A first draft genome of the Sugarcane borer, Diatraea saccharalis.

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.

Sex pheromone biosynthesis in the sugarcane borer Diatraea saccharalis: paving the way for biotechnological production

“…Desaturases and reductases for which expression in the transcriptome analysis was considered both female‐biased (female:male >10) and relatively high (> 100 TPM), and all remaining full‐length desaturases found in the transcriptome, were together with the desaturase Dsac_NPAQ from the published genome, 56 functionally characterised in a yeast expression system. After expression, their products were methylated and analysed by GC/MS (Fig.…”

“…Two such sequences would be more easily resolved if one of them had lower expression, and then a certain coverage cut-off level could be used to unambiguously assemble only the sequence with high expression level. 63 The D. saccharalis genome assembly presented in Borges dos Santos et al 56 is 87% complete assessed by the BUSCO Insecta dataset, and does resolve two full-length genes, Dsac_NPAQ (genome) and Dsac_NPTQ (genome), differing in 35 amino acid residues and also in their intron sequences. These are highly similar to Dsac_NPAQ from this study's transcriptome assembly and Dsac_NPTQ amplified from the transcriptome cDNA, respectively (Supporting Information, Fig.…”

“…Sometimes fragmented sequences can be completed by increasing the k‐mer size in the assembly parameters, but highly similar transcripts resulting in chimeras (or lowly expressed paralogs, with low coverage) might possibly only be resolved by lowering the k‐mer size, which in turn can result in a highly fragmented assembly 63 . If the consensus sequence for Dsac_NPAQ is chosen as the transcript assembly most similar to Dsac_NPAQ from the available D. saccharalis genome assembly, 56 it is 17 amino acid residues different from the Dsac_NPTQ sequence amplified from cDNA. It might not be possible to resolve two such highly similar sequences with similar expression levels, by short‐read transcriptome sequencing and de novo assembly.…”

Unraveling the population structure of the sugarcane borer,Diatraea saccharalis, in Argentina

“…Additional work is necessary to unravel whether some of the outlier SNP markers detected in this study indeed have biological significance (Barrett & Hoekstra, 2011). In this context, the recent data about the genome of D. saccharalis will be an essential resource for future genetic studies of the species (Borges dos Santos et al, 2020).…”