Evidence map›Paper›PMID 36792983›Full record

ArticleBMC genomics2023

Chromosome-length genome assembly of Teladorsagia circumcincta - a globally important helminth parasite in livestock.

Shamshad Ul Hassan, Eng Guan Chua, Erwin A Paz, Chin Yen Tay, Johan C Greeff, Dieter G Palmer, Olga Dudchenko, Erez Lieberman Aiden, Graeme B Martin, Parwinder Kaur

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
2.4field-weighted citation impact, top 12% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 8 citations in OpenAlex.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 4 institutions in 3 countries.

Shamshad Ul HassanUWA School of Agriculture and Environment, The University of Western Australia, 6009, Crawley, WA, Australia.
Eng Guan ChuaHelicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia.
Erwin A PazUWA School of Agriculture and Environment, The University of Western Australia, 6009, Crawley, WA, Australia.
Chin Yen TayHelicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia.
Johan C GreeffDepartment of Primary Industries and Regional Development, Western Australia 3 Baron Hay Court, South Perth, 6151, WA, Australia.
Dieter G PalmerDepartment of Primary Industries and Regional Development, Western Australia 3 Baron Hay Court, South Perth, 6151, WA, Australia.
Olga DudchenkoThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, 77030, Houston, TX, USA.
Erez Lieberman AidenThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, 77030, Houston, TX, USA.
Graeme B MartinUWA School of Agriculture and Environment, The University of Western Australia, 6009, Crawley, WA, Australia.
Parwinder KaurUWA School of Agriculture and Environment, The University of Western Australia, 6009, Crawley, WA, Australia. parwinder.kaur@uwa.edu.au.
The University of Western Australia · AUDepartment of Primary Industries and Regional Development · AUBaylor College of Medicine · USBroad Institute · US

Funding

GENOME WIDE MAPPING OF LOOPS USING IN SITU HI-CUM1HG009375 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI LIEBERMAN-AIDEN, EREZ · 2017 to 2021
$4.7M
NHGRI NIH HHS UM1 HG009375
6 · The paper itself

Abstract

backgroundGastrointestinal (GIT) helminthiasis is a global problem that affects livestock health, especially in small ruminants. One of the major helminth parasites of sheep and goats, Teladorsagia circumcincta, infects the abomasum and causes production losses, reductions in weight gain, diarrhoea and, in some cases, death in young animals. Control strategies have relied heavily on the use of anthelmintic medication but, unfortunately, T. circumcincta has developed resistance, as have many helminths. Vaccination offers a sustainable and practical solution, but there is no commercially available vaccine to prevent Teladorsagiosis. The discovery of new strategies for controlling T. circumcincta, such as novel vaccine targets and drug candidates, would be greatly accelerated by the availability of better quality, chromosome-length, genome assembly because it would allow the identification of key genetic determinants of the pathophysiology of infection and host-parasite interaction. The available draft genome assembly of T. circumcincta (GCA_002352805.1) is highly fragmented and thus impedes large-scale investigations of population and functional genomics.

resultsWe have constructed a high-quality reference genome, with chromosome-length scaffolds, by purging alternative haplotypes from the existing draft genome assembly and scaffolding the result using chromosome conformation, capture-based, in situ Hi-C technique. The improved (Hi-C) assembly resulted in six chromosome-length scaffolds with length ranging from 66.6 Mbp to 49.6 Mbp, 35% fewer sequences and reduction in size. Substantial improvements were also achieved in both the values for N50 (57.1 Mbp) and L50 (5 Mbp). A higher and comparable level of genome and proteome completeness was achieved for Hi-C assembly on BUSCO parameters. The Hi-C assembly had a greater synteny and number of orthologs with a closely related nematode, Haemonchus contortus.

conclusionThis improved genomic resource is suitable as a foundation for the identification of potential targets for vaccine and drug development.

Indexed as

HaemonchusNematodaParasitesSheep DiseasesAnimalsGenomicsLivestockSheep3D-DNABioinformaticsBrown stomach wormGenome assemblyHi-C sequencingTeladorsagia circumcincta

Identifiers

PMID36792983
PMCPMC9933375
OpenAlexW4321003238

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.