Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons.
Filarial parasitic nematodes (Filarioidea) cause substantial disease burden to humans and animals around the world. Recently there has been a coordinated global effort to generate, annotate, and curate genomic data from nematode species of medical and veterinary importance. This has resulted in two...
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ftdoajarticles:oai:doaj.org/article:64913c8e992d4e2bacfb8e895689ff30 2023-05-15T15:16:42+02:00 Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons. Nicolas J Wheeler Paul M Airs Mostafa Zamanian 2020-11-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0008869 https://doaj.org/article/64913c8e992d4e2bacfb8e895689ff30 EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pntd.0008869 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0008869 https://doaj.org/article/64913c8e992d4e2bacfb8e895689ff30 PLoS Neglected Tropical Diseases, Vol 14, Iss 11, p e0008869 (2020) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2020 ftdoajarticles https://doi.org/10.1371/journal.pntd.0008869 2022-12-31T04:32:54Z Filarial parasitic nematodes (Filarioidea) cause substantial disease burden to humans and animals around the world. Recently there has been a coordinated global effort to generate, annotate, and curate genomic data from nematode species of medical and veterinary importance. This has resulted in two chromosome-level assemblies (Brugia malayi and Onchocerca volvulus) and 11 additional draft genomes from Filarioidea. These reference assemblies facilitate comparative genomics to explore basic helminth biology and prioritize new drug and vaccine targets. While the continual improvement of genome contiguity and completeness advances these goals, experimental functional annotation of genes is often hindered by poor gene models. Short-read RNA sequencing data and expressed sequence tags, in cooperation with ab initio prediction algorithms, are employed for gene prediction, but these can result in missing clade-specific genes, fragmented models, imperfect mapping of gene ends, and lack of isoform resolution. Long-read RNA sequencing can overcome these drawbacks and greatly improve gene model quality. Here, we present Iso-Seq data for B. malayi and Dirofilaria immitis, etiological agents of lymphatic filariasis and canine heartworm disease, respectively. These data cover approximately half of the known coding genomes and substantially improve gene models by extending untranslated regions, cataloging novel splice junctions from novel isoforms, and correcting mispredicted junctions. Furthermore, we validated computationally predicted operons, manually curated new operons, and merged fragmented gene models. We carried out analyses of poly(A) tails in both species, leading to the identification of non-canonical poly(A) signals. Finally, we prioritized and assessed known and putative anthelmintic targets, correcting or validating gene models for molecular cloning and target-based anthelmintic screening efforts. Overall, these data significantly improve the catalog of gene models for two important parasites, and they ... Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 14 11 e0008869 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Nicolas J Wheeler Paul M Airs Mostafa Zamanian Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
Filarial parasitic nematodes (Filarioidea) cause substantial disease burden to humans and animals around the world. Recently there has been a coordinated global effort to generate, annotate, and curate genomic data from nematode species of medical and veterinary importance. This has resulted in two chromosome-level assemblies (Brugia malayi and Onchocerca volvulus) and 11 additional draft genomes from Filarioidea. These reference assemblies facilitate comparative genomics to explore basic helminth biology and prioritize new drug and vaccine targets. While the continual improvement of genome contiguity and completeness advances these goals, experimental functional annotation of genes is often hindered by poor gene models. Short-read RNA sequencing data and expressed sequence tags, in cooperation with ab initio prediction algorithms, are employed for gene prediction, but these can result in missing clade-specific genes, fragmented models, imperfect mapping of gene ends, and lack of isoform resolution. Long-read RNA sequencing can overcome these drawbacks and greatly improve gene model quality. Here, we present Iso-Seq data for B. malayi and Dirofilaria immitis, etiological agents of lymphatic filariasis and canine heartworm disease, respectively. These data cover approximately half of the known coding genomes and substantially improve gene models by extending untranslated regions, cataloging novel splice junctions from novel isoforms, and correcting mispredicted junctions. Furthermore, we validated computationally predicted operons, manually curated new operons, and merged fragmented gene models. We carried out analyses of poly(A) tails in both species, leading to the identification of non-canonical poly(A) signals. Finally, we prioritized and assessed known and putative anthelmintic targets, correcting or validating gene models for molecular cloning and target-based anthelmintic screening efforts. Overall, these data significantly improve the catalog of gene models for two important parasites, and they ... |
format |
Article in Journal/Newspaper |
author |
Nicolas J Wheeler Paul M Airs Mostafa Zamanian |
author_facet |
Nicolas J Wheeler Paul M Airs Mostafa Zamanian |
author_sort |
Nicolas J Wheeler |
title |
Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons. |
title_short |
Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons. |
title_full |
Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons. |
title_fullStr |
Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons. |
title_full_unstemmed |
Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons. |
title_sort |
long-read rna sequencing of human and animal filarial parasites improves gene models and discovers operons. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2020 |
url |
https://doi.org/10.1371/journal.pntd.0008869 https://doaj.org/article/64913c8e992d4e2bacfb8e895689ff30 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 14, Iss 11, p e0008869 (2020) |
op_relation |
https://doi.org/10.1371/journal.pntd.0008869 https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0008869 https://doaj.org/article/64913c8e992d4e2bacfb8e895689ff30 |
op_doi |
https://doi.org/10.1371/journal.pntd.0008869 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
14 |
container_issue |
11 |
container_start_page |
e0008869 |
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1766346998383902720 |