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There has been long taxonomic debate on mulberry species (genus Morus) because the classification of mulberry species has relied on morphological characteristics. Although attempts for classifying mulberry species using molecular markers have been performed, phylogenetic relationships among diploid mulberry species remain unclear. In this study, we aim to investigate the genetic relationship between 54 diploid mulberry varieties belonging to seven different Morus species (M. alba, M. indica, M. bombycis, M. acidosa, M. latifolia, M. kagayamae, and M. rotundiloba) and one unspecified Morus species ('Enbu') using genome-wide SNP discovery and phylogenetic analysis via double-digest restriction site-associated DNA sequencing (ddRAD-seq). Genome-wide 2229 homozygous SNPs of 54 mulberry varieties in the eight species were identified by ddRAD-seq. Results of the phylogenetic analysis identified only three clear monophyletic clades in two Japanese native species, M. acidosa and M. kagayamae, which are found on different geographically isolated islands and a Thai species, M. rotundiloba, whereas the other species were non-monophyletic. Varieties of M. bombycis, another Japanese native species, were roughly classified into three groups. Of these, two M. bombycis groups were monophyletic with M. acidosa and M. kagayamae, respectively, while another M. bombycis group was not monophyletic. Varieties of M. indica, an Indian native species, were classified into two different monophyletic clades. Of these, one clade was clearly monophyletic with an indigenous variety in Kenya, 'Enbu', while another clade was monophyletic with M. rotundiloba and one M. latifolia variety. There were no clear monophyletic clades within M. alba and M. latifolia varieties, which could be a result of several hybridization events after their introductions from China to Japan. Our results suggested that it was difficult to clearly classify the hybridized mulberry varieties even with genome-wide DNA markers. In addition to phylogenetic analysis, we also evaluated morphological characteristics of mulberry leaves for each variety. The results of morphological evaluation indicated that leaf tip ratio may correlate to genetic difference among the two M. bombycis groups in monophyletic clades and another M. bombycis group in non-monophyletic clades. These results suggested that leaf tip ratio might be used for evaluating hybridization of M. bombycis varieties. Over all, our results may provide new insights into taxonomic debate of mulberry species.

BRCA2 is a breast tumour susceptibility factor with functions in maintaining genome stability through ensuring efficient double-strand DNA break (DSB) repair via homologous recombination. Although best known in vertebrates, fungi, and higher plants also possess BRCA2-like genes. To investigate the role of Arabidopsis BRCA2 genes in DNA repair in somatic cells, transposon insertion mutants of the AtBRCA2a and AtBRCA2b genes were identified and characterized. atbrca2a-1 and atbrca2b-1 mutant plants showed hypersensitivity to genotoxic stresses compared to wild-type plants. An atbrca2a-1/atbrca2b-1 double mutant showed an additive increase in sensitivity to genotoxic stresses compared to each single mutant. In addition, it was found that atbrca2 mutant plants displayed fasciation and abnormal phyllotaxy phenotypes with low incidence, and that the ratio of plants exhibiting these phenotypes is increased by gamma-irradiation. Interestingly, these phenotypes were also induced by gamma-irradiation in wild-type plants. Moreover, it was found that shoot apical meristems of the atbrca2a-1/atbrca2b-1 double mutant show altered cell cycle progression. These data suggest that inefficient DSB repair in the atbrca2a-1/atbrca2b-1 mutant leads to disorganization of the programmed cell cycle of apical meristems.

Guineagrass (Panicum maximum Jacq.) is one of the most important tropical forage grasses due to its high productivity and good forage qualities. Although P. maximum is important forage, basic genomic information such as genome size and ribosomal DNA (rDNA) ideogram information have not been reported. In this study, the DNA contents of one diploid strain and three tetraploid cultivars of P. maximum were examined by flow cytometry and rDNA loci were physical mapped by fluorescence in situ hybridization (FISH). The DNA content of the diploid strain was determined to be approximately 500 Mbp, which is of similar size to Oryza sativa and represents a relatively small genome size when compared to other members of the plant kingdom. The tetraploid cultivars were determined to exhibit a genome size of approximately 1000 Mbp. FISH with rDNA probes was applied to diploid and tetraploid strains. The numbers of 5S rDNA loci in the diploid and the tetraploids were two and four, respectively. The number of 45S rDNA loci varied from four to eight among the tetraploids. Constructed quantitative ideograms of diploid strain by image analysis indicated that the difference in the number of 45S rDNA is dependent on the presence or absence of the locus on chromosome 2. The determined DNA content and constructed ideograms in this study are useful for future research efforts on P. maximum in areas focused on cultivar development, gene isolation of apomixis loci and mutation research.

A genomic DNA containing a rice (Oryza sativa L., cv. Norin-8) gene coding for a pullulanase-type starch debranching enzyme (EC 3.2.1. 41) was sequenced (EMBL/GenBank/DDBJ accession number AB012915). Along the 15, 248 bp DNA, the pullulanase gene is split into 26 exons. The four pullulanase consensus regions are positioned in the middle portion of the sequence and are separated by long introns and 1-3 exons. Comparison of the rice cv. Norin-8 pullulanase genomic structure with that of barley pullulanase (limit dextrinase) (F. Lok et al., EMBL/GenBank/DDBJ accession number AF022725) indicates that most of the pullulanase exons are highly conserved. Alignment of the nucleotide bases of rice exon 8 with those of barley exon 8-intron 8-exon 9 fragment suggests that the 85 bp internal sequence of rice exon 8 was originally an intron, a possibility further indicated by the absence in barley and spinach (A. Renz et al., EMBL/GenBank/DDBJ accession number X83969) pullulanases of amino acid residues encoded by the 85 bp fragment.

Two isoforms of starch branching enzyme (Q-enzyme), QEI and QEII, have been purified to honlogeneity from developing rice endosperm. QEI and QEII, with molecular weights of about 80 and 85 kDa, respectively, could be fully separated by anion-exchange or hydrophobic chromatography. The peptide maps obtained after V8 proteinase digestion were quite different between the two enzymes. Antibodies prepared against QEI showed no immunological cross-reaction with the QEII protein in Western blot experiments, and anti-QEII serum did not react with the QEI protein. The data indicate that QEI and QEII are distinct proteins encoded by different genes in rice plants.

Rad51 paralogs belong to the Rad52 epistasis group of proteins and are involved in homologous recombination (HR), especially the assembly and stabilization of Rad51, which is a homolog of RecA in eukaryotes. We previously cloned and characterized two RAD51 paralogous genes in Arabidopsis, named AtRAD51C and AtXRCC3, which are considered the counterparts of human RAD51C and XRCC3, respectively. Here we describe the identification of RAD51B homologue in Arabidopsis, AtRAD51B. We found a higher expression of AtRAD51B in flower buds and roots. Expression of AtRAD51B was induced by genotoxic stresses such as ionizing irradiation and treatment with a cross-linking reagent, cisplatin. Yeast two-hybrid analysis showed that AtRad51B interacted with AtRad51C. We also found and characterized T-DNA insertion mutant lines. The mutant lines were devoid of AtRAD51B expression, viable and fertile. The mutants were moderately sensitive to gamma-ray and hypersensitive to cisplatin. Our results suggest that AtRAD51B gene product is involved in the repair of double-strand DNA breaks (DSBs) via HR.