Biology subjects

Tsuchimatsu, T.

Publications and source records attributed to Tsuchimatsu, T..

12 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↗

bioRxiv2025

Genomic architecture of the self-incompatibility locus in apple provides insights into the evolution of collaborative non-self recognition

Self-incompatibility (SI) systems prevent self-fertilization, thereby maintaining genetic diversity in flowering plants. Among them, collaborative non-self recognition (CNSR) is the most widespread, yet the genomic organization and evolutionary maintenance of its multigenic recognition system remain poorly understood. Using 27 haplotype-resolved genomes from wild and domesticated apples (Malus spp.), we dissected the structure and evolution of the S-locus. We identified 17 S-RNase alleles and 500 pollen-expressed S-locus F-box brother (SFBB) genes across 18 families. The S-locus shows extensive structural divergence among alleles and transposable element accumulation, consistent with long-term restricted effective recombination. Despite this divergence, haplotypes carrying the same S-RNase allele retain remarkably conserved SFBB repertoires and gene organization, even across species boundaries, indicating that long-term balancing selection preserves highly conserved S-haplotype architectures associated with specific S-RNase lineages. Tandem duplication, positive selection, and signatures consistent with gene conversion contribute to the diversification of pollen-expressed SFBB genes while S-RNase-associated SFBB repertoires remain conserved across haplotypes carrying the same S-RNase allele. Our results reveal how a structurally dynamic yet evolutionarily constrained genomic region can sustain long-term S-allele diversity and preserve complex multigenic haplotype architectures in flowering plants.

genomics↗

bioRxiv2025

Genomic and evolutionary factors influencing the prediction accuracy of optimal growth temperature in prokaryotes

Bacteria and archaea have evolved diverse genomic adaptations to thrive across various temperatures. These adaptations include genome sequence optimizations, such as increased GC content in rRNA and tRNA, shifts in codon and amino acids usage, and the acquisition of functional genes conferring adaptation for specific temperatures. Since the experimental determination of optimal growth temperatures (OGT) is only possible for cultured species, predicting OGT from genomic information has become increasingly important given the exponential increase in genomic data. Although previous studies developed prediction models integrating multiple features based on genome composition using machine learning, the accuracy was variable depending on the target species, with models performing well for thermophiles but less accurately for psychrophiles. In this study, we curated the OGT and genomic data of 2,869 bacterial species to develop a novel prediction model incorporating features reflecting genomic adaptation toward lower temperatures. We found that species with rapid OGT shifts from their ancestors, including psychrophiles, showed less accuracy in genome composition-based models. Incorporating the gene presence/absence information associated with the rapid changes in OGT improved the prediction accuracy for psychrophiles. We also observed that OGT in archaea is phylogenetically more conserved than in bacteria, which may lead to the long-term optimization of the genome composition and explain high predictability of OGT in archaea. These findings highlight the importance of integrating long- and short-term evolutionary adaptations for phenotype prediction models.

genomics↗

bioRxiv2025

Life-history trade-offs explain local adaptation in Arabidopsis thaliana

Local adaptation has been demonstrated in many organisms, but the traits involved, and the temporal and spatial scales at which selection acts are generally unknown. We carried out a multi-year study of 200 accessions (natural inbred lines) of Swedish Arabidopsis thaliana using local field sites and a combination of common-garden experiments that measured adult survival and fecundity, and selection experiments that measured fitness over the full life cycle. We found evidence of strong and variable selection, with particular genotypes favored more than five-fold in certain years and locations. Fecundity showed evidence of classical local adaptation, with accessions generally performing better closer to their home. However, relative to other accessions, southern ones usually had the highest fecundity---but were far more sensitive to harsh winters and slug herbivory, which strongly decreased both survival and fecundity. Furthermore, accessions originally sampled on beaches had low fecundity in all common-garden experiments, but massively outperformed all other accessions in the selection experiments, presumably due to an advantage during seedling establishment associated with their very large seeds. We conclude that local adaptation in A. thaliana reflects strong temporally and spatially varying selection on multiple traits, generally involving trade-offs and different life-history strategies, making fitness difficult to predict and measure.

genetics↗

bioRxiv2024

Long-read sequencing reveals the allelic diversity of the self-incompatibility gene across natural populations in Petunia (Solanaceae)

Self-incompatibility (SI) is a genetic mechanism to prevent self-fertilization and thereby promote outcrossing in hermaphroditic plant species through discrimination of self and non-self pollen by pistils. In many SI systems, recognition between pollen and pistils is controlled by a single multiallelic locus (called S-locus), in which numbers of alleles (called S-alleles) are segregating. Because of the extreme level of polymorphism of the S-locus, identifications of S-alleles have been a major issue in many SI studies for decades. Here we report an RNA-seq-based method to explore allelic diversity of the S-locus by employing the long-read sequencing technology of the Oxford Nanopore MinION, and applied it for the gametophytic SI system of Petunia (Solanaceae), in which the female determinant is a secreted ribonuclease called S-RNase that inhibits the elongation of self-pollen tubes by degrading RNA. We developed a method to identify S-alleles by the search of S-RNase sequences, using the previously reported sequences as queries, and found in total 62 types of S-RNase including 45 novel types. We validated this method through Sanger sequencing and crossing experiments, confirming the sequencing accuracy and SI phenotypes corresponding to genotypes. Then, using the obtained sequence data together with PCR-based genotyping in a larger sample set of 187 plants, we investigated the diversity, frequency, and the level of shared polymorphism of S-alleles across populations and species. The method as well as the dataset obtained in Petunia will be an important basis for further studying the evolution of S-RNase-based gametophytic SI systems in natural populations. Significance statementFlowering plants have evolved molecular mechanisms called self-incompatibility (SI) for discriminating self and non-self pollen at pistils to prevent self-fertilization, which is often deleterious due to inbreeding depression. The specificity of SI is usually determined by numbers of highly divergent alleles (called S-alleles) segregating at a single locus, and identifications of S-alleles have been a major issue in many SI systems. Here we report a new method to identify S-alleles by employing a long-read sequencing technology and applied it for the gametophytic SI system of Petunia, identifying 62 types of S-alleles including 45 novel types. The method as well as the dataset obtained in this study will be an important basis for the research of SI evolution.

evolutionary biology↗

bioRxiv2024

Population genomics reveals demographic history and climate adaptation in Japanese Arabidopsis halleri

Climate oscillations in the Quaternary forced species to major latitudinal or altitudinal range shifts. It has been suggested that adaptation concomitant with range shifts plays key roles in species responses during climate oscillations, but the role of selection for local adaptation to climatic changes remains largely unexplored. Here, we investigated population structure, demographic history, and signatures of climate-driven selection based on genome-wide polymorphism data of 141 Japanese Arabidopsis halleri individuals, with European ones as outgroups. Coalescent-based analyses suggested a genetic differentiation between Japanese subpopulations since the Last Glacial Period (LGP), which would have contributed to shaping the current pattern of population structure. Population demographic analysis revealed the population size fluctuations in the LGP, which were particularly prominent since the subpopulations started to diverge ([~]50 kya). The ecological niche modeling predicted the range shifts from southern coastal regions to northern coastal and mountainous areas, possibly in association with the population size fluctuations. Through genome-wide association analyses of bioclimatic variables and selection scans, we investigated whether climate-associated loci are enriched in the extreme tails of selection scans, and demonstrated the prevailing signatures of selection, particularly toward a warmer climate in southern subpopulations and a drier environment in northern subpopulations, which may have taken place during or after the LGP. Our study highlights the importance of integrating climate associations, selection scans, and population demographic analyses for identifying genomic signatures of population-specific adaptation, which would also help us predict the evolutionary responses to future climate changes.

evolutionary biology↗

bioRxiv2023

Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum-strigosum-littorale Complex

Genome sizes are known to vary within and among closely related species, but the knowledge about genomic factors contributing to the variation and their impacts on gene functions is limited to only a small number of species. This study identified a more than twofold heritable genome size variation among the unicellular Zygnematophycean alga, Closterium peracerosum-strigosum-littorale (C. psl.) complex, based on short-read sequencing analysis of 22 natural strains and F1 segregation analysis. Six de novo assembled genomes revealed that genome size variation is largely attributable to genome-wide copy number variation (CNV) among strains rather than mating type-linked genomic regions or specific repeat sequences such as rDNA. Notably, about 30% of genes showed CNV even between strains that can mate with each other. Transcriptome and gene ontology analysis demonstrated that CNV is distributed nonrandomly in terms of gene functions, such that CNV was more often observed in the gene set with stage-specific expression. Furthermore, in about 30% of these genes with CNV, the expression level does not increase proportionally with the gene copy number, suggesting presence of dosage compensation, which was overrepresented in genes involved in basic biological functions, such as translation. Nonrandom patterns in gene duplications and corresponding expression changes in terms of gene functions may contribute to maintaining the high level of CNV associated with extensive genome size variation in the C. psl. complex, despite its possible detrimental effects.

evolutionary biology↗

bioRxiv2023

Diversity of genome size and chromosome number in homothallic and heterothallic strains of the Closterium peracerosum-strigosum-littorale complex (desmidiales, zygnematophyceae, streptophyta)

Members of the Closterium peracerosum-strigosum-littorale (C. psl.) complex are unicellular zygnematophycean algae, which are suggested to be closely related to land plants. A zygospore is typically formed as a result of conjugation between mating-type plus (mt+) and mating-type minus (mt-) cells during sexual reproduction in heterothallic strains. On the other hand, zygospores are formed between genetically identical cells in homothallic strains. In this study, we isolated novel homothallic strains in the C. psl. complex. Phylogenetic analysis revealed the polyphyly of homothallic strains, suggesting multiple transitions between homothallism and heterothallism in the C. psl. complex. We measured the 1C genome size of the C. psl. complex by using flow cytometry after staining nuclei with propidium iodide, which ranged from 0.53 to 1.42 Gbp. We counted chromosome numbers using confocal microscope images, finding that two homothallic strains had fewer chromosomes than four heterothallic strains. Genome size positively correlated with both the cell size and chromosome number. Chromosome numbers differed even within the same mating group, suggesting a mechanism tolerating chromosomal rearrangements during meiosis in the C. psl. complex.

plant biology↗

bioRxiv2020

Massive rhizobial genomic variations associated with partner quality in Lotus-Mesorhizobium symbiosis

In diverse mutualistic relationships, genetic variations in impact on the growth of interacting partners--variations in partner quality--are common, despite the theoretical prediction that selection favoring high-quality partners should eliminate such variations. Here, we investigated how variations in partner quality could be maintained in the nitrogen-fixing mutualism between Lotus japonicus and Mesorhizobium bacteria. We reconstructed de novo assembled full-genome sequences from nine rhizobial symbionts, finding massive variations in the core genome and the contrastingly similar symbiotic islands, indicating recent horizontal gene transfer (HGT) of the symbiosis islands into diverse Mesorhizobium lineages. A cross-inoculation experiment using nine sequenced rhizobial symbionts and 15 L. japonicus accessions revealed extensive quality variations represented by plant growth phenotypes, including genotype-by-genotype interactions. Quality variations were not associated with the presence/absence variations of known symbiosis-related genes in the symbiosis island, but rather, showed significant correlations with the core genome variations, supported by SNP- and kinship matrix-based association analyses. These findings highlight the novel role of HGT of symbiosis islands, which indirectly supply mutations of core genomes into L. japonicus-associated bacteria, thereby contributing to the maintenance of variations in partner quality.

evolutionary biology↗

bioRxiv2018

Adaptive Reduction of Male Gamete Number in a Selfing Species

The number of male gametes produced is critical for reproductive success and varies greatly between and within species1-3. Evolutionary reduction of male gamete production has been widely reported in plants as a hallmark of the selfing syndrome, as well as in humans. Such a reduction may simply represent deleterious decay4-7, but evolutionary theory predicts that breeding systems could act as a major selective force on male gamete number: while large numbers of sperm should be produced in highly promiscuous species because of male-male gamete competition1, reduced sperm numbers may be advantageous at lower outcrossing rates because of the cost of gamete production. Here we used genome-wide association study (GWAS) to show a signature of polygenic selection on pollen number in the predominantly selfing plant Arabidopsis thaliana. The top associations with pollen number were significantly more strongly enriched for signatures of selection than those for ovule number and 107 phenotypes analyzed previously, indicating polygenic selection8. Underlying the strongest association, responsible for 20% of total pollen number variation, we identified the gene REDUCED POLLEN NUMBER 1 affecting cell proliferation in the male germ line. We validated its subtle but causal allelic effects using a quantitative complementation test with CRISPR-Cas9-generated null mutants in a nonstandard wild accession. Our results support polygenic adaptation underlying reduced male gamete numbers.

evolutionary biology↗

bioRxiv2017

Plant genes influence microbial hubs that shape beneficial leaf communities

Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200 A. thaliana genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial OTUs. Host genetics disproportionately influenced hubs within the microbial communities, with their impact then percolating through the community, as evidenced by a decline in the heritability of particular OTUs with their distance to the nearest hub. By simultaneously measuring host performance, we found that host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants grown in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins and the immune system. Using untargeted metabolomics, we corroborate the consistent association of variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host natural variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.

microbiology↗

bioRxiv2017

Patterns of polymorphism at the self-incompatibility locus in 1,083 Arabidopsis thaliana genomes

Although the transition to selfing in the model plant Arabidopsis thaliana involved the loss of the self-incompatibility (SI) system, it clearly did not occur due to the fixation of a single inactivating mutation at the locus determining the specificities of SI (the S-locus). At least three groups of divergent haplotypes (haplogroups), corresponding to ancient functional S-alleles, have been maintained at this locus, and extensive functional studies have shown that all three carry distinct inactivating mutations. However, the historical process of loss of SI is not well understood, in particular its relation with the last glaciation. Here, we took advantage of recently published genomic re-sequencing data in 1,083 Arabidopsis thaliana accessions that we combined with BAC sequencing to obtain polymorphism information for the whole S-locus region at a species-wide scale. The accessions differed by several major rearrangements including large deletions and inter-haplogroup recombinations, forming a set of haplogroups that are widely distributed throughout the native range and largely overlap geographically. Relict A. thaliana accessions that directly derive from glacial refugia are polymorphic at the S-locus, suggesting that the three haplogroups were already present when glacial refugia from the last Ice Age became isolated. Inter-haplogroup recombinant haplotypes were highly frequent, and detailed analysis of recombination breakpoints suggested multiple independent origins. These findings suggest that the complete loss of SI in A. thaliana involved independent self-compatible mutants that arose prior to the last Ice Age, and experienced further rearrangements during post-glacial colonization.

evolutionary biology↗