Biology subjects

Horiuchi, A.

Publications and source records attributed to Horiuchi, A..

3 recordsLinked to original sources

bioRxiv2023

Rapid and dynamic evolution of a giant Y chromosome in Silene latifolia

To test hypotheses about the evolution of massive sex-linked regions in plants, we sequenced the genome of Silene latifolia, whose giant heteromorphic sex chromosomes were first discovered in 1923. It has long been known that the Y consists mainly of a male-specific region which does not recombine with the X in male meiosis, and that this region carries the primary sex-determining genes, and other genes contributing to male functioning. However, only with a whole Y chromosome assembly can the candidates be validated experimentally, as we describe. Our new results also illuminate the genomic changes as the ancestral chromosome evolved into the current XY pair, testing ideas about why large regions of sex-linkage evolve, and the mechanisms creating the present recombination pattern. One sentence summaryBased on the whole genome sequences of Silene latifolia, a model species for plant sex chromosome evolution, we describe discovery of genes underlying male-female flower differences, and relate the results to ideas about the evolution of the vast non-recombining regions of the Y chromosome.

genetics↗

bioRxiv2023

Genetic basis of lineage-specific evolution of fruit traits in hexaploid persimmon

Frequent polyploidization events in plants have led to the establishment of many lineage-specific traits representing each species. Little is known about the genetic bases for these specific traits in polyploids, presumably due to plant genomic complexity and their difficulties of applying genetic approaches. Hexaploid Oriental persimmon (Diospyros kaki) has evolved specific fruit characters, including wide variations in fruit shapes and astringency. In this study, using whole-genome diploidized/quantitative genotypes from ddRAD-Seq data of 173 persimmon cultivars, we examined their population structures and potential correlations between their structural transitions and variations in nine fruit traits. The population structures of persimmon cultivars were highly randomized and not substantially correlated with the representative fruit traits focused on in this study, except for fruit astringency. With genome-wide association analytic tools considering polyploid alleles, we identified the loci associated with the nine fruit traits; we mainly focused on fruit-shape variations, which have been numerically characterized by principal component analysis of elliptic Fourier descriptors. The genomic regions that putatively underwent selective sweep exhibited no overlap with the loci associated with these persimmon-specific fruit traits. These insights will contribute to understanding of the genetic mechanisms by which fruit traits are independently established, possibly due to polyploidization events.

plant biology↗

bioRxiv2022

Ongoing rapid evolution of a post-Y region revealed by chromosome-scale genome assembly of a hexaploid monoecious persimmon (Diospyros kaki)

Sex chromosomes have evolved independently in many plant lineages. They have often undergone rapid structural degeneration and extension of non-recombining regions, which is conventionally considered to be strongly associated with the expression of sexually dimorphic traits. In this study, we assembled a monoecious hexaploid persimmon (Diospyros kaki) in which the Y chromosome had lost its function in male determination. Comparative genomic analysis among D. kaki and its dioecious relatives revealed that the non-functional Y chromosome (Ym) via silencing of the sex-determining gene, OGI, arose approximately two million years ago. Comparative analyses of the whole X and Ym chromosomes suggested that the non-functional male-specific region of the Y-chromosome (MSY), or post-MSY, retained certain conserved characteristics of the original functional MSY. Specifically, comparison of the functional MSY in D. lotus and the non-functional post-MSY in D. kaki indicated that the post-MSY had been rapidly rearranged mainly via ongoing transposable element bursts, as well as in the functional MSY. These results suggest a novel interpretation that the rapid evolution of the post-MSY (and possibly also MSYs in dioecious Diospyros species) might reflect the ancestral genomic properties of these regions, rather than the evolution of male-determining functions and/or sexually dimorphic traits.

plant biology↗