Evidence map›Paper›PMID 36522771›Full record

ArticleBMC genomics2022

Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus.

G J Etherington, W Nash, A Ciezarek, T K Mehta, A Barria, C Peñaloza, M G Q Khan, A Durrant, N Forrester, F Fraser and 12 more

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Article in BMC genomics, 2022. 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
–field-weighted citation impact
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.

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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

22 authors.

G J Etherington *Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
W Nash *Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
A Ciezarek *Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
T K Mehta *Earlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
A BarriaThe Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
C PeñalozaThe Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
M G Q KhanThe Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
A DurrantEarlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
N ForresterEarlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
F FraserEarlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
N IrishEarlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
G G KaithakottilEarlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
J LipscombeEarlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
T TrongWorldFish, 10670, Penang, Malaysia.
C WatkinsEarlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
D SwarbreckEarlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
E AngioliniEarlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
A CnaaniDepartment of Poultry and Aquaculture, Institute of Animal Science, Agricultural Research Organization - Volcani Institute, Rishon LeTsiyon, Israel.
K GharbiEarlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK.
R D HoustonThe Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
J A H BenzieWorldFish, 10670, Penang, Malaysia. J.Benzie@cgiar.org.
W HaertyEarlham Institute, Norwich Research Park, Colney Ln, Norwich, NR4 7UZ, UK. wilfried.haerty@earlham.ac.uk.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary.

resultsUsing a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11 Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate.

conclusionBecause of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits.

Indexed as

CichlidsTilapiaAnimalsAquacultureChromosomesGenomicsAquacultureIntrogressionReference genomeTilapia

Identifiers

PMID36522771
PMCPMC9756657

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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.