Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing
1
Issued Date
2022-11-01
Resource Type
eISSN
19326203
Scopus ID
2-s2.0-85141542003
Pubmed ID
36331983
Journal Title
PLoS ONE
Volume
17
Issue
11 November
Rights Holder(s)
SCOPUS
Bibliographic Citation
PLoS ONE Vol.17 No.11 November (2022)
Suggested Citation
Shaw P.J., Kaewprommal P., Wongsombat C., Ngampiw C., Taechalertpaisarn T., Kamchonwongpaisan S., Tongsima S., Piriyapongsa J. Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing. PLoS ONE Vol.17 No.11 November (2022). doi:10.1371/journal.pone.0276956 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/86462
Title
Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing
Other Contributor(s)
Abstract
The Plasmodium falciparum human malaria parasite genome is incompletely annotated and does not accurately represent the transcriptomic diversity of this species. To address this need, we performed long-read transcriptomic sequencing. 50 capped mRNA was enriched from samples of total and nuclear-fractionated RNA from intra-erythrocytic stages and converted to cDNA library. The cDNA libraries were sequenced on PacBio and Nanopore longread platforms. 12,495 novel isoforms were annotated from the data. Alternative 50 and 30 ends represent the majority of isoform events among the novel isoforms, with retained introns being the next most common event. The majority of alternative 50 ends correspond to genomic regions with features similar to those of the reference transcript 50 ends. However, a minority of alternative 50 ends showed markedly different features, including locations within protein-coding regions. Alternative 30 ends showed similar features to the reference transcript 30 ends, notably adenine-rich termination signals. Distinguishing features of retained introns could not be observed, except for a tendency towards shorter length and greater GC content compared with spliced introns. Expression of antisense and retained intron isoforms was detected at different intra-erythrocytic stages, suggesting developmental regulation of these isoform events. To gain insights into the possible functions of the novel isoforms, their protein-coding potential was assessed. Variants of P. falciparum proteins and novel proteins encoded by alternative open reading frames suggest that P. falciparum has a greater proteomic repertoire than the current annotation. We provide a catalog of annotated transcripts and encoded alternative proteins to support further studies on gene and protein regulation of this pathogen.