Genetic characteristics of Apodemus speciosus at Akiyoshidai Quasi-National Park in Yamaguchi Prefecture

The large Japanese field mouse (Apodemus speciosus) is a small rodent endemic to Japan. The mice have a genetic characteristic in which the number of chromosomes differs between those from western Japan and those from eastern Japan. A. spesiosus, found throughout Japan, is used as a model animal for geogenetics and monitoring of radiation effects of wildlife. In this present study, to elucidate the genetic characteristics of the mice Akiyoshidai Quasi-National Park in Yamaguchi Prefecture, we investigated mitochondrial DNA and chromosome numbers. As a result, A. speciosus from Yamaguchi Prefecture were classified into the Honshu-Shikoku-Kyushu group and had a western Japan-type chromosome set of 2n=46; however, some Yamaguchi Prefecture mice formed a genetic cluster in Yamaguchi Prefecture, suggesting that continuous monitoring is needed to reveal the dynamics of genetic diversity.

Shift and adapt: the costs and benefits of karyotype variations

Variation is the spice of life or, in the case of evolution, variation is the necessary material on which selection can act to enable adaptation. Karyotypic variation in ploidy (the number of homologous chromosome sets) and aneuploidy (imbalance in the number of chromosomes) are fundamentally different than other types of genomic variants. Karyotypic variation emerges through different molecular mechanisms than other mutational events, and unlike mutations that alter the genome at the base pair level, rapid reversion to the wild type chromosome number is often possible. Although karyotypic variation has long been noted and discussed by biologists, interest in the importance of karyotypic variants in evolutionary processes has spiked in recent years, and much remains to be discovered about how karyotypic variants are produced and subsequently selected.

USING CONTEXTUAL INFORMATION TO CLARIFY CROSS-SPECIES GENE NORMALIZATION AMBIGUITY

The goal of Gene Normalization (GN) is to identify the unique database IDs of genes and proteins mentioned in biomedical literature. A major difficulty in GN comes from the ambiguity of gene names. That is, the same gene name can refer to different database IDs depending on the species in question. In this paper, we introduce a method to exploit contextual information in an abstract, like tissue type, chromosome location, etc., to tackle this problem. Using this technique, we have been able to improve system performance (F-score) by 14.3% on the BioCreAtIvE-II GN task test set. We also examined our method on a full-text dataset with cross-species genes. The experimental results show a promising performance (AUC) of 42.94%. Our experimental results also show that with full text, versus abstract only, the system performance was 12.24% higher.

Variations in Ribosomal RNA Gene Loci in Spider Lily (Lycoris spp.)

Lycoris species of the Amaryllidaceae are important ornamental and medicinal plants in Asia. Karyotypes of Lycoris species have been studied extensively since the time when their chromosome numbers were first counted over 80 years ago. Based on karyotype, Lycoris taxa can be classified into the monomorphic A group, dimorphic MT group, and the sterile dikaryotype MT-A group. Numerous reports dealing with karyotype analysis and phylogenetic relationship in the genus Lycoris have been published. However, there are disputes and controversies regarding karyotype evolution resulting from lacking efficient and reliable markers for chromosome identification in the genus Lycoris. In this study, we applied fluorescent in situ hybridization (FISH) to visualize the 5S and 45S rDNA loci on chromosomes as landmarks for chromosome identification in Lycoris taxa. In total, 12 accessions of three karyotype groups, including nine species and three artificial dikaryotype hybrids, were investigated. A high degree of variation in the number and position of 5S and 45S rDNA loci was detected among Lycoris taxa. There were four to 14 FISH signals of 5S rDNAs and two to 12 FISH signals of 45S rDNAs observed in each investigated Lycoris accession. Lycoris accessions with the same karyotype 2n = 22A may have different numbers of rDNA loci, which distributed at different chromosomal positions. In an interspecific hybrid, the number and chromosomal position of both 5S and 45S rDNA loci were either the combinations of those in their parental species or considerably modified. Overlapping FISH signals of 5S and 45S rDNAs were colocalized with a 4′, 6-diamidino-2-phenylindole-positive band at the end of the p-arm on almost every T-type chromosome (but not the A-type chromosomes). Based on the features of T-type chromosomes, the possibility of centromeric fission in karyotypic evolution of Lycoris is discussed.

Two Chimeric Chromosomes of Streptomyces coelicolor A3(2) Generated by Single Crossover of the Wild-Type Chromosome and Linear Plasmid SCP1

ABSTRACT Streptomyces coelicolor A3(2) strain 2106 carries a 1.85-Mb linear plasmid, SCP1′-cysD, in addition to a 7.2-Mb linear chromosome. Macrorestriction analysis indicated that both linear DNAs are hybrids of the wild-type chromosome and the linear plasmid SCP1 on each side. Nucleotide sequencing of the fusion junctions revealed no homology between the recombination regions. SCP1′-cysD contains an SCP1 telomere and a chromosomal telomere at each end and therefore does not have terminal inverted repeats. In addition, SCP1′-cysD could not be eliminated from strain 2106 by various mutagenic treatments. Thus, we concluded that both the 7.2-Mb chromosome and SCP1′-cysD are chimeric chromosomes generated by a single crossover of the wild-type chromosome and SCP1. This may be regarded as a model of chromosomal duplication in genome evolution.