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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.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Methods<\/ns3:bold>\n                    : 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\n                    <ns3:italic>Schistocerca gregaria<\/ns3:italic>\n                    was assembled using the ABySS pipeline, scaffolding was improved using LINKS.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Results<\/ns3:bold>\n                    : 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.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Conclusions<\/ns3:bold>\n                    : 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\u2019s 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.\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.25148.2","type":"journal-article","created":{"date-parts":[[2021,5,21]],"date-time":"2021-05-21T11:15:09Z","timestamp":1621595709000},"page":"775","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["First draft genome assembly of the desert locust, Schistocerca 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.27753.r71637, Uwe Homberg, Animal Physiology, Department of Biology, Center for Mind, Brain and Behavior (CMBB), University of Marburg, Giessen, Germany, 05 Oct 2020, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/9-775\/v1#referee-response-71637","order":0,"name":"referee-response-71637","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Heleen Verlinden<\/b>; \n<i>Posted: 06 May 2021<\/i>; The authors would like to thank the reviewer for this very positive feedback on their manuscript.","URL":"https:\/\/f1000research.com\/articles\/9-775\/v2#referee-comment-6649","order":1,"name":"referee-comment-6649","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.27753.r72656, Surya Saha, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA, 27 Oct 2020, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/9-775\/v1#referee-response-72656","order":2,"name":"referee-response-72656","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Heleen Verlinden<\/b>; \n<i>Posted: 06 May 2021<\/i>; We would like to thank the reviewer for this positive feedback, as well as for recognising the challenges we have faced. Since sequencing technologies are evolving very fast, we agree that future work will further improve the current genome assembly. Therefore, we designated this as the \u201cfirst genome assembly\u201d. In addition, with the release of our genome data, we are convinced that many additional analyses are becoming possible. Locusts have always been -and still are- research models for studying a wide range of research questions in different areas of interest. With this manuscript, we therefore chose not to focus on a very specific research question, but communicate the main results obtained of our genome sequencing effort. Moreover, given the current locust situation, we felt that it was important to make available this first genome draft to the international scientific community and to stimulate readers -worldwide- to address their specific research question(s).  1) We agree that these analyses will be of great value and sincerely hope to include these in future research, however they are out of scope of this first draft publication. 2)We took many precautions to reduce the risk of contamination. The locust cages were meticulously cleaned multiple times a week, all material that entered the facility was either new or sterilised or both. Food was bred separately and washed carefully. Gloves, lab coats, face masks were worn upon entering the rooms. Our animals all looked healthy, with no signs of infections. During the dissections, we were extremely careful not to damage the gut and did not include any digestive tissues. We checked for contamination by BLASTX and BLASTN with sequence databases from a number of vertebrate, plant, fungi, gregarina, amoeba, bacteria and protoctista and could not find any significant contamination. We therefore did not perform any form of filtering for endosymbiont\/microbial contamination. Following sentences have now been adapted\/added to the supplementary materials and methods to make this clearer for the reader: \u201cThe entire breeding facility was meticulously cleaned multiple times a week throughout the entire breeding period to avoid any form of contamination. All materials that entered the facility were either new or sterilised or even both. Food was bred separately and washed carefully. Gloves, lab coats and face masks were worn upon entering the facility. The locusts showed no external signs of disease or contamination, displayed clear phenotypic characteristics of solitarious locusts and underwent the sixth larval stage characteristic of the solitarious phase (Pener and Simpson, 2009; Cullen et al., 2017). The animals were very carefully dissected and specific attention was paid to avoid any contamination with gut material.\u201d \u201cWe checked for contamination by BLASTX and BLASTN with sequence databases from a number of vertebrate, plant, fungi, gregarina, amoeba, bacteria and protoctista and could not find any contamination. We therefore did not perform any form of filtering for endosymbiont\/microbial contamination.\u201d  Minor points: 1. In general, a bigger genome takes more reads and thus also more budget to obtain enough sequencing coverage. Although we did not concretely know how expanded the non-coding portion of the genome would be, we had expected the presence of many repetitive regions, which can indeed make assembly more complicated and challenging. We therefore anticipated to this by including a long-read technology like PacBio, to improve the assembly process of short Illumina reads. We specified that we also expected more repetitive regions and added two references here: Dominguez Del Angel, V., Hjerde, E., Sterck, L., et al.: Ten steps to get started in Genome Assembly and Annotation [version 1; peer review: 2 approved]. F1000Research 2018, 7(ELIXIR), 148. T&oslash;rresen, O.K., Star, B., Mier, P., et al.: Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res 2019; 47(21), 10994\u201311006. 2. As clarified above, we took many precautions to avoid contaminations and indeed checked if there was contamination. Since no significant contamination was observed, we did not perform any form of filtering. 3. We performed PacBio sequencing, in addition to the Illumina sequencing, to obtain long reads.&nbsp; We agree that newer technologies may be very useful to further optimise the genome sequence assembly.","URL":"https:\/\/f1000research.com\/articles\/9-775\/v2#referee-comment-6650","order":3,"name":"referee-comment-6650","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.27753.r72658, Joshua B. Benoit, Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA, 02 Nov 2020, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/9-775\/v1#referee-response-72658","order":4,"name":"referee-response-72658","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Heleen Verlinden<\/b>; \n<i>Posted: 06 May 2021<\/i>; We would like to thank the reviewer for this positive feedback and for recognising the challenges we have faced. Since sequencing technologies are evolving very fast, we agree that future work will further improve the current genome assembly. This is why we designated this as the \u201cfirst genome assembly\u201d. In addition, with the release of our genome data, we are convinced that many additional analyses are becoming possible. Locusts have always been -and still are- research models for studying a wide range of research questions in different areas of interest. With this manuscript, we therefore chose not to focus on a very specific research question, but communicate the main results obtained of our genome sequencing effort. Moreover, given the current locust situation, we felt that it was important to make available this first genome draft to the international scientific community and to stimulate readers -worldwide- to address their specific research question(s).  The BUSCO assessment on the Trinity assembly shows that it includes 91.2% complete genes in insecta_odb10 dataset. Compared with the BUSCO values (genomic 80.9% vs geneset 79.4%) of our current genome assembly this indeed indicates that our genome assembly still misses some BUSCO genes that are present in our transcript databases. It proves that our current genome assembly can still be further improved, as we are of course aware. The Trinity assembly is included in the gene set we made available.  As already clarified in our answer to a very similar comment made by reviewer 2, we took many precautions to avoid contaminations and we did not observe any. This is now specified in the supplementary materials and methods.  We fully agree with the reviewer that additional techniques may further improve this draft genome assembly.","URL":"https:\/\/f1000research.com\/articles\/9-775\/v2#referee-comment-6651","order":5,"name":"referee-comment-6651","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"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). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":6,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}