmodium falciparum
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Recurrent bottlenecks in the malaria life cycle obscure signals of positive selection
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Adaptive protein evolution at the Adh locus in Drosophila
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Genome sequence of the human malaria parasite Plasmodium falciparum
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Origin of the human malaria parasite Plasmodium falciparum in gorillas
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Structure of malaria invasion protein RH5 with erythrocyte basigin and blocking antibodies
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A novel locus of resistance to severe malaria in a region of ancient balancing selection
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Making ubiquitin specific
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Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria
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Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts
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Ape parasite origins of human malaria virulence genes
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Inferring human population size and separation history from multiple genome sequences
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Bayesian inference of ancient human demography from individual genome sequences
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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
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Revising the human mutation rate: implications for understanding human evolution
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An algorithm for progressive multiple alignment of sequences with insertions
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Evidence for an ancient adaptive episode of convergent molecular evolution
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African great apes are natural hosts of multiple related malaria species, including Plasmodium falciparum
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Maurer's clefts, the enigma of Plasmodium falciparum
inferredcites →https://doi.org/10.1073/pnas.1320771110openalex-snapshot
RH5–Basigin interaction plays a major role in the host tropism of Plasmodium falciparum
inferredcites →https://doi.org/10.1073/pnas.1603008113openalex-snapshot
Ape malaria transmission and potential for ape-to-human transfers in Africa
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A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences
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BamView: visualizing and interpretation of next-generation sequencing read alignments
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Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
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Jalview Version 2—a multiple sequence alignment editor and analysis workbench
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Fast and accurate short read alignment with Burrows–Wheeler transform
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ABACAS: algorithm-based automatic contiguation of assembled sequences
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SNP-o-matic
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Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology
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The variant call format and VCFtools
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Optimized Whole-Genome Amplification Strategy for Extremely AT-Biased Template
inferredcites →https://doi.org/10.1093/gbe/evw128openalex-snapshot
Multigenomic Delineation ofPlasmodiumSpecies of theLaveraniaSubgenus Infecting Wild-Living Chimpanzees and Gorillas
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Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msp259openalex-snapshot
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building
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The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection
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The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection
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A New Method for Estimating Species Age Supports the Coexistence of Malaria Parasites and Their Mammalian Hosts
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Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkl200openalex-snapshot
AUGUSTUS: ab initio prediction of alternative transcripts
inferredcites →https://doi.org/10.1093/nar/gkq1268openalex-snapshot
RATT: Rapid Annotation Transfer Tool
inferredcites →https://doi.org/10.1093/nar/gku989openalex-snapshot
UniProt: a hub for protein information
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026201openalex-snapshot
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1098/rspb.2014.3027openalex-snapshot
Hybridization and pre-zygotic reproductive barriers inPlasmodium
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.115949.110openalex-snapshot
High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1111/j.1365-2958.2006.05284.xopenalex-snapshot
Malaria transmission‐blocking antigen, Pfs230, mediates human red blood cell binding to exflagellating male parasites and oocyst production
inferredcites →https://doi.org/10.1111/j.1365-2958.2007.05736.xopenalex-snapshot
Variable switching rates of malaria virulence genes are associated with chromosomal position
inferredcites →https://doi.org/10.1126/science.1059878openalex-snapshot
Recent Origin of Plasmodium falciparum from a Single Progenitor
inferredcites →https://doi.org/10.1126/science.1158395openalex-snapshot
Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
inferredcites →https://doi.org/10.1126/science.1210829openalex-snapshot
A DOC2 Protein Identified by Mutational Profiling Is Essential for Apicomplexan Parasite Exocytosis
inferredcites →https://doi.org/10.1128/cmr.15.4.564-594.2002openalex-snapshot
Evolutionary and Historical Aspects of the Burden of Malaria
inferredcites →https://doi.org/10.1186/1471-2148-11-299openalex-snapshot
Timing the origin of human malarias: the lemur puzzle
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Isolation of Plasmodium falciparum by flow-cytometry: implications for single-trophozoite genotyping and parasite DNA purification for whole-genome high-throughput sequencing of archival samples
inferredcites →https://doi.org/10.1186/s12936-015-0622-6openalex-snapshot
Diversity of malaria parasites in great apes in Gabon
inferredcites →https://doi.org/10.1186/s12936-015-0820-2openalex-snapshot
Genetic evidence for contribution of human dispersal to the genetic diversity of EBA-175 in Plasmodium falciparum
inferredcites →https://doi.org/10.1186/s12936-016-1641-7openalex-snapshot
Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification
inferredcites →https://doi.org/10.1371/journal.pgen.1003293openalex-snapshot
Mitotic Evolution of Plasmodium falciparum Shows a Stable Core Genome but Recombination in Antigen Families
inferredcites →https://doi.org/10.1371/journal.pgen.1004812openalex-snapshot
Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis
inferredcites →https://doi.org/10.1371/journal.pone.0022213openalex-snapshot
An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing
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Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
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A New Malaria Agent in African Hominids
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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1101/gr.218123.116openalex-snapshot
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Defining the ecological and evolutionary drivers of Plasmodium knowlesi transmission within a multi-scale framework
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Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution
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The Plasmodium berghei RC strain is highly diverged and harbors putatively novel drug resistance variants
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