Biology subjects

Aoyagi, Y. B.

Publications and source records attributed to Aoyagi, Y. B..

3 recordsLinked to original sources

bioRxiv2026

Chromosome-scale genome assembly of Cycas revoluta provides insights into cycad diversification and species diversity

Cycads are an ancient group of seed plants. Despite their ancient origin, many extant cycad genera exhibit high species diversity. The specialized reproductive traits in cycads, dioecy governed by the XY sex-determination system and the elaborate co-evolutionary synergy with insect pollinators, may facilitate lineage diversification. Here, we present a chromosome-scale genome sequence of Cycas revoluta, the species in which plant spermatozoids were discovered in 1896. The genome sequence spanned 11.6 Gb, 98.4% of which were anchored onto the 11 cycad chromosomes. Repetitive sequences occupied 9.8 Gb, and 31,481 genes were predicted. Based on this genome assembly, the X- and Y-associated genomic regions were characterized, and candidate genes for sex determination were identified. In addition, the genomic positions of genes for sex-related traits were determined. Subsequently, we analyzed transcriptomes for thermogenesis responsible for attracting insect pollinators. Through these comprehensive analyses, we provide new insights into the genomic basis of cycad diversification and species diversity.

genomics↗

bioRxiv2026

Genomic basis of rapid urban evolution revealed by the subgenome-resolved genome of octoploid Oxalis corniculata

Urbanization is a major driver of contemporary evolution, yet the genomic basis of urban adaptation remains poorly understood, particularly in non-model plants with complex polyploid genomes. Here, we investigate the genetic mechanisms underlying leaf color variation in the octoploid Oxalis corniculata, a phenotype associated with heat tolerance in urban environments. By integrating high-fidelity long-read sequencing and chromosome conformation capture, we generated the subgenome-resolved, chromosome-scale genome assemblies for both red- and green-leaved lines, resolving four distinct subgenomes. LTR insertion timing revealed a two-step hybridization history that established this octoploid genome within the last 1 million years. Leveraging a nationwide citizen science initiative, we collected and analyzed over 1,700 samples across a broad geographic range. We identified a major locus on one subgenome underlying this variation and implicate a coding-sequence repeat-length polymorphism in a MYB transcription factor as the candidate causal variant. This simple sequence repeat likely acts as a molecular "tuning knob" for rapid adaptation to urban heat islands. This study provides a new baseline for evolutionary ecological genomics in plants and highlights the power of integrating advanced genomics with public participation to forecast evolutionary responses in an increasingly urbanized world.

genomics↗

bioRxiv2025

Chromosome-level genome assembly of the gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies

Gerbera hybrida is one of the most popular ornamental plants and also serves as a valuable model plant within the Asteraceae family. Here, we report both the nuclear and organellar genome assemblies and annotations of G. hybrida, which was developed through hybridization of two wild species. Sequencing was performed using a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). The total span of the nuclear genome assembly is 2.32 gigabases, and 99.3% of the sequence assembled into 25 scaffolds, consistent with the known chromosome number. Genome annotation of the nuclear genome identified 36,160 protein-coding genes and 11,572 non-coding transcripts. The mitochondrial genome had 363,511 bp and contains 36 protein-coding genes, 3 rRNAs, and 21 tRNAs, while the chloroplast genome is 151,898 bp in length and includes 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. This reference genome provides a foundational resource for future molecular breeding and genetic research in Gerbera and the broader Asteraceae family.

plant biology↗