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Table 1 Key advances from recent omics studies

From: Recent advances in malaria genomics and epigenomics

Research area Key findings Reference(s)
Genome sequencing WGS and refinement of genome sequences of primate and rodent infectious Plasmodium species [13, 154157, 179]
  Genome sequence of cryptic chimpanzee Plasmodium species [158]
Gene expression regulation Discovery of AP2-G as master regulator of gametocytogenesis in Pf and Pb [49, 50]
  AP2-G2 functions as a transcription regulator driving gametocyte development [51]
  Functional analysis of Pf lifecycle dynamics using transcriptional profiling [180]
  Genome-wide TSS mapping in Pf [42]
  Acetylome analysis reveals post-translational PTM of ApiAP2 transcription factors [55]
  Genome-wide analysis of AP2-O target genes [48]
Post-transcriptional/translational control Genome-wide analysis reveals features of the Pf translatome [59, 66]
  Analysis of the Pb maternal repressome [64]
Epigenetic control SETvs functions as a regulator of var gene silencing in Pf [98]
  Involvement of HP1 in clonal variant gene expression and sexual development [29]
  HDA2 mediates var gene silencing and sexual commitment in Pf [27]
  BDP1 regulates expression of invasion-related genes [31]
  Profiling of histone PTMs in Pf [22]
Gene silencing/editing First description of the use of ZFN and CRISPR-Cas9 genome editing in Plasmodium [115, 116, 140]
  Functional adaptation of an AID-based conditional knockdown system in Pb [159]
Antibiotic resistance Analysis of KELCH13-propellermutations in Plasmodium field isolates confirms relation to artemisinin resistance [115, 116]
  Identification of UPR pathway involvement in Plasmodium artemisinin resistance [123, 126]
Genome structure First profiling of genome-wide chromosome interactions [39]
  Strong correlation between spatial genome structure and gene expression [37]
ncRNAs PfRNaseII exonuclease is involved in group A var gene silencing [84]
  Genome-wide search revealed over 1000 novel ncRNAs in Pf [181]
  Strand-specific RNA sequencing reveals widespread transcription of antisense RNAs in Pf [1618]
  Antisense lncRNAs regulate expression of cognate var genes in Pf [87]
Virulence/transmission Vector transmission of P. chabaudi chabaudi impacts on parasite virulence [182]
  Transcriptome changes during early phase of mosquito infection [183]
Development Global phosphoproteome analysis identified PKG as major intracellular Ca2+ level regulator [184]
  PKG regulates Plasmodium egress and evasion [185]
  Systematic subtractive bioinformatic analysis identified sex-specific stage V gametocyte protein marker [186]
  Protein phosphatases are key regulators of Plasmodium development [187]
Population genomics Identification of a novel malaria resistance locus through GWAS in African children [5]
  Genomic epidemiology study revels global KELCH13 mutation distribution [160]
Metablomics Lipid metabolism analysis in Pf [151]
  1. AID auxin-inducible degron, CRISPR clustered regularly interspaced short palindromic repeats, GWAS genome-wide association study, lncRNA long non-coding RNA, ncRNA non-coding RNA, Pb P. berghei, Pf P. falciparum, PTM post-translational modification, SNP single-nucleotide polymorphism, TSS transcription start site, UPR unfolded protein response, WGS whole-genome sequencing, ZFN zinc finger nuclease