Biology subjects

Mattila, T. M.

Publications and source records attributed to Mattila, T. M..

4 recordsLinked to original sources

bioRxiv2026

The Nature of Centromeric Repeat Turnovers in the genus Arabidopsis

Centromeres are critical for accurate segregation of chromosomes and are often composed of megabases of tandemly arranged satellite repeats. Yet, despite their conserved function, the DNA sequence of centromeres is, paradoxically, rapidly evolving. To understand the nature of centromeric sequence turnover, we assembled 417 centromeres from nine species representing the entire Arabidopsis genus. In the genus, centromeres are formed by four main satellite repeats with homologous sequences forming central arrays and minor repeat types. We identify the ancestral centromeric repeat type for the Arabidopsis genus and three independent turnovers to different repeats: (1) a complete turnover in A. thaliana, (2) a turnover of seven out of the eight centromeres in the ancestor of A. cebennensis and A. pedemontana, (3) turnovers of three to five centromeres in the genomes of A. halleri and A. lyrata. Most centromeric repeats are also present throughout the genome with shared syntenic locations between Arabidopsis species, and some being similar to parts of transposable elements and genes, suggesting that centromeric repeats originate outside of the centromeres. In allotetraploid A. suecica we find that the repeats from centromeric arrays on one subgenome can transpose and invade the other, likely via transposable element activity. All four main centromeric repeats can recruit the CENH3 (CENP-A) histone variant, however, when a new repeat successfully proliferates in an old array, CENH3 is primarily recruited to the new array marking functional take over. Complete centromeric turnovers occurred in species that experienced severe bottlenecks in their evolutionary history, where new centromeric alleles may have been fixed by genetic drift. Yet, we also observe segregation distortion between two different centromeric repeat types in A. lyrata, suggestive of centromere drive and we propose that both drift and drive contribute to centromeric repeat turnover. Together, our findings reveal the origin of centromeric repeats, mechanisms of repeat proliferation and spread, and the evolutionary dynamics of centromeric repeat turnovers in the Arabidopsis genus.

evolutionary biology↗

bioRxiv2024

Optimizing Exome Captures in Species with Large Genomes Using Species-specific Repetitive DNA Blocker

Large and highly repetitive genomes are common. However, research interests usually lie within the non-repetitive parts of the genome, as they are more likely functional, and can be used to answer questions related to adaptation, selection, and evolutionary history. Exome capture is a cost-effective method for providing sequencing data from protein-coding parts of the genes. C0t-1 DNA blockers consist of repetitive DNA and are used in exome captures to prevent the hybridization of repetitive DNA sequences to capture baits or bait-bound genomic DNA. Universal blockers target repetitive regions shared by many species, while species-specific c0t-1 DNA is prepared from the DNA of the studied species, thus perfectly matching the repetitive DNA contents of the species. So far the use of species-specific c0t-1 DNA has been limited to a few model species. Here, we evaluated the performance of blocker treatments in exome captures of Pinus sylvestris, a widely distributed conifer species with a large (> 20 Gbp) and highly repetitive genome. We compared treatment with a commercial universal blocker to treatments with species-specific c0t-1 (30,000 ng and 60,000 ng). Species-specific c0t-1 captured more unique exons than the initial set of targets, reduced sequencing of tandem repeats, and produced more target regions with high read coverage and narrower depth distribution than the universal blocker. Based on our results, we recommend optimizing exome captures by using at least 60,000 ng species-specific c0t-1 DNA. It is relatively easy and fast to prepare and can also be used with existing bait set designs.

genomics↗

bioRxiv2023

Strong purifying selection in haploid tissue-specific genes of Scots pine supports the masking theory

The masking theory states that genes expressed in haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploid organisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intra-specific competition. Evidence from other plant groups is scarce and results show no support for the masking theory. Here we have used a gymnosperm Scots pine megagametophyte, a maternally-derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects (DFE) of new mutations in haploid and diploid tissue-specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue, and that this signal of strong selection is not an artifact driven by high expression levels

evolutionary biology↗

bioRxiv2021

Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

Scots pine (Pinus sylvestris) is the most widespread coniferous tree in the boreal forests of Eurasia and has major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies and genomic selection. We present a new 50K SNP genotyping array for Scots pine research, breeding programs, and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array, and identified 47 712 high-quality SNPs for the final array (called PiSy50k). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns, and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from breeding populations from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.92%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the amount of Mendelian error was negligible. In addition, array genotypes successfully discriminate Scots pine populations from different geographic origins. The PiSy50k array will be a valuable tool for future genetic studies and forestry applications. Significance statementScots pine is an evolutionary, economically and ecologically impressive coniferous species but its gigantic genome has limited studying e.g. the genetic basis of its functional trait variation. We have developed a genotyping array that facilitates Scots pine genetic research and linking its trait variation to genetic polymorphisms and gene expression levels across the genome.

genomics↗