First draft genome assembly of the desert locust, Schistocerca gregaria

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.

Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

“…The genomes of four chromosomal races of the viatica species group that we assembled here with 2.94–3.27 Gb assembly sizes are the third largest assembled insect genomes so far, with the largest being the two locust grasshoppers L. migratoria and Schistocerca gregaria with 6.5 and 8.6 Gb assembly sizes, respectively [ 55 , 56 ]. We believe that genome size estimates based on k-mer analysis better represent the genome size of these grasshoppers than the genome assembly sizes because highly repetitive sequences (e.g., centromeres, telomeres, satDNAs, non-recombining part of sex chromosomes) are likely collapsed during the assembly process [ 66 , 67 , 78 , 79 ].…”

“…However, the two different k-mer approaches yielded quite different estimates between the chromosomal races (3.30–3.82 Gb by Supernova, and 5.42–6.32 Gb by findGSE), the reasons for which remain unclear. The large differences in contig size (contig N50 29.11–35.69 kb) of the assembled genomes of the viatica species group, L. migratoria (contig N50 10.78 kb) [ 55 ] and S. gregaria (contig N50 12.03 kb) [ 56 ] are probably due to the difference in the DNA library preparation and sequencing methods. The L. migratoria genome is based on Illumina short reads (2 × 45–150 bp paired-end) with multiple insert-size libraries (i.e., four paired-end libraries ranging from 170 to 800 bp and five mate-pair libraries ranging from 2 to 40 kb) while we used linked reads (150 bp paired-end Illumina short reads with barcode information from long input DNA molecules), and the S. gregaria assembly used paired-end and mate-pair Illumina short reads and PacBio long reads.…”

“…The scaffold N50 (158 kb) of the S. gregaria genome assembly (8.6 Gb) is smaller than the scaffold N50 (326 kb) of L. migratoria and the scaffold N50 (317 kb) that we obtained in the P24X0 race. In addition, the S. gregaria genome assembly is even more fragmented than the L. migratoria as indicated by the BUSCO scores (see [ 56 ]), indicating that assembling such large grasshopper genomes is challenging even using the combination of technologies above. Although the smaller genome assemblies of the viatica species group were more contiguous than the assembly of L. migratoria , they still contained missing and fragmented genes.…”

“…Grasshoppers generally have large genomes (9 Gb on average, minimum 1.5 Gb and maximum 16.6 Gb [ 54 ]) likely because of large amounts of repetitive DNA [ 55 , 56 ]. They provide ample opportunities to investigate the influence of the repeatome on karyotype evolution because grasshoppers are also karyotypically divergent between closely related species [ 57 – 59 ] .…”

“…They provide ample opportunities to investigate the influence of the repeatome on karyotype evolution because grasshoppers are also karyotypically divergent between closely related species [ 57 – 59 ] . However, comparative genomic studies in grasshoppers have been hampered by their large genome sizes [ 55 , 56 ]. The Australian morabine (Morabinae) grasshopper of the genus Vandiemenella (hereafter referred to as the viatica species group) is a relatively young species complex with estimated divergence time < 0.5–3.1 Myr based on a mitochondrial marker [ 58 ] and is karyotypically diverse [ 58 – 60 ] .…”