Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

Dermatoglyphics on volar skin of mice: the normal pattern

BACKGROUND

Mouse volar skin has many protrusions, both large and small. They can be observed more clearly after removal of the epidermis, as they are chiefly constructed of dermal structures. They form "dermatoglyphs." This report describes the normal pattern of these protrusions to establish a normal standard for detection of abnormalities.

METHODS

Limbs of young and adult mice were fixed in 10% formalin and treated with 5% KOH to remove the epidermis layer. They were observed under a dissecting microscope after toluidine blue staining, or by scanning electron microscopy. Several limbs were used for light microscopic observation.

RESULTS

Four types of protrusions are observed. 1) Digital pads: single large pads on each digital tip. They locate over the distal phalanx. 2) Interdigital pads and carpal (tarsal) pads (or thenar and hypothenar pads): large pads similar to digital pads. There are five on the palm and six on the sole. 3) Caterpillar pads: elongated thin protrusions on the ventral side of the digits. They form stripes transverse to the axis of the digits. 4) Cobblestone pads: many small protrusions between the interdigital and carpal (tarsal) pads. "Caterpillar pads" and "cobblestone pads" are reported here for the first time. Each pad contains sweat glands and has sweat duct openings and dermal ridges on its top.

CONCLUSIONS

A detailed description of the normal pattern is indispensable for identification of abnormal patterns. The present description, therefore, can be used as a normal standard when genetically or environmentally induced anomalies are assessed.