A step forward in the genome characterization of the sugarcane borer, Diatraea saccharalis: karyotype analysis, sex chromosome system and repetitive DNAs through a cytogenomic approach

Author(s)

Gasparotto, Ana E. ; Milani, Diogo ; Marti, Emiliano ; Ferretti, Ana Beatriz S. M. ; Bardella, Vanessa B. ; Hickmann, Frederico ; Zrzava, Magda ; Marec, Frantisek ; Cabral-de-Mello, Diogo C.

• Document type: Journal article
• Source: CHROMOSOMA; v. 131, n. 4, p. 15-pg., 2022-10-11.

Abstract

Moths of the family Crambidae include a number of pests that cause economic losses to agricultural crops. Despite their economic importance, little is known about their genome architecture and chromosome evolution. Here, we characterized the chromosomes and repetitive DNA of the sugarcane borer Diatraea saccharalis using a combination of low-pass genome sequencing, bioinformatics, and cytogenetic methods, focusing on the sex chromosomes. Diploid chromosome numbers differed between the sexes, i.e., 2n = 33 in females and 2n = 34 in males. This difference was caused by the occurrence of a WZ(1)Z(2) trivalent in female meiosis, indicating a multiple sex-chromosome system WZ(1)Z(2)/Z(1)Z(1)Z(2)Z(2). A strong interstitial telomeric signal was observed on the W chromosome, indicating a fusion of the ancestral W chromosome with an autosome. Among repetitive DNAs, transposable elements (TEs) accounted for 39.18% (males) to 41.35% (females), while satDNAs accounted for only 0.214% (males) and 0.215% (females) of the genome. FISH mapping revealed different chromosomal organization of satDNAs, such as single localized clusters, spread repeats, and non-clustered repeats. Two TEs mapped by FISH were scattered. Although we found a slight enrichment of some satDNAs in the female genome, they were not differentially enriched on the W chromosome. However, we found enriched FISH signals for TEs on the W chromosome, suggesting their involvement in W chromosome degeneration and differentiation. These data shed light on karyotype and repetitive DNA dynamics due to multiple chromosome fusions in D. saccharalis, contribute to the understanding of genome structure in Lepidoptera and are important for future genomic studies. (AU)

• FAPESP's process: 21/05908-7 - Genome architecture and evolution of sex chromosomes in Pentatomidae pest bugs and related species
• Grantee: Diogo Milani
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 20/06188-5 - Molecular content, patterns of epigenetic changes and interference of supernumerary chromosomes in Drosophila melanogaster
• Grantee: Ana Beatriz Stein Machado Ferretti
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 19/19069-7 - Investigating the evolution of satellite DNAs in holocentric chromosomes of pest species
• Grantee: Diogo Cavalcanti Cabral de Mello
• Support Opportunities: Regular Research Grants
• FAPESP's process: 18/21772-5 - Cytogenomics of the treehoppers pest Aetalion reticulatum: analysis of repetitive DNAs and B chromosomes
• Grantee: Vanessa Bellini Bardella
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 18/20351-6 - Dormancy and host adaptation of two allopatric lineages of Euschistus heros (Hemiptera: Pentatomidae)
• Grantee: Frederico Hickmann
• Support Opportunities: Scholarships in Brazil - Doctorate