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

Gasparotto, Ana Elisa; Milani, Diogo; Martí, Emiliano; Ferretti, Ana Beatriz Stein Machado; Bardella, Vanessa Bellini; Hickmann, Frederico; Zrzavá, Magda; Marec, František; Cabral-de-Mello, Diogo Cavalcanti

doi:10.1007/s00412-022-00781-4

Cited by 7 publications

(3 citation statements)

References 83 publications

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“…The use of NGS data has also been employed for the studies of evolution of B and sex chromosomes, e.g., to characterize the composition and putative ancestry of B chromosomes in grasshopper species Rhammatocerus brasiliensis , Schistocerca rubiginosa, Xyleus discoideus angulatus, Abracris flavolineata, Eumigus monticola [ 93 , 102 , 112 ] or in characid fish Characidium gomesi [ 96 ]. An understanding of karyotype diversification, genome architecture and sex chromosome evolution was forwarded, for example, in Crambidae moths [ 92 ], Triportheidae fishes [ 140 ], grasshopper Ronderosia bergii [ 115 ], sugarcane borer Diatraea saccharalis [ 100 ], etc. Further questions can be addressed in viewing the satellitome in relation to the repeatome as a whole, especially in the context of the hetero/euchromatin content and distribution.…”

Section: Genomic Content or How Many Satdnas Are In The Genomementioning

confidence: 99%

Satellite DNAs—From Localized to Highly Dispersed Genome Components

Šatović-Vukšić

Plohl

2023

Genes

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According to the established classical view, satellite DNAs are defined as abundant non-coding DNA sequences repeated in tandem that build long arrays located in heterochromatin. Advances in sequencing methodologies and development of specialized bioinformatics tools enabled defining a collection of all repetitive DNAs and satellite DNAs in a genome, the repeatome and the satellitome, respectively, as well as their reliable annotation on sequenced genomes. Supported by various non-model species included in recent studies, the patterns of satellite DNAs and satellitomes as a whole showed much more diversity and complexity than initially thought. Differences are not only in number and abundance of satellite DNAs but also in their distribution across the genome, array length, interspersion patterns, association with transposable elements, localization in heterochromatin and/or in euchromatin. In this review, we compare characteristic organizational features of satellite DNAs and satellitomes across different animal and plant species in order to summarize organizational forms and evolutionary processes that may lead to satellitomes’ diversity and revisit some basic notions regarding repetitive DNA landscapes in genomes.

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Section: Genomic Content or How Many Satdnas Are In The Genomementioning

confidence: 99%

Satellite DNAs—From Localized to Highly Dispersed Genome Components

Šatović-Vukšić

Plohl

2023

Genes

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“…The origin of multiple sex chromosomes through X-chromosome fission appears to be common in other Heteroptera species as well (Panzera et al, 2021;Papeschi & Bressa, 2006), in contrast to some other insects where the formation of multiple sex chromosome systems primarily involves translocation or fusion events between autosomes and ancient sex chromosomes, such as observed in Melanoplinae grasshoppers (Castillo et al, 2010;Palacios-Gimenez et al, 2013), certain Coleoptera species (Galián et al, 2002) and termites (Bergamaschi et al, 2007). Translocations and fusions contributing to the generation of multiple sex chromosomes have also been observed in other groups with holocentric chromosomes, such as Lepidoptera (Gasparotto et al, 2022;Yoshido et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

The spread of satellite DNAs in euchromatin and insights into the multiple sex chromosome evolution in Hemiptera revealed by repeatome analysis of the bug Oxycarenus hyalinipennis

Cabral‐de‐Mello,

Mora,

Rico‐Porras

et al. 2023

Insect Molecular Biology

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Satellite DNAs (satDNAs) are highly repeated tandem sequences primarily located in heterochromatin, although their occurrence in euchromatin has been reported. Here, our aim was to advance the understanding of satDNA and multiple sex chromosome evolution in heteropterans. We combined cytogenetic and genomic approaches to study, for the first time, the satDNA composition of the genome in an Oxycarenidae bug, Oxycarenus hyalinipennis. The species exhibits a male karyotype of 2n = 19 (14A + 2 m + X1X2Y), with a highly differentiated Y chromosome, as demonstrated by C‐banding and comparative genomic hybridization, revealing an enrichment of repeats from the male genome. Additionally, comparative analysis between males and females revealed that the 26 identified satDNA families are significantly biased towards male genome, accumulating in discrete regions in the Y chromosome. Exceptionally, the OhyaSat04‐125 family was found to be distributed virtually throughout the entire extension of the Y chromosome. This suggests an important role of satDNA in Y chromosome differentiation, in comparison of other repeats, which collectively shows similar abundance between sexes, about 50%. Furthermore, chromosomal mapping of all satDNA families revealed an unexpected high spread in euchromatic regions, covering the entire extension, irrespective of their abundance. Only discrete regions of heterochromatin on the Y chromosome and of the m‐chromosomes (peculiar chromosomes commonly observed in heteropterans) were enriched with satDNAs. The putative causes of the intense enrichment of satDNAs in euchromatin are discussed, including the possible existence of burst cycles similar to transposable elements and as a result of holocentricity. These data challenge the classical notion that euchromatin is not enriched with satDNAs.

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“…In this study, we identified 10 putative W-enriched repeats of P. rhomboidaria , most of them being classified as LINE or LTR retrotransposons. Their identification was done by comparative analysis with the RepeatExplorer software, a novel approach for Lepidoptera as it only has been used for mapping satellite sequences in Crambidae 10 , and for the identification and characterization of W-enriched repetitive sequences in Diatraea saccharalis (Crambidae) 50 .…”

Section: Discussionmentioning

confidence: 99%

Accumulation of retrotransposons contributes to W chromosome differentiation in the willow beauty Peribatodes rhomboidaria (Lepidoptera: Geometridae)

Hejníčková

Dalíková

Zrzavá

et al. 2023

Sci Rep

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The W chromosome of Lepidoptera is typically gene-poor, repeat-rich and composed of heterochromatin. Pioneering studies investigating this chromosome reported an abundance of mobile elements. However, the actual composition of the W chromosome varies greatly between species, as repeatedly demonstrated by comparative genomic hybridization (CGH) or fluorescence in situ hybridization (FISH). Here we present an analysis of repeats on the W chromosome in the willow beauty, Peribatodesrhomboidaria (Geometridae), a species in which CGH predicted an abundance of W-enriched or W-specific sequences. Indeed, comparative analysis of male and female genomes using RepeatExplorer identified ten putative W chromosome-enriched repeats, most of which are LTR or LINE mobile elements. We analysed the two most abundant: PRW LINE-like and PRW Bel-Pao. The results of FISH mapping and bioinformatic analysis confirmed their enrichment on the W chromosome, supporting the hypothesis that mobile elements are the driving force of W chromosome differentiation in Lepidoptera. As the W chromosome is highly underrepresented in chromosome-level genome assemblies of Lepidoptera, this recently introduced approach, combining bioinformatic comparative genome analysis with molecular cytogenetics, provides an elegant tool for studying this elusive and rapidly evolving part of the genome.

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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

Cited by 7 publications

References 83 publications

Satellite DNAs—From Localized to Highly Dispersed Genome Components

Satellite DNAs—From Localized to Highly Dispersed Genome Components

The spread of satellite DNAs in euchromatin and insights into the multiple sex chromosome evolution in Hemiptera revealed by repeatome analysis of the bug Oxycarenus hyalinipennis

Accumulation of retrotransposons contributes to W chromosome differentiation in the willow beauty Peribatodes rhomboidaria (Lepidoptera: Geometridae)

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