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Kishida, T.

Publications and source records attributed to Kishida, T..

3 recordsLinked to original sources

Integrative taxonomic revision of turtle barnacle genus Platylepas (Cirripedia: Coronuloidea): an ancient host-range expansion to sea snakes and sirenians

The barnacle genus Platylepas contains obligate epibionts of marine vertebrates, but the taxonomic status and evolutionary history of the sea-snake specialist, P. ophiophila, have remained unclear. Here, we reassess species boundaries and host associations in Platylepas using shell-morphological comparisons and sequence data from mitochondrial COI and nuclear H3 genes from specimens collected from sea turtles, sea snakes, and a dugong. Our results show that P. ophiophila is a valid species, phylogenetically and morphologically distinct from the widespread turtle barnacles P. decorata and P. hexastylos. Furthermore, we report the first record of P. ophiophila from a sirenian host (Dugong dugon), a discovery that necessitates the re-examination of historical records of barnacles on sirenians worldwide. Our phylogeny places P. decorata, a turtle epibiont, as the earliest diverging lineage within the genus. This is consistent with the hypothesis that the ancestor of Platylepas was associated with sea turtles, a conclusion supported by the ichnofossil record. The subsequent divergence of the P. ophiophila clade may represent an important host-use transition: an ancient host shift from sea turtles to the taxonomically disparate but ecologically linked inhabitants--sea snakes and sirenians--of seagrass ecosystems. This study clarifies species limits within Platylepas and provides a framework for discussing host associations and potential host shifts in light of existing molecular and fossil evidence.

zoology↗

Chromosome-scale genomes of two wild flowering cherrys (Cerasus itosakura and C. jamasakura) provide insights into structural evolution in Prunus

Flowering cherries (genus Cerasus) are iconic trees in Japan, celebrated for their cultural and ecological significance. Despite their prominence, high-quality genomic resources for wild Cerasus species have been limited. Here, we report chromosome-level genome assemblies of two representative Japanese cherries: Cerasus itosakura, a progenitor of the widely cultivated C. xyedoensis Somei-yoshino, and Cerasus jamasakura, a traditional popular wild species endemic to Japan. Using deep PacBio long-read and Illumina short-read sequencing, combined with reference-guided scaffolding based on near-complete C. speciosa genome, we generated assemblies of 259.1 Mbp (C. itosakura) and 312.6 Mbp (C. jamasakura), with both >98% BUSCO completeness. Consistent with their natural histories, C. itosakura showed low heterozygosity, while C. jamasakura displayed high genomic diversity. Comparative genomic analyses revealed structural variations, including large chromosomal inversions. Notably, the availability of both the previously published C. speciosa genome and our new C. itosakura genome enabled the reconstruction of proxy haplotypes for both parental lineages of Somei-yoshino. Comparison with the phased genome of Somei-yoshino revealed genomic discrepancies, suggesting that the cultivar may have arisen from genetically distinct or admixed individuals, and may also reflect intraspecific diversity. Our results offer genomic foundations for evolutionary and breeding studies in Cerasus and Prunus.

genomics↗

Decoding the Centromeric Region with a Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa

The Oshima cherry (Cerasus speciosa), which is endemic to Japan, has significant cultural and horticultural value. In this study, we present a near complete telomere-to-telomere genome assembly for C. speciosa, derived from the old growth "Sakurakkabu" tree on Izu Oshima Island. Using Illumina short-read, PacBio long-read, and Hi-C sequencing, we constructed a 269.3 Mbp genome assembly with a contig N50 of 32.0 Mbp. We examined the distribution of repetitive sequences in the assembled genome and identified regions that appeared to be centromeric. Detailed structural analysis of these putative centromeric regions revealed that the centromeric regions of C. speciosa comprised repetitive sequences with monomer lengths of 166 or 167 bp. Comparative genomic analysis with Prunus sensu lato genome revealed structural variations and conserved syntenic regions. This high-quality reference genome provides a crucial tool for studying the genetic diversity and evolutionary history of Cerasus species, facilitating advancements in horticultural research and the preservation of this iconic species.

genomics↗