Transposons and satellite DNA: on the origin of the major satellite DNA family in the Chenopodium genome

Alexander Belyayev,Michaela Jandová,Václav Mahelka,Karol Krak,Jiřina Josefiová,Bohumil Mandák

doi:10.1186/s13100-020-00219-7

Alexander Belyayev, Michaela Jandová + Show 4 more

Open Access

https://doi.org/10.1186/s13100-020-00219-7

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Abstract

Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome structure, function and evolution. Here, we report a novel case of mutual relationships between TEs and satDNA. In the genomes of Chenopodium s. str. species, the deletion derivatives of tnp2 conserved domain of the newly discovered CACTA-like TE Jozin are involved in generating monomers of the most abundant satDNA family of the Chenopodium satellitome. The analysis of the relative positions of satDNA and different TEs utilizing assembled Illumina reads revealed several associations between satDNA arrays and the transposases of putative CACTA-like elements when an ~ 40 bp fragment of tnp2 served as the start monomer of the satDNA array. The high degree of identity of the consensus satDNA monomers of the investigated species and the tnp2 fragment (from 82.1 to 94.9%) provides evidence of the genesis of CficCl-61-40 satDNA family monomers from analogous regions of their respective parental elements. The results were confirmed via molecular genetic methods and Oxford Nanopore sequencing. The discovered phenomenon leads to the continuous replenishment of species genomes with new identical satDNA monomers, which in turn may increase species satellitomes similarity.

Highlights

Transposable elements (TEs) and satellite DNA are the major components of the eukaryotic genome repeatome, accounting for up to 90% of plant nuclear DNA [1]
In contig 22 of the C. acuminatum CficCl-61-40 satellite DNA (satDNA) family array of 94.4 monomers with a consensus sequence of 39 bp was attached to the incomplete tnp2 TPase domain of 115 bp, and the start monomer of the array was simultaneously a tnp2 fragment of 41 bp oriented in the same direction (Fig. 1a, Additional file 1)
In the genome of C. acuminatum, significant nucleotide similarities were found between monomers of the CficCl-61-40 satDNA family and the ~ 40 bp fragment of the tnp2 domain, and it is possible to claim with a high probability that these monomers are derived from a similar region of their parent element, the ~ 40 bp fragment of tnp2 of the putative CACTA-like transposon

Summary

Introduction

Transposable elements (TEs) and satellite DNA (satDNA) are the major components of the eukaryotic genome repeatome, accounting for up to 90% of plant nuclear DNA [1]. SatDNA, which consists of long, latereplicating, noncoding arrays of tandemly arranged. The relationships between these two large fractions are fascinating. Extensive and complex links between TEs and satDNAs exist in eukaryotic genome, creating a complex network of sequences that has a crucial effect on genome structure, function and evolution [10]. There is growing evidence of the involvement of TEs in generating a library of tandem repeats that can be dispersed throughout the genome and, in some cases, amplified into long arrays of new satDNAs [10,11,12]. The Belyayev et al Mobile DNA (2020) 11:20 possibility of elucidating the details of this process by using next-generation sequencing (NGS) technology has arisen through the comparative analysis of entire species repeatomes

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