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Gasparotto AE, Milani D, Martí E, Ferretti ABSM, Bardella VB, Hickmann F, Zrzavá M, Marec F, Cabral-de-Mello DC. 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. Chromosoma 2022; 131:253-267. [PMID: 36219241 DOI: 10.1007/s00412-022-00781-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022]
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 WZ1Z2 trivalent in female meiosis, indicating a multiple sex-chromosome system WZ1Z2/Z1Z1Z2Z2. 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.
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Affiliation(s)
- Ana E Gasparotto
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Emiliano Martí
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Ana Beatriz S M Ferretti
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Vanessa B Bardella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Frederico Hickmann
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, (USP/ESALQ), University of São Paulo, Piracicaba, SP, Brazil
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil.
- Department of Experimental Biology, Genetics Area, University of Jaen, Paraje las Lagunillas s/n, 23071, Jaen, Spain.
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