The Low-Copy-Number Satellite DNAs of the Model Beetle <i>Tribolium castaneum</i>
The red flour beetle <i>Tribolium castaneum</i> is an important pest of stored agricultural products and the first beetle whose genome was sequenced. So far, one high-copy-number and ten moderate-copy-number satellite DNAs (satDNAs) have been described in the assembled part of its genome...
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MDPI AG
2023-04-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/5/999 |
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| author | Tena Gržan Mira Dombi Evelin Despot-Slade Damira Veseljak Marin Volarić Nevenka Meštrović Miroslav Plohl Brankica Mravinac |
| author_facet | Tena Gržan Mira Dombi Evelin Despot-Slade Damira Veseljak Marin Volarić Nevenka Meštrović Miroslav Plohl Brankica Mravinac |
| author_sort | Tena Gržan |
| collection | DOAJ |
| description | The red flour beetle <i>Tribolium castaneum</i> is an important pest of stored agricultural products and the first beetle whose genome was sequenced. So far, one high-copy-number and ten moderate-copy-number satellite DNAs (satDNAs) have been described in the assembled part of its genome. In this work, we aimed to catalog the entire collection of <i>T. castaneum</i> satDNAs. We resequenced the genome using Illumina technology and predicted potential satDNAs via graph-based sequence clustering. In this way, we discovered 46 novel satDNAs that occupied a total of 2.1% of the genome and were, therefore, considered low-copy-number satellites. Their repeat units, preferentially 140–180 bp and 300–340 bp long, showed a high A + T composition ranging from 59.2 to 80.1%. In the current assembly, we annotated the majority of the low-copy-number satDNAs on one or a few chromosomes, discovering mainly transposable elements in their vicinity. The current assembly also revealed that many of the in silico predicted satDNAs were organized into short arrays not much longer than five consecutive repeats, and some of them also had numerous repeat units scattered throughout the genome. Although 20% of the unassembled genome sequence masked the genuine state, the predominance of scattered repeats for some low-copy satDNAs raises the question of whether these are essentially interspersed repeats that occur in tandem only sporadically, with the potential to be satDNA “seeds”. |
| first_indexed | 2024-03-11T03:42:13Z |
| format | Article |
| id | doaj.art-178d7f40cb374d62a3d0687841922421 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T03:42:13Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-178d7f40cb374d62a3d06878419224212023-11-18T01:29:04ZengMDPI AGGenes2073-44252023-04-0114599910.3390/genes14050999The Low-Copy-Number Satellite DNAs of the Model Beetle <i>Tribolium castaneum</i>Tena Gržan0Mira Dombi1Evelin Despot-Slade2Damira Veseljak3Marin Volarić4Nevenka Meštrović5Miroslav Plohl6Brankica Mravinac7Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, CroatiaRuđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, CroatiaRuđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, CroatiaRuđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, CroatiaRuđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, CroatiaRuđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, CroatiaRuđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, CroatiaRuđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, CroatiaThe red flour beetle <i>Tribolium castaneum</i> is an important pest of stored agricultural products and the first beetle whose genome was sequenced. So far, one high-copy-number and ten moderate-copy-number satellite DNAs (satDNAs) have been described in the assembled part of its genome. In this work, we aimed to catalog the entire collection of <i>T. castaneum</i> satDNAs. We resequenced the genome using Illumina technology and predicted potential satDNAs via graph-based sequence clustering. In this way, we discovered 46 novel satDNAs that occupied a total of 2.1% of the genome and were, therefore, considered low-copy-number satellites. Their repeat units, preferentially 140–180 bp and 300–340 bp long, showed a high A + T composition ranging from 59.2 to 80.1%. In the current assembly, we annotated the majority of the low-copy-number satDNAs on one or a few chromosomes, discovering mainly transposable elements in their vicinity. The current assembly also revealed that many of the in silico predicted satDNAs were organized into short arrays not much longer than five consecutive repeats, and some of them also had numerous repeat units scattered throughout the genome. Although 20% of the unassembled genome sequence masked the genuine state, the predominance of scattered repeats for some low-copy satDNAs raises the question of whether these are essentially interspersed repeats that occur in tandem only sporadically, with the potential to be satDNA “seeds”.https://www.mdpi.com/2073-4425/14/5/999satellite DNAtandem repeatsrepetitive DNAsatellitome<i>Tribolium castaneum</i> |
| spellingShingle | Tena Gržan Mira Dombi Evelin Despot-Slade Damira Veseljak Marin Volarić Nevenka Meštrović Miroslav Plohl Brankica Mravinac The Low-Copy-Number Satellite DNAs of the Model Beetle <i>Tribolium castaneum</i> Genes satellite DNA tandem repeats repetitive DNA satellitome <i>Tribolium castaneum</i> |
| title | The Low-Copy-Number Satellite DNAs of the Model Beetle <i>Tribolium castaneum</i> |
| title_full | The Low-Copy-Number Satellite DNAs of the Model Beetle <i>Tribolium castaneum</i> |
| title_fullStr | The Low-Copy-Number Satellite DNAs of the Model Beetle <i>Tribolium castaneum</i> |
| title_full_unstemmed | The Low-Copy-Number Satellite DNAs of the Model Beetle <i>Tribolium castaneum</i> |
| title_short | The Low-Copy-Number Satellite DNAs of the Model Beetle <i>Tribolium castaneum</i> |
| title_sort | low copy number satellite dnas of the model beetle i tribolium castaneum i |
| topic | satellite DNA tandem repeats repetitive DNA satellitome <i>Tribolium castaneum</i> |
| url | https://www.mdpi.com/2073-4425/14/5/999 |
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