A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Background

Tilapias are the second most farmed fishes in the world and a sustainable source of food. Like many other fish, tilapias are sexually dimorphic and sex is a commercially important trait in these fish. In this study, we developed a significantly improved assembly of the tilapia genome using the latest genome sequencing methods and show how it improves the characterization of two sex determination regions in two tilapia species.

Results

A homozygous clonal XX female Nile tilapia ( Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing. Dozens of candidate de novo assemblies were generated and an optimal assembly (contig NG50 of 3.3Mbp) was selected using principal component analysis of likelihood scores calculated from several paired-end sequencing libraries. Comparison of the new assembly to the previous O. niloticus genome assembly reveals that recently duplicated portions of the genome are now well represented. The overall number of genes in the new assembly increased by 27.3%, including a 67% increase in pseudogenes. The new tilapia genome assembly correctly represents two recent vasa gene duplication events that have been verified with BAC sequencing. At total of 146Mbp of additional transposable element sequence are now assembled, a large proportion of which are recent insertions. Large centromeric satellite repeats are assembled and annotated in cichlid fish for the first time. Finally, the new assembly identifies the long-range structure of both a ~9Mbp XY sex determination region on LG1 in O. niloticus, and a ~50Mbp WZ sex determination region on LG3 in the related species O. aureus.

Conclusions

This study highlights the use of long read sequencing to correctly assemble recent duplications and to characterize repeat-filled regions of the genome. The study serves as an example of the need for high quality genome assemblies and provides a framework for identifying sex determining genes in tilapia and related fish species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3723-5) contains supplementary material, which is available to authorized users.

Related collections

Most cited references 43

Record: found
Abstract: found
Article: not found

FLASH: fast length adjustment of short reads to improve genome assemblies.

T. Magoc, S. L. Salzberg (2013)

Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.

0 comments Cited 5875 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

The genomic substrate for adaptive radiation in African cichlid fish

David Brawand, Catherine E. Wagner, Yang I. Li … (2014)

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

0 comments Cited 416 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

REAPR: a universal tool for genome assembly evaluation

Martin Hunt, Taisei Kikuchi, Mandy Sanders … (2013)

Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked. Here we present REAPR, a tool that precisely identifies errors in genome assemblies without the need for a reference sequence. We have validated REAPR on complete genomes or de novo assemblies from bacteria, malaria and Caenorhabditis elegans, and demonstrate that 86% and 82% of the human and mouse reference genomes are error-free, respectively. When applied to an ongoing genome project, REAPR provides corrected assembly statistics allowing the quantitative comparison of multiple assemblies. REAPR is available at http://www.sanger.ac.uk/resources/software/reapr/.

0 comments Cited 233 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Matthew A. Conte: mconte@umd.edu

William J. Gammerdinger: wgammerd@umd.edu

Kerry L. Bartie: k.l.bartie1@stir.ac.uk

David J. Penman: d.j.penman@stir.ac.uk

Thomas D. Kocher: tdk@umd.edu

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 2 May 2017

Publication date PMC-release: 2 May 2017

Publication date Collection: 2017

Volume: 18

Electronic Location Identifier: 341

Affiliations

[1 ]ISNI 0000 0001 0941 7177, GRID grid.164295.d, Department of Biology, , University of Maryland, ; 20742 College Park, MD USA

[2 ]ISNI 0000 0001 2248 4331, GRID grid.11918.30, Institute of Aquaculture, School of Natural Sciences, , University of Stirling, ; Stirling, FK9 4LA Scotland UK

Article

Publisher ID: 3723

DOI: 10.1186/s12864-017-3723-5

PMC ID: 5414186

PubMed ID: 28464822

SO-VID: 7b2d1272-5183-41d2-b9d8-44705b9da4b9

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 9 February 2017

Date accepted : 25 April 2017

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100000199, U.S. Department of Agriculture;

Award ID: MD.W-2014-05906

Award Recipient : Thomas D. Kocher

Funded by: FundRef http://dx.doi.org/http://dx.doi.org/10.13039/100000002, National Institutes of Health;

Award ID: R01-EY024639

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: genome assembly,pacific biosciences smrt sequencing,transposable elements,gene duplication,sex chromosome,sex determination,aquaculture,tilapia

Data availability:

ScienceOpen disciplines: Genetics

Keywords: genome assembly, pacific biosciences smrt sequencing, transposable elements, gene duplication, sex chromosome, sex determination, aquaculture, tilapia

Comments

Comment on this article

scite_

Smart Citations

Citing PublicationsSupportingMentioningContrasting

View Citations

See how this article has been cited at scite.ai

scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.

A high quality assembly of the Nile Tilapia ( Oreochromis niloticus) genome reveals the structure of two sex determination regions

Read this article at

Abstract

Background

Results

Conclusions

Electronic supplementary material

Related collections

Genome Integrity

Most cited references 43

FLASH: fast length adjustment of short reads to improve genome assemblies.

The genomic substrate for adaptive radiation in African cichlid fish

REAPR: a universal tool for genome assembly evaluation

Author and article information

Contributors

Journal

Affiliations

Article

History

Funding

Categories

Custom metadata

Comments

Comment on this article

Similar content 809

Cited by 94

Most referenced authors 2,831