Marsupial satellite DNA as faithful reflections of long-terminal repeat retroelement structure

Abstract

Long terminal repeat (LTR) retroelements, including endogenous retroviruses, are one of the origins of satellite DNAs. However, the vast majority of satellite DNAs originating from LTR retroelements consist of parts of the element. In addition, they frequently contain sequences unrelated to that element. Here we report a novel marsupial satellite DNA (named walbRep) that contains, and consists solely of, the entire sequence of an LTR retroelement (the <i>walb</i> element). As is common with LTR retroelements, <i>walb</i> copies exhibit length variation. We focused on the abundance of copies of a specific length (2.7 kb) in the genome of the red-necked wallaby. Cloning and analyses of long genomic DNA fragments revealed a satellite DNA in which the LTR sequence (0.4 kb) and the sequence of the internal region of a nonautonomous <i>walb</i> copy (2.3 kb) were repeated alternately. The junctions between these two components exhibited the same end-to-end arrangements as those in the <i>walb</i> element. This satellite organization could be accounted for by a simple formation model that includes slippage during chromosome pairing followed by homologous recombination but does not invoke any other types of rearrangements. We discuss the possible reasons why satellite DNAs having such structures are rarely found in mammals.

Marsupial genome analysis suggests that satellite DNA formation from walb endogenous retrovirus is an event specific to the red‐necked wallaby

“…This is an extension of our previous studies, in which we analyzed the walb retrovirus (Hayashi, Honda, et al, 2022) and the walbRep satellite (Hayashi, Shimizu, et al, 2022). The genomic DNA samples of red‐necked and tammar wallabies used in the present study were the same as those used in the previous studies.…”

“…In the present study, as an approach with a lower risk of representation bias, we performed NCBI BLAST searches of the Illumina short‐read data collections of two tammar wallaby individuals (Figure 2). Focusing on the large (5.5 kb) internal deletion that characterizes the walbRep repeat unit (see Figure S1 of Hayashi, Shimizu, et al, 2022 for sequence alignment), we used two different 190‐nucleotide parts of the repeat unit sequence as queries. QyW1 (nucleotides 1717–1906 of GenBank LC704881) included the deletion breakpoint at its center.…”

“…Among possible changes, a change at the 3′‐terminal nucleotide site needs particular attention because mismatching at this site has a highly deleterious effect on the amplification efficiency. There remains the possibility of such an incident at approximately 1% because the average nucleotide identity among repeat units was 99.5% (Hayashi, Shimizu, et al, 2022) and lack of product could be caused by mismatching in one of the two primers. In our previous study, PCR using a different primer pair produced fragments of the expected size from Red but no detectable fragment from Tam (Figure 4 of Hayashi, Honda, et al, 2022).…”

“…We recently found a satellite DNA of this structure that resides in the genome of the red‐necked wallaby Notamacropus rufogriseus (Hayashi, Shimizu, et al, 2022). It originates from the walb endogenous retrovirus, which was identified as an insertion sequence in a pigment‐related gene of a body color mutant wallaby (Hayashi, Honda, et al, 2022). The satellite DNA, named walbRep, consisted of the LTR (0.4 kb) and internal region (2.4 kb) of a nonautonomous walb copy (Hayashi, Shimizu, et al, 2022).…”

“…The repeat units of walbRep were highly homogeneous in nucleotide sequence; the average pairwise nucleotide identity was 99.5% (Hayashi, Honda, et al, 2022). This high homogeneity suggested a recent formation of walbRep: the time span after the formation is so short that few mutational changes have occurred.…”