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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Funding
This study was supported in part by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) (process number 2019/19069–7), the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (CAPES), Conselho Nacional de Desenvolvimento Científiico e Tecnológico (CNPq). DM, VBB, ABSMF, and FH were supported by FAPESP (processes numbers 2021/05908–7, 2018/21772–5, 2020/06188–5, and 2018/20351–6) and AEGS and EM by CAPES. DCC-d-M is a recipient of a research productivity fellowship from the Conselho Nacional de Desenvolvimento Científico e Tecnológico-CNPq (process number 308290/2020–8). MZ and FM acknowledge support from grant 20-13784S of the Czech Science Foundation.
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Ana E Gasparotto: performed the research, analyzed the data and wrote the original draft.
Diogo Milani: performed the research and analyzed the data.
Emiliano Martí: performed the research and analyzed the data.
Ana BSM Ferretti: performed the research.
Vanessa B Bardella: performed the research.
Frederico Hickmann: performed the research.
Magda Zrzavá: analyzed the data and wrote the original draft.
František Marec: conceived, designed the study, analyzed the data and wrote the original draft.
Diogo C Cabral-de-Mello: conceived, designed the study, analyzed the data and wrote the original draft.
All authors revised and edited the text.
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Supplementary file1 Supplementary Fig. 1 Polyploid nuclei obtained from Malpighian tubule cells of (a) male and (b) female larvae, stained with orcein. The arrow in (b) points to the deeply stained W chromatin body. Bar = 10 µm(JPG 75 KB)
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Supplementary file2 Supplementary Table 1 DNA oligo sequences designed to obtain probes for the repetitive DNAs that were identified for the first time in this work. Asterisks indicate oligos directly labeled with biotin-14-dATP to be used as probes (DOCX 14 KB)
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Supplementary file3 Supplementary Table 2 General characteristics of TEs identified in the genome of Diatraea saccharalis, including number of elements, genome abundance, abundance ratio between female/male genomes, and genome divergence (DOCX 49 KB)
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Gasparotto, A.E., Milani, D., Martí, E. et al. 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 131, 253–267 (2022). https://doi.org/10.1007/s00412-022-00781-4
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DOI: https://doi.org/10.1007/s00412-022-00781-4