First draft genome assembly of the desert locust, Schistocerca gregaria [version 1; peer review: 2 approved, 1 approved with reservations]
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 li...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2020-07-01
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| Series: | F1000Research |
| Online Access: | https://f1000research.com/articles/9-775/v1 |
| _version_ | 1811292431525609472 |
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| author | 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 Peer Jozef Vanden Broeck |
| author_facet | 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 Peer Jozef Vanden Broeck |
| author_sort | Heleen Verlinden |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T04:45:17Z |
| format | Article |
| id | doaj.art-b24967d4624b4e94b39b384b04b3f79e |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-04-13T04:45:17Z |
| publishDate | 2020-07-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-b24967d4624b4e94b39b384b04b3f79e2022-12-22T03:01:51ZengF1000 Research LtdF1000Research2046-14022020-07-01910.12688/f1000research.25148.127753First draft genome assembly of the desert locust, Schistocerca gregaria [version 1; peer review: 2 approved, 1 approved with reservations]Heleen Verlinden0Lieven Sterck1Jia Li2Zhen Li3Anna Yssel4Yannick Gansemans5Rik Verdonck6Michiel Holtof7Hojun Song8Spencer T. Behmer9Gregory A. Sword10Tom Matheson11Swidbert R. Ott12Dieter Deforce13Filip Van Nieuwerburgh14Yves Van de Peer15Jozef Vanden Broeck16Laboratory of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, 3000, BelgiumLaboratory of Bioinformatics and Evolutionary Genomics, Ghent University, Ghent, 9000, BelgiumLaboratory of Bioinformatics and Evolutionary Genomics, Ghent University, Ghent, 9000, BelgiumCenter for Plant Systems Biology, Ghent University - VIB, Ghent, 9052, BelgiumDepartment of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South AfricaLaboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, 9000, BelgiumStation d' Ecologie Théorique et Expérimentale, UMR 5321 CNRS et Université Paul Sabatier, Moulis, 09200, FranceLaboratory of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, 3000, BelgiumDepartment of Entomology, Texas A&M University, College Station, Texas, TX 77843-2475, USADepartment of Entomology, Texas A&M University, College Station, Texas, TX 77843-2475, USADepartment of Entomology, Texas A&M University, College Station, Texas, TX 77843-2475, USADepartment of Neuroscience, Physiology and Behaviour, University of Leicester, Leicester, LE1 7RH, UKDepartment of Neuroscience, Physiology and Behaviour, University of Leicester, Leicester, LE1 7RH, UKNXTGNT, Ghent University, Ghent, 9000, BelgiumNXTGNT, Ghent University, Ghent, 9000, BelgiumLaboratory of Bioinformatics and Evolutionary Genomics, Ghent University, Ghent, 9000, BelgiumLaboratory of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, 3000, BelgiumBackground: 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.https://f1000research.com/articles/9-775/v1 |
| spellingShingle | 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 Peer Jozef Vanden Broeck First draft genome assembly of the desert locust, Schistocerca gregaria [version 1; peer review: 2 approved, 1 approved with reservations] F1000Research |
| title | First draft genome assembly of the desert locust, Schistocerca gregaria [version 1; peer review: 2 approved, 1 approved with reservations] |
| title_full | First draft genome assembly of the desert locust, Schistocerca gregaria [version 1; peer review: 2 approved, 1 approved with reservations] |
| title_fullStr | First draft genome assembly of the desert locust, Schistocerca gregaria [version 1; peer review: 2 approved, 1 approved with reservations] |
| title_full_unstemmed | First draft genome assembly of the desert locust, Schistocerca gregaria [version 1; peer review: 2 approved, 1 approved with reservations] |
| title_short | First draft genome assembly of the desert locust, Schistocerca gregaria [version 1; peer review: 2 approved, 1 approved with reservations] |
| title_sort | first draft genome assembly of the desert locust schistocerca gregaria version 1 peer review 2 approved 1 approved with reservations |
| url | https://f1000research.com/articles/9-775/v1 |
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