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Abstract Herein, we present the first high-quality long-read-based chromosome-level genome assemblies and gene annotations of the genomes of three endangered Tokudaia species: Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki. These species, which are endemic to different islands of the Ryukyu Islands, Japan, exhibited unique karyotypes and sex chromosomal characteristics. The genome assemblies generated using PacBio, Illumina, and Hi-C sequence data consisted of 13 (corresponded to 12 autosomes and one X chromosome), 23 (corresponded to 22 autosomes and one X chromosome), and 23 (corresponded to 21 autosomes and the neo- and ancestral X regions) chromosome-level scaffolds that contained 2,445, 2,477, and 2,661 Mbp of sequence data, respectively. Annotations of protein-coding genes were performed using RNA-Seq-based, homology-based, and Ab initio methods. BUSCO completeness values for every species exceeded 96% for genomes and 98% for genes. These data can be an important resource for contributing to our understanding of species genomes resulting from allopatric speciation and provide insights into mammalian sex-determination mechanisms and sex chromosome evolution.

DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.