DNA barcode information for the sugar cane moth borer Diatraea saccharalis

Joyce A, Pereira de Souza A, Gabriela Murúa M, J. Clough S, Imaculada Zucchi M. A first draft genome of the Sugarcane borer, Diatraea saccharalis

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.

Identification of Diatraea spp. (Lepidoptera: Crambidae) based on cytochrome oxidase II

Diatraea spp. (Lepidoptera: Crambidae) are a group of insects that are agriculture pests in many economically relevant crops such as sugarcane, sorghum, corn and rice. Recognized species for this genus respond differentially to natural enemies used in their biological control, emphasizing the importance of species in a regional approach. Currently, identification is based on the male genitalia. However, the availability of specimens collected from field and subjectivity based on the character recognition can seriously hamper species identification, and therefore result in inadequate pest management. To overcome this, individuals of Diatraea spp. preliminarily classified male genitalia and obtained from reared conditions and the field (both derived from natural populations occurring in Colombia) were analyzed using genitalic morphometry and molecular biology specifically using a fragment of the cytochrome oxidase subunit II (CO II) mitochondrial gene. Although morphometric analysis did not show any overriding results regarding genitalia morphology, the bioinformatics analyses of CO II sequences resulted in an adequate classification of the individuals within the recognized species. It also, revealed that the occurrence of clades associated with geographical distribution may be associated with cryptic species. The latter was also confirmed by a Single-Strand Conformation Polymorphism (SSCP) methodology evaluating the same fragment of CO II. This experimental approach allows properly recognizing each species and in consequence is proposed as an effective tool in Diatraea species identification.

Geographic population structure of the sugarcane borer, Diatraea saccharalis (F.) (Lepidoptera: Crambidae), in the southern United States

The sugarcane borer moth, Diatraea saccharalis, is widespread throughout the Western Hemisphere, and is considered an introduced species in the southern United States. Although this moth has a wide distribution and is a pest of many crop plants including sugarcane, corn, sorghum and rice, it is considered one species. The objective was to investigate whether more than one introduction of D. saccharalis had occurred in the southern United States and whether any cryptic species were present. We field collected D. saccharalis in Texas, Louisiana and Florida in the southern United States. Two molecular markers, AFLPs and mitochondrial COI, were used to examine genetic variation among these regional populations and to compare the sequences with those available in GenBank and BOLD. We found geographic population structure in the southern United States which suggests two introductions and the presence of a previously unknown cryptic species. Management of D. saccharalis would likely benefit from further investigation of population genetics throughout the range of this species.

Mitochondrial pseudogenes in insect DNA barcoding: differing points of view on the same issue

Molecular tools have been used in taxonomy for the purpose of identification and classification of living organisms. Among these, a short sequence of the mitochondrial DNA, popularly known as DNA barcoding, has become very popular. However, the usefulness and dependability of DNA barcodes have been recently questioned because mitochondrial pseudogenes, non-functional copies of the mitochondrial DNA incorporated into the nuclear genome, have been found in various taxa. When these paralogous sequences are amplified together with the mitochondrial DNA, they may go unnoticed and end up being analyzed as if they were orthologous sequences. In this contribution the different points of view regarding the implications of mitochondrial pseudogenes for entomology are reviewed and discussed. A discussion of the problem from a historical and conceptual perspective is presented as well as a discussion of strategies to keep these nuclear mtDNA copies out of sequence analyzes.

Genetic diversity analysis with RAPD linked to sex identification in the sugar cane borer Diatraea saccharalis

Diatraea saccharalis is an insect that causes considerable losses in the sugar cane crop. Our aim was to contribute to the knowledge of the biology of D. saccharalis, with the report of DNA fragments involved in the differentiation between the male and female of this species using the RAPD sex molecular marker GyakuU-13, which is specific for the W chromosome of Bombyx mori. Another point evaluated in this study was the genetic diversity of a D. saccharalis population maintained by inbreeding in a laboratory culture. The profile of sex-specific fragments was analyzed, and the genetic variability of this population was estimated. An analysis of the molecular markers showed only one fragment, of approximately 700 bp, that could be considered as a female sex marker in D. saccharalis.

Structural characteristics and phylogenetic analysis of the mitochondrial genome of the sugarcane borer, Diatraea saccharalis (Lepidoptera: Crambidae)

The sugarcane borer, Diatraea saccharalis (F.), is an economically important pest of several major crops in North and South America. There is great concern over potential resistance development to the valuable transgenic Bacillus thuringiensis corn. Cost-effective monitoring methods, especially regarding molecular markers that could detect early changes in resistance allele frequency in field populations of D. saccharalis, are needed. This article reports the complete mitochondrial genome sequence of D. saccharalis (GenBank: FJ240227). The mitochondrial genome sequence of D. saccharalis has the typical metazoan mitogenome structure including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes, with a total size of 15,490 bp. The A+T content of the full mitogenome is 80.1% and the significant A+T bias is at the control region (94.9%), as compared to the extremely low G content (0.6%). In all 13 protein coding genes, 9 start with the common Met initiator codon (ATA or ATG) and 3 use ATT (Ile), whereas CGA (Arg) is used as a start codon in COI. Eleven of the 13 protein coding genes use complete termination codon (TAA), whereas COI and COII use incomplete ones, which terminated with a single T-nucleotide abutting on tRNA. There are seven major noncoding spacers (628 bp), including six intergenic spacers and an A+T-rich region, which are scattered in the mitogenome. Several microsatellite-like elements were observed in these noncoding regions. The complete mitochondrial sequences of D. saccharalis reported in this study can provide useful data in analyzing divergence of lepidopteran insects and in developing DNA-based diagnoses and genetic makers.