Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons

PLoS Neglected Tropical Diseases
Nicolas J WheelerMostafa Zamanian

Abstract

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 disea...Continue Reading

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Citations

Jun 9, 2021·Parasites & Vectors·Yue XieGuangyou Yang
May 25, 2021·International Journal for Parasitology. Drugs and Drug Resistance·Sandra NoackPaul M Selzer

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Methods Mentioned

BETA
chip
PCR
RNA-seq
Iso-Seq
restriction digest

Software Mentioned

HISAT2
R package topGO
BEDTools
blastx
Iso
SQANTI3
ParaSite
BioPython
ExPASy translate
blastx ParaSite

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