Identifying transcript 5′ capped ends in <i>Plasmodium falciparum</i>

Shaw, Philip; Piriyapongsa, Jittima; Kaewprommal, Pavita; Wongsombat, Chayaphat; Chaosrikul, Chadapohn; Teeravajanadet, Krirkwit; Boonbangyang, Manon; Uthaipibull, Chairat; Kamchonwongpaisan, Sumalee; Tongsima, Sissades

doi:10.7717/peerj.11983

Cited by 3 publications

(5 citation statements)

References 87 publications

(257 reference statements)

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“…RNA-Seq data to filter P. falciparum isoforms. The majority of 5 0 capped nucleotide signals are broad, with a mean interquartile width >100 bp [18]. We selected candidate isoforms with 5 0ends not further than 50 bp from the dominant 5 0 capped nucleotide in each signal.…”

Section: Plos Onementioning

confidence: 99%

Section: Analysis Of External Short-read Rna-seq Datamentioning

confidence: 99%

“…Annotation of 5 0 capped nucleotides for validating 5 0 ends of novel isoforms 5 0 capped nucleotide signals were obtained from CAPture-enrichment [18] and 5 0 cap end sequencing [17] experimental data reported previously. The signals were annotated from these data using the CAGEr program [94] as previously reported [18]. The signals (CAGEr clusters) were concatenated, i.e., the union of signals from different data sources, into a single "CAGE peak BED file" for SQANTI3 [35].…”

Section: Analysis Of External Short-read Rna-seq Datamentioning

confidence: 99%

“…Transcript 5 0 end positions were obtained from the.gff annotation files for reference and novel isoform transcripts. H2A.Z ChIP-seq data reported in a previous study [32] were used to calculate genome-wide normalized occupancy as described previously [18]. The normalized occupancy values at the transcript 5 0 end positions were natural log-transformed and the distributions were plotted using the ggplot2 package in R. Principal component scores of the log-transformed normalized occupancy values at novel isoform 5 0 end positions were calculated using the MacroPCA package in R [99].…”

Section: Analysis Of Transcript 5 0 Endsmentioning

confidence: 99%

“…The current P. falciparum 3D7 nuclear genome annotation (PlasmoDB [16] release 58) includes UTR features for the majority of the 5,318 protein-coding genes (not including pseudogenes) based on these data. 67(1%) of the genes have annotated alternative transcripts; however, RNA-Seq studies using specialized protocols to enrich fragments of 5 0 capped transcript ends have indicated that isoforms with alternative 5 0 ends showing differential abundance across the IDC are expressed from many more genes [17,18].…”

Section: Introductionmentioning

confidence: 99%

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Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing

et al. 2022

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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. 5′ 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 long-read platforms. 12,495 novel isoforms were annotated from the data. Alternative 5′ and 3′ ends represent the majority of isoform events among the novel isoforms, with retained introns being the next most common event. The majority of alternative 5′ ends correspond to genomic regions with features similar to those of the reference transcript 5′ ends. However, a minority of alternative 5′ ends showed markedly different features, including locations within protein-coding regions. Alternative 3′ ends showed similar features to the reference transcript 3′ 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.

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Section: Plos Onementioning

confidence: 99%

Section: Analysis Of External Short-read Rna-seq Datamentioning

confidence: 99%

Section: Analysis Of External Short-read Rna-seq Datamentioning

confidence: 99%

Section: Analysis Of Transcript 5 0 Endsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing

et al. 2022

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A single cell atlas of sexual development inPlasmodium falciparum

Dogga

Rop

Cudini

et al. 2023

Preprint

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The developmental decision made by malaria parasites to become sexual underlies all malaria transmission. Here, we describe a rich atlas of short and long-read single-cell transcriptomes of over 37,000 Plasmodium falciparum cells across intraerythrocytic asexual and sexual development. We used the atlas to explore transcriptional modules and exon usage along sexual development, and expanded it to include malaria parasites collected from a Malian individual naturally infected with multiple P. falciparum strains. We investigated genotypic and transcriptional heterogeneity within and among these wild strains at a single-cell level for the first time, finding considerable differential expression between different strains even within the same host. This work is a key addition to the Malaria Cell Atlas, enabling a deeper understanding of the biology and diversity of transmission stages.

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A single cell atlas of sexual development in Plasmodium falciparum

Dogga,

Rop,

Cudini

et al. 2024

Science

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The developmental decision made by malaria parasites to become sexual underlies all malaria transmission. Here, we describe a rich atlas of short- and long-read single-cell transcriptomes of over 37,000 Plasmodium falciparum cells across intraerythrocytic asexual and sexual development. We used the atlas to explore transcriptional modules and exon usage along sexual development and expanded it to include malaria parasites collected from four Malian individuals naturally infected with multiple P. falciparum strains. We investigated genotypic and transcriptional heterogeneity within and among these wild strains at the single-cell level, finding differential expression between different strains even within the same host. These data are a key addition to the Malaria Cell Atlas interactive data resource, enabling a deeper understanding of the biology and diversity of transmission stages.

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Identifying transcript 5′ capped ends in Plasmodium falciparum

Cited by 3 publications

References 87 publications

Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing

Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing

A single cell atlas of sexual development inPlasmodium falciparum

A single cell atlas of sexual development in Plasmodium falciparum

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