An improved Raphanus sativus cv. WK10039 genome localizes centromeres, uncovers variation of DNA methylation and resolves arrangement of the ancestral Brassica genome blocks in radish chromosomes.

KEY MESSAGE: This study presents an improved genome of Raphanus sativus cv. WK10039 uncovering centromeres and differentially methylated regions of radish chromosomes. Comprehensive genome comparison of radish and diploid Brassica species of U's triangle reveals that R. sativus arose from the Brassica B genome lineage and is a sibling species of B. nigra. Radish (Raphanus sativus L.) is a key root vegetable crop closely related to the Brassica crop species of the family Brassicaceae. We reported a draft genome of R. sativus cv. WK10039 (Rs1.0), which had 54.6 Mb gaps. To study the radish genome and explore previously unknown regions, we generated an improved genome assembly (Rs2.0) by long-read sequencing and high-resolution genome-wide mapping of chromatin interactions. Rs2.0 was 434.9 Mb in size with 0.27 Mb gaps, and the N50 scaffold length was 37.3 Mb (40-fold larger assembly compared to Rs1.0). Approximately 38% of Rs2.0 was comprised of repetitive sequences, and 52,768 protein-coding genes and 4845 non-protein-coding genes were predicted and annotated. The improved contiguity and coverage of Rs2.0, along with the detection of highly methylated regions, enabled localization of centromeres where R. sativus-specific centromere-associated repeats, full-length OTA and CRM LTR-Gypsy retrotransposons, hAT-Ac, CMC-EnSpm and Helitron DNA transposons, and sequences highly homologous to B. nigra centromere-specific CENH3-associated CL sequences were enriched. Whole-genome bisulfite sequencing combined with mRNA sequencing identified differential epigenetic marks in the radish genome related to tissue development. Synteny comparison and genomic distance analysis of radish and three diploid Brassica species of U's triangle suggested that the radish genome arose from the Brassica B genome lineage through unique rearrangement of the triplicated ancestral Brassica genome after splitting of the Brassica A/C and B genomes.

Seeded Ising Model and Distributed Biometric Template Storage and Matching.

It is known that a variant of Ising model, called Seeded Ising Model, can be used to recover the information content of a biometric template from a fraction of information therein. The method consists in reconstructing the whole template, which is called the intruder template in this paper, using only a small portion of the given template, a partial template. This reconstruction method may pose a security threat to the integrity of a biometric identity management system. In this paper, based on the Seeded Ising Model, we present a systematic analysis of the possible security breach and its probability of accepting the intruder templates as genuine. Detailed statistical experiments on the intruder match rate are also conducted under various scenarios. In particular, we study (1) how best a template is divided into several small pieces called partial templates, each of which is to be stored in a separate silo; (2) how to do the matching by comparing partial templates in the locked-up silos, and letting only the results of these intra-silo comparisons be sent to the central tallying server for final scoring without requiring the whole templates in one location at any time.

The Formation and Invariance of Canine Nose Pattern of Beagle Dogs from Early Puppy to Young Adult Periods.

The formation and invariance of the canine nose pattern is studied. Nose images of ten beagle dogs were collected for ten months from month two to month eleven. The nose patterns in these images are examined visually and by a biometric algorithm. It is found that the canine nose pattern is fully formed at the end of the second month since birth and remains invariant until the end of the eleventh month. This study also strongly indicates that the canine nose pattern can be used as a unique biometric marker for each individual dog.

Study on the Viability of Canine Nose Pattern as a Unique Biometric Marker.

The uniqueness of the canine nose pattern was studied. A total of 180 nose images of 60 dogs of diverse age, gender, and breed were collected. The canine nose patterns in these images were examined visually and by a biometric algorithm. It was found that the canine nose pattern remains invariant regardless of when the image is taken; and that the canine nose pattern is indeed unique to each dog. The same study was also performed on an enlarged dataset of 278 nose images of 70 dogs of 19 breeds. The study of the enlarged dataset also leads to the same conclusion. The result of this paper confirms and enhances the claims of earlier works by others that the canine nose pattern is indeed unique to each animal and serves as a unique biometric marker.