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 Transposable Elements in Genus Calliptamus Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation

“…The transposable elements (TE) account for the largest proportion of the genomes [ 1 , 6 ]. The first two locust species documented in literature, Locusta migratoria and Schistocerca gregaria , have the largest genome assemblies, with 6.5 and 8.6 GB, respectively [ 46 , 47 ]. The recently published assembled genome of the morabine grasshopper is the third-largest assembled genome [ 48 ].…”

Grasshopper genome reveals long-term conservation of the X chromosome and temporal variation in X chromosome evolution

“…Sutton’s success was partly attributed to the large chromosomes in grasshoppers, which result from extreme genome size, which in turn has hampered effective genome assembly and subsequent molecular studies. As a result, the two currently available grasshopper genome assemblies, Locusta migratoria (Wang et al 2014) and Schistocerca gregaria (Verlinden et al 2021) remain fragmented.…”

A Chromosome-Level Genome Assembly of the Pygmy Mole CricketXya riparia

“…The reasons behind Orthoptera’s large genome remain unclear. Presently, the available genome resources of orthopteran insects is limited and only a few studies on the genome of orthopteran insects have been conducted ( Wang et al 2014 ; Blankers et al 2018 ; Verlinden et al 2020 ). Further research to obtain high-quality genome data is the only way to determine the cause of the orthopteran order’s genome enlargement and to establish more robust phylogenetic relationships among species contained in the order Orthoptera.…”