Repair and Reconstruction of Telomeric and Subtelomeric Regions and Genesis of New Telomeres: Implications for Chromosome Evolution

Abstract

DNA damage repair within telomeres are suppressed to maintain the integrity of linear chromosomes, but the accidental activation of repairs can lead to genome instability. This review develops the concept that mechanisms to repair DNA damage in telomeres contribute to genetic variability and karyotype evolution, rather than catastrophe. Spontaneous breaks in telomeres can be repaired by telomerase, but in some cases DNA repair pathways are activated, and can cause chromosomal rearrangements or fusions. The resultant changes can also affect subtelomeric regions that are adjacent to telomeres. Subtelomeres are actively involved in such chromosomal changes, and are therefore the most variable regions in the genome. The case of Caenorhabditis elegans in the context of changes of subtelomeric structures revealed by long-read sequencing is also discussed. Theoretical and methodological issues covered in this review will help to explore the mechanism of chromosome evolution by reconstruction of chromosomal ends in nature.

Atlas of telomeric repeat diversity inArabidopsis thaliana

“…These duplications could be the result of simple expansion by the same mechanisms that cause other HORs. Alternatively, they could be caused by telomerase-independent repair triggered by a double-strand break (DSB; Kim et al 2020). At the end of chr2q of Hum-2, a unique sequence fragment interrupted the variant telomeric repeats, and a related arrangement was found at chr5q of the same accession.…”

Intraspecific de novo gene birth revealed by presence–absence variant genes in Caenorhabditis elegans

“…These cut-and-paste processes cause double-strand breaks in areas from where the transposon has been pulled out and must be repaired by either homologous recombination or non-homologous end-joining (49). In particular, non-homologous end-joining may cause small indels, increase mutation rate of surrounding sequences and/or insert substantially large sequences (50–52). This process may probably contribute to the generation of genes and alternative alleles that we found.…”

A beginner’s guide to assembling a draft genome and analyzing structural variants with long-read sequencing technologies

“…Note: For the PacBio CLR mode and ONT, high-quality DNA would have >10-kb N50 read lengths, and a high-quality genome assembly would have >1-Mb N50 contig lengths ( Kim et al, 2019a , Kim et al, 2020 , Kim et al, 2021 ).…”