The subtelomeric region of the Arabidopsis thaliana chromosome IIIR contains potential genes and duplicated fragments from other chromosomes

Abstract

The subtelomere and a portion of the associated telomeric region (together named 3RTAS) of chromosome IIIR from the Arabidopsis thaliana ecotypes Columbia (Col) and Wassilewskija (Ws) were specifically amplified by polymerase chain reaction and subsequently cloned and sequenced. The centromere-proximal portion of 3RTAS from both ecotypes contained two newly identified potential genes, one encoding the chloroplast luminal 19-kDa protein precursor and the other encoding three potential alternatively spliced CCCH-type zinc finger proteins. The telomere-proximal portion of 3RTAS from the Col ecotype contained short duplicated fragments derived from chromosomes I, II, and III, and that from the Ws ecotype contained a duplicated fragment derived from chromosome V. Each duplicated fragment has diverged somewhat in sequence from that of the ectopic template. Small patches of homologous nucleotides were found within the flanking sequences of both the duplicated fragments and the corresponding ectopic template sequences. The structural characteristics of these duplicated fragments suggest that they are filler DNAs captured by non-homologous end joining during double-strand break repair. Our characterization of 3RTAS not only filled up a gap in the chromosome IIIR sequence of A. thaliana but also identified new genes with unknown functions.

Organization and Evolution of Subtelomeric Satellite Repeats in the Potato Genome

“…This region showed dynamic sequence changes and rearrangements with characteristics of nonhomologous end-joining (NHEJ) events associated with double-strand break (DSB) repair. Such NHEJ events were also detected in the subtelomeric regions of the right arm of chromosome 3 (Wang et al 2010). Thus, NHEJ events may play an important role in generating the sequence variation associated with the subtelomeric regions of A. thaliana chromosomes.…”

Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii

“…Transposition also contributes to subtelomere variations ( 10 , 14 , 39 , 46 ). These mechanisms, along with others such as non-homologous end-joining (NHEJ)-mediated translocations and fusions, have been described in a variety of species and can lead to segmental duplications and amplification of repeated elements ( 14 , 44 , 46 , 47 ). Consistently, mutation rates and chromosomal rearrangements are elevated at chromosome ends, even more so in the absence of telomerase, as reported in yeast, Drosophila , mammals and plants ( 35 , 38 , 49–52 ).…”

Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii

“…Transposition also contributes to subtelomere variations (Kim et al 1998; Kuo et al 2006; Rudd et al 2009; Chen et al 2018). All of these mechanisms, along with others such as non-homologous end-joining (NHEJ)-mediated translocations and fusions, can lead to segmental duplications and amplification of repeated elements (Linardopoulou et al 2005; Kuo et al 2006; Wang et al 2010; Chen et al 2018). Consistently, mutation rates and chromosomal rearrangements are elevated at chromosome ends, even more so in the absence of telomerase (Horowitz and Haber 1984; Hackett et al 2001; Siroky et al 2003; Londono-Vallejo et al 2004; Anderson et al 2008; Coutelier et al 2018).…”

“…An early study evidenced a high level of similarity in the sequences adjacent to a few cloned C. reinhardtii telomeres (Petracek et al 1990). Subtelomere architecture has also been partially outlined in a limited number of plant species, including Arabidopsis thaliana , Silene latifolia and Phaseolus vulgaris (Kotani et al 1999; Sykorova et al 2003; Kuo et al 2006; Wang et al 2010; Richard et al 2013; Chen et al 2018), and the green alga Coccomyxa subellipsoidea (Blanc et al 2012). To probe the structure of these repetitive regions, we recently generated a contiguous de novo assembly from published Oxford Nanopore Technologies long reads (Liu et al 2019; O'Donnell et al 2020), which we analyze alongside soon-to-be-released PacBio-generated assemblies (Craig et al, in prep ).…”