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First draft genome assembly of the desert locust, Schistocerca gregaria

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Abstract
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.
Keywords
Eco-devo, large genome size, locust plague, Orthoptera, pest insect, phenotypic plasticity, polyphenism, swarm

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MLA
Verlinden, Heleen, et al. “First Draft Genome Assembly of the Desert Locust, Schistocerca Gregaria.” F1000RESEARCH, vol. 9, 2020, doi:10.12688/f1000research.25148.1.
APA
Verlinden, H., Sterck, L., Li, J., Li, Z., Yssel, A., Gansemans, Y., … Vanden Broeck, J. (2020). First draft genome assembly of the desert locust, Schistocerca gregaria. F1000RESEARCH, 9. https://doi.org/10.12688/f1000research.25148.1
Chicago author-date
Verlinden, Heleen, Lieven Sterck, Jia Li, Zhen Li, Anna Yssel, Yannick Gansemans, Rik Verdonck, et al. 2020. “First Draft Genome Assembly of the Desert Locust, Schistocerca Gregaria.” F1000RESEARCH 9. https://doi.org/10.12688/f1000research.25148.1.
Chicago author-date (all authors)
Verlinden, Heleen, 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 Peer, and Jozef Vanden Broeck. 2020. “First Draft Genome Assembly of the Desert Locust, Schistocerca Gregaria.” F1000RESEARCH 9. doi:10.12688/f1000research.25148.1.
Vancouver
1.
Verlinden H, Sterck L, Li J, Li Z, Yssel A, Gansemans Y, et al. First draft genome assembly of the desert locust, Schistocerca gregaria. F1000RESEARCH. 2020;9.
IEEE
[1]
H. Verlinden et al., “First draft genome assembly of the desert locust, Schistocerca gregaria,” F1000RESEARCH, vol. 9, 2020.
@article{8670858,
  abstract     = {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.},
  articleno    = {775},
  author       = {Verlinden, Heleen and Sterck, Lieven and Li, Jia and Li, Zhen and Yssel, Anna and Gansemans, Yannick and Verdonck, Rik and Holtof, Michiel and Song, Hojun and Behmer, Spencer T. and Sword, Gregory A. and Matheson, Tom and Ott, Swidbert R. and Deforce, Dieter and Van Nieuwerburgh, Filip and Van de Peer, Yves and Vanden Broeck, Jozef},
  issn         = {2046-1402},
  journal      = {F1000RESEARCH},
  keywords     = {Eco-devo,large genome size,locust plague,Orthoptera,pest insect,phenotypic plasticity,polyphenism,swarm},
  language     = {eng},
  pages        = {11},
  title        = {First draft genome assembly of the desert locust, Schistocerca gregaria},
  url          = {http://dx.doi.org/10.12688/f1000research.25148.1},
  volume       = {9},
  year         = {2020},
}

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