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First draft genome assembly of the desert locust, Schistocerca gregaria

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journal contribution
posted on 16.03.2021, 14:10 by Heleen Verlinden, Lieven Sterck, Jia Li, Zhen Li, Anna Yssel, Yannick Gansemans, Rik Verdonck, Michiel Holtof, Hojun Song, Spencer T Behmer, Gregory A Sword, Tom Matheson, Swidbert R Ott, Dieter Deforce, Filip Van Nieuwerburgh, Yves Van de PeerYves Van de Peer, Jozef Vanden Broeck
Background: At the time of publication, the most devastating desert locust crisis in decades is affecting East Africa, the Arabian Peninsula and South-West Asia. The situation is extremely alarming in East Africa, where Kenya, Ethiopia and Somalia face an unprecedented threat to food security and livelihoods. Most of the time, however, locusts do not occur in swarms, but live as relatively harmless solitary insects. The phenotypically distinct solitarious and gregarious locust phases differ markedly in many aspects of behaviour, physiology and morphology, making them an excellent model to study how environmental factors shape behaviour and development. A better understanding of the extreme phenotypic plasticity in desert locusts will offer new, more environmentally sustainable ways of fighting devastating swarms.
Methods: High molecular weight DNA derived from two adult males was used for Mate Pair and Paired End Illumina sequencing and PacBio sequencing. A reliable reference genome of Schistocerca gregaria was assembled using the ABySS pipeline, scaffolding was improved using LINKS.
Results: In total, 1,316 Gb Illumina reads and 112 Gb PacBio reads were produced and assembled. The resulting draft genome consists of 8,817,834,205 bp organised in 955,015 scaffolds with an N50 of 157,705 bp, making the desert locust genome the largest insect genome sequenced and assembled to date. In total, 18,815 protein-encoding genes are predicted in the desert locust genome, of which 13,646 (72.53%) obtained at least one functional assignment based on similarity to known proteins.
Conclusions: The desert locust genome data will contribute greatly to studies of phenotypic plasticity, physiology, neurobiology, molecular ecology, evolutionary genetics and comparative genomics, and will promote the desert locust’s use as a model system. The data will also facilitate the development of novel, more sustainable strategies for preventing or combating swarms of these infamous insects.

Funding

This work was supported by the Special Research Fund of KU Leuven (BOF grant C14/15/050 to JVdB and HV), the Research Foundation of Flanders (FWO grants: postdoctoral fellowship 64322 to HV, G0F2417N to JVdB, G090919N to JVdB and YVdP); the Special Research Fund of Ghent University (BOFPDO2018001701 to ZL), the Department of Research and Innovation of the University of Pretoria (grant A0C827 to AY); the U.S. National Science Foundation (IOS-1253493 and IOS-1636632 to HS), the U.S. Department of Agriculture (hatch grant TEX0-1-6584 to HS) and the Biotechnology and Biological Sciences Research Council UK (BBSRC; research grant BB/L02389X/1 to SRO and TM).

History

Citation

F1000Research 2020, 9:775 (https://doi.org/10.12688/f1000research.25148.1)

Author affiliation

Department of Neuroscience, Psychology and Behaviour, College of Life Sciences

Version

VoR (Version of Record)

Published in

F1000Research

Volume

9

Pagination

775

Publisher

F1000 Research Ltd

eissn

2046-1402

Copyright date

2020

Available date

16/03/2021

Language

en