A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel Limnoperna fortunei

Uliano-Silva, M., Dondero, F., Otto, T. D. , Costa, I., Lima, N. C. B., Americo, J. A., Mazzoni, C. J., Prosdocimi, F. and Rebelo, M. d. F. (2018) A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel Limnoperna fortunei. GigaScience, 7(2), pp. 1-10. (doi: 10.1093/gigascience/gix128) (PMID:29267857)

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Abstract

Background: For more than 25 years, the golden mussel Limnoperna fortunei has aggressively invaded South American freshwaters, having travelled more than 5,000 km upstream across five countries. Along the way, the golden mussel has outcompeted native species and economically harmed aquaculture, hydroelectric powers, and ship transit. We have sequenced the complete genome of the golden mussel to understand the molecular basis of its invasiveness and search for ways to control it. Findings: We assembled the 1.6 Gb genome into 20548 scaffolds with an N50 length of 312 Kb using a hybrid and hierarchical assembly strategy from short and long DNA reads and transcriptomes. A total of 60717 coding genes were inferred from a customized transcriptome-trained AUGUSTUS run. We also compared predicted protein sets with those of complete molluscan genomes, revealing an exacerbation of protein-binding domains in L. fortunei. Conclusions: We built one of the best bivalve genome assemblies available using a cost-effective approach using Illumina pair-end, mate pair, and PacBio long reads. We expect that the continuous and careful annotation of L. fortunei’s genome will contribute to the investigation of bivalve genetics, evolution, and invasiveness, as well as to the development of biotechnological tools for aquatic pest control.

Item Type:Articles
Keywords:Amazon, TLR, binding domain, bivalves, genomics, transposon.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Authors: Uliano-Silva, M., Dondero, F., Otto, T. D., Costa, I., Lima, N. C. B., Americo, J. A., Mazzoni, C. J., Prosdocimi, F., and Rebelo, M. d. F.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:GigaScience
Publisher:Oxford University Press
ISSN:2047-217X
ISSN (Online):2047-217X
Published Online:15 December 2017
Copyright Holders:Copyright © 2017 The Authors
First Published:First published in GigaScience 7(2):1-10
Publisher Policy:Reproduced under a Creative Commons License

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