Abstract
Background: The sugarcane borer (Diatraea saccharalis), a widely distributed moth throughout the Americas, is a pest that affects economically important crops such as sugarcane, sorghum, wheat, maize and rice. Given its significant impact on yield reduction, whole-genome information of the species is needed. Here, we report the first draft assembly of the D. saccharalis genome. Methods: The genomic sequences were obtained using the Illumina HiSeq 2500 whole-genome sequencing of a single adult male specimen. We assembled the short-reads using the SPAdes software and predicted protein-coding genes using MAKER. Genome assembly completeness was assessed through BUSCO and the repetitive content by RepeatMasker. Results: The 453 Mb assembled sequences contain 1,445 BUSCO gene orthologs and 1,161 predicted gene models identified based on homology evidence to the domestic silk moth, Bombyx mori. The repeat content composes 41.18% of the genomic sequences which is in the range of other lepidopteran species. Conclusions: Functional annotation reveals that predicted gene models are involved in important cellular mechanisms such as metabolic pathways and protein synthesis. Thus, the data generated in this study expands our knowledge on the genomic characteristics of this devastating pest and provides essential resources for future genetic studies of the species.
Highlights
Diatraea saccharalis (Fabricius), commonly known as the sugarcane borer, is an important moth pest of the family Crambidae (Lepidoptera; Crambidae) that is distributed throughout the Americas, including South America, the Caribbean, Central America, and the southeastern United States (Box, 1931; CAB International, 1989; Dyar & Heinrich, 1927)
GenomeScope estimated a haploid genome size of 359 Megabase pairs (Mb). This analysis revealed 0.69% of variation across the genomic sequences, indicating that the D. saccharalis genome of the selected individual had low heterozygosity properties, most likely due to the inbred nature of the colony used in this experiment
The assembly of the reduced data set using SPAdes resulted in 50,460 scaffolds larger than 1 kb having a cumulative length of 453 Mb, and a scaffold N50, an indication of assembly contiguity, of 16.3 kb
Summary
Diatraea saccharalis (Fabricius), commonly known as the sugarcane borer, is an important moth pest of the family Crambidae (Lepidoptera; Crambidae) that is distributed throughout the Americas, including South America, the Caribbean, Central America, and the southeastern United States (Box, 1931; CAB International, 1989; Dyar & Heinrich, 1927). D. saccharalis host plants include important crops such as sugarcane (Saccharum spp.), sorghum (Sorghum bicolor), wheat (Triticum spp.), maize (Zea mays L.), and rice (Oryza sativa L.) (Myers, 1932; Rodríguez-del-Bosque et al, 1988; Roe, 1981). As a result of the borer behavior, the physical strength of the mature plant stalk is reduced, decreasing the plant biomass and sugar content in more developed crops, and have an increased susceptibility to plant pathogens due to the holes made by the larvae (Cruz, 2007; Wilson et al, 2017). The sugarcane borer (Diatraea saccharalis), a widely distributed moth throughout the Americas, is a pest that affects economically important crops such as sugarcane, sorghum, wheat, maize and rice. Results: The 453 Mb assembled sequences contain 1,445 BUSCO gene orthologs and 1,161 predicted gene models identified based on homology evidence to the domestic silk moth, Bombyx mori.
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