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. 2018 Mar 12;16(3):e2004328. doi: 10.1371/journal.pbio.2004328

Fig 6. Summary of PfEMP1 transcripts, domains, and segments that were up-regulated in severe malaria.

Fig 6

Sequences up-regulated in severe malaria are organised in columns for each analysis method separated by grey bars. Multiple domains found in the same single transcripts from the combined or separate assemblies are on a single row. Closely related sequences found in multiple analyses are colour coded for each of the major domain types and are grouped together across analyses by unbroken horizontal lines. Domains and/or segments that clustered together by expression profile in multiple individuals within a single analysis are also grouped by unbroken horizontal lines. Grey shaded sequences at the bottom of the diagram are unrelated to each other. For example, in the case of DC4, 2 transcripts from the combined assembly were amongst the closest BLAST hits to the DC4-like transcripts from the CORSET cluster of the separate assembly; 6 domains and 5 blocks identified by HMM in the separate assembly are found in DC4 domains; and clusters for 1 domain and 4 segments identified by hierarchical analysis contained DC4 domain sequences, including those from the DC4-like transcripts from the CORSET cluster of the separate assembly. aCombined assembly transcripts up-regulated in severe malaria were all adjusted p < 0.05 except for domains marked b (adjusted p < 0.153). Domains HMM and blocks HMM were identified using the HMM of [14]. Domains and segments %ID were identified using the novel hierarchical approach developed for this study. cNon–DC8-like DBLδ1 and non–DC4-like DBLβ3 that clustered by expression profile in the same patients with a highly conserved CIDRβ1. A dashed line separates DBLβ12 from DC8 because DC8 typically contain DBLβ12, but these DBLβ12 formed a phylogenetic cluster with non-DC8 DBLβ12. Dashed lines separate putative DC9 components because transcripts containing all components were not up-regulated in the combined assembly or the Corset analysis, but the clusters from which the up-regulated segments were identified contained multiple transcripts carrying the DC9 domains. ATS, acidic terminal sequence; CIDR, cysteine-rich interdomain region; DBL, Duffy binding-like; DC, domain cassette; HMM, Hidden Markov Model; PfEMP1, Plasmodium falciparum Erythrocyte Membrane Protein 1; TM, transmembrane.