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

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-frac...

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Autores principales: Shaw, Philip J., Kaewprommal, Pavita, Wongsombat, Chayaphat, Ngampiw, Chumpol, Taechalertpaisarn, Tana, Kamchonwongpaisan, Sumalee, Tongsima, Sissades, Piriyapongsa, Jittima
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9635732/
https://www.ncbi.nlm.nih.gov/pubmed/36331983
http://dx.doi.org/10.1371/journal.pone.0276956
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author Shaw, Philip J.
Kaewprommal, Pavita
Wongsombat, Chayaphat
Ngampiw, Chumpol
Taechalertpaisarn, Tana
Kamchonwongpaisan, Sumalee
Tongsima, Sissades
Piriyapongsa, Jittima
author_facet Shaw, Philip J.
Kaewprommal, Pavita
Wongsombat, Chayaphat
Ngampiw, Chumpol
Taechalertpaisarn, Tana
Kamchonwongpaisan, Sumalee
Tongsima, Sissades
Piriyapongsa, Jittima
author_sort Shaw, Philip J.
collection PubMed
description 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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spelling pubmed-96357322022-11-05 Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing Shaw, Philip J. Kaewprommal, Pavita Wongsombat, Chayaphat Ngampiw, Chumpol Taechalertpaisarn, Tana Kamchonwongpaisan, Sumalee Tongsima, Sissades Piriyapongsa, Jittima PLoS One Research Article 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. Public Library of Science 2022-11-04 /pmc/articles/PMC9635732/ /pubmed/36331983 http://dx.doi.org/10.1371/journal.pone.0276956 Text en © 2022 Shaw et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Shaw, Philip J.
Kaewprommal, Pavita
Wongsombat, Chayaphat
Ngampiw, Chumpol
Taechalertpaisarn, Tana
Kamchonwongpaisan, Sumalee
Tongsima, Sissades
Piriyapongsa, Jittima
Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing
title Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing
title_full Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing
title_fullStr Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing
title_full_unstemmed Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing
title_short Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing
title_sort transcriptomic complexity of the human malaria parasite plasmodium falciparum revealed by long-read sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9635732/
https://www.ncbi.nlm.nih.gov/pubmed/36331983
http://dx.doi.org/10.1371/journal.pone.0276956
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