Movilli, A. | bioRxiv Science

bioRxiv2023

Atlas of telomeric repeat diversity in Arabidopsis thaliana

Telomeric repeat arrays at the ends of chromosomes are highly dynamic but their repetitive nature and technological limitations have made it difficult to assess the variation in genome diversity surveys. Here we present a comprehensive characterization of the sequence variation immediately adjacent to the canonical telomeric repeat arrays at the very ends of chromosomes in 49 genetically diverse Arabidopsis thaliana accessions. We reveal several types of distinct telomeric repeat units and identify evolutionary processes such as local homogenization and higher-order repeat formation that shape diversity of chromosome ends. The identification of segmental duplications and at least one recombination event suggests a plausible history of telomerase-independent maintenance generation. By comparing largely isogenic samples, we are able to determine variant telomeric repeat number variation at both the germline and somatic levels. Analysis of haplotype structure uncovers chromosome end-specific as well as genetic group-specific patterns in telomeric repeat diversity and provides evidence for linkage disequilibrium between repeat arrays and their adjacent non-coding regions. Together, our findings illustrate the fine-scale telomeric repeat spectrum in A. thaliana, expanding our knowledge of the evolution of chromosome ends.

genomics↗

bioRxiv2023

Transposon dynamics in the emerging oilseed crop Thlaspi arvense

Genome evolution is partly driven by the mobility of transposable elements (TEs) which often leads to deleterious effects, but their activity can also facilitate genetic novelty and catalyze local adaptation. We explored how the intraspecific diversity of TE polymorphisms is shaping the broad geographic success and adaptation capacity of the emerging oil crop Thlaspi arvense. We achieved this by classifying the TE inventory of this species based on a high-quality genome assembly, age estimation of retrotransposon TE families and a comprehensive assessment of their mobilization potential. Our survey of TE insertion polymorphisms (TIPs) captured 280 accessions from 12 regions across the Northern hemisphere. We quantified over 90,000 TIPs, with their distribution mirroring genetic differentiation as measured by single nucleotide polymorphisms (SNPs). The number and types of mobile TE families vary substantially across populations, but there are also shared patterns common to all accessions. We found that Ty3/Athila elements are the main drivers of TE diversity in T. arvense populations, while a single Ty1/Alesia lineage might be particularly important for molding transcriptome divergence. We further observed that the number of retrotransposon TIPs is associated with variation at genes related to epigenetic regulation while DNA transposons are associated with variation at a Heat Shock Protein (HSP19). We propose that the high rate of mobilization activity can be harnessed for targeted gene expression diversification, which may ultimately present a toolbox for the potential use of transposition in breeding and domestication of T. arvense.

genomics↗