The Low-Copy-Number Satellite DNAs of the Model Beetle Tribolium castaneum

Gržan, Tena; Dombi, Mira; Despot-Slade, Evelin; Veseljak, Damira; Volarić, Marin; Meštrović, Nevenka; Plohl, Miroslav; Mravinac, Brankica (2023) The Low-Copy-Number Satellite DNAs of the Model Beetle Tribolium castaneum. Genes, 14 (5). ISSN 2073-4425

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Abstract

The red flour beetle Tribolium castaneum is an important pest of stored agricultural products and the first beetle whose genome was sequenced. So far, one high-copy-number and ten moderatecopy- 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 T. castaneum 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”.

Item Type:	Article
Uncontrolled Keywords:	satellite DNA ; tandem repeats ; repetitive DNA ; satellitome ; Tribolium castaneum
Subjects:	NATURAL SCIENCES > Biology
Divisions:	Division of Molecular Biology
Projects:	Project title Project leader Project code Project type Rasvjetljavanje evolucije satelitnih DNA visokoprotočnim analizama satelitoma srodnih vrsta Mravinac, Brankica IP-2019-04-5522 HRZZ Centromerna genomika beskralježnjaka Plohl, Miroslav IP-2014-09-3183 HRZZ
Depositing User:	Brankica Mravinac
Date Deposited:	16 Jun 2023 09:03
URI:	http://fulir.irb.hr/id/eprint/8023
DOI:	10.3390/genes14050999

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