Soil bacterial community structures of six dominant phyla (Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, Bacteroidetes and Actinobacteria) and unclassified bacteria detected in tropical Sarawakian and temperate Japanese forests were compared based on 16S rRNA gene sequence variation. The class composition in each phylum was similar among the studied forests; however, significant heterogeneities of class frequencies were detected. Acidobacteria and Proteobacteria were the most dominant phyla in all six forests, but differed in the level of bacterial species diversity, pattern of species occurrence and association pattern of species composition with physicochemical properties in soil. Species diversity among Acidobacteria was approximately half that among Proteobacteria, based on the number of clusters and the Chao1 index, even though a similar number of sequence reads were obtained for these two phyla. In contrast, species diversity within Planctomycetes and Bacteroidetes was nearly as high as within Acidobacteria, despite many fewer sequence reads. The density of species (the number of sequence reads per cluster) correlated negatively with species diversity, and species density within Acidobacteria was approximately twice that within Proteobacteria. Although the percentage of forest-specific species was high for all bacterial groups, sampling site-specific species varied among bacterial groups, indicating limited inter-forest migration and differential movement of bacteria in forest soil. For five of the seven bacterial groups, including Acidobacteria, soil pH appeared to strongly influence species composition, but this association was not observed for Proteobacterial species. Topology of UPGMA trees and pattern of NMDS plots among the forests differed among the bacterial groups, suggesting that each bacterial group has adapted and evolved independently in each forest.

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Allopolyploidization in plants is an important event that enhances heterosis and environmental adaptation. Common wheat, Triticum aestivum (AABBDD), which is an allohexaploid that evolved from an allopolyploidization event between T. turgidum (AABB) and Aegilops tauschii (DD), shows more growth vigor and wider adaptation than tetraploid wheats. To better understand the molecular basis for the heterosis of hexaploid wheat, we systematically analyzed the genome-wide gene expression patterns of two combinations of newly hybridized triploids (ABD), their chromosome-doubled hexaploids (AABBDD), stable synthetic hexaploids (AABBDD) and natural hexaploids, in addition to their parents, T. turgidum (AABB) and Ae. tauschii (DD), using a microarray to reconstruct the events of allopolyploidization and genome stabilization. Overall comparisons of gene expression profiles showed that the newly generated hexaploids exhibited gene expression patterns similar to those of their maternal tetraploids, irrespective of hybrid combination. With successive generations, the gene expression profiles of nascent hexaploids became less similar to the maternal profiles, and belonged to a separate cluster from the natural hexaploids. Triploids revealed characteristic expression patterns, suggesting endosperm effects. In the newly hybridized triploids (ABD) of two independent synthetic lines, approximately one-fifth of expressed genes displayed non-additive expression; the number of these genes decreased with polyploidization and genome stabilization. Approximately 20% of the non-additively expressed genes were transmitted across generations throughout allopolyploidization and successive self-pollinations, and 43 genes overlapped between the two combinations, indicating that shared gene expression patterns can be seen during allohexaploidization. Furthermore, four of these 43 genes were involved in starch and sucrose metabolism, suggesting that these metabolic events play key roles in the hybrid vigor of hexaploid wheat.

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Flowering time is an important trait for Japanese wheat breeding. Aegilops tauschii, the D-genome donor of hexaploid wheat, is a useful resource to enlarge the D-genome diversity of common wheat. Previously, we identified flowering-related QTLs in F₂ populations of synthetic hexaploid wheat lines between the tetraploid wheat cultivar Langdon and Ae. tauschii accessions. Here, to evaluate the usefulness of the early-flowering alleles from Ae. tauschii for Japanese wheat breeding, QTL analyses were conducted in two F₂ populations derived from crosses between Japanese wheat cultivars and early-flowering lines of synthetic hexaploid wheat. Only two chromosomal regions controlling flowering-related traits were identified, on chromosomes 2DS and 5AL in the mapping populations, and no previously identified QTLs were found in the synthetic hexaploid lines. The strong effect of the 2DS QTL, putatively corresponding to Ppd-D1, was considered to hide any significant expression of other QTLs with small effects on flowering-related traits. When F₂ individuals carrying Ae. tauschii-homozygous alleles around the 2DS QTL region were selected, the Ae. tauschii-derived alleles of the previously identified flowering QTLs partly showed an early-flowering phenotype compared with the Japanese wheat-derived alleles. Thus, some early-flowering alleles from Ae. tauschii may be useful for production of early-flowering Japanese wheat cultivars.

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Toll-interacting protein (Tollip) is a critical regulator of Toll-like receptor (TLR)-mediated innate immune responses. However, the Tollip gene has not been systematically characterized in shellfish. In this study, we identified and characterized a Tollip gene, PyTollip, in Yesso scallop (Patinopecten yessoensis). Phylogenetic and protein structural analyses were conducted to determine its sequence identities and evolutionary relationships. Compared with Tollip genes from other invertebrate and vertebrate species, the PyTollip gene is highly conserved in its sequence and structural features, except that a unique asparagine residue was found at a conserved site in the C2 domain of PyTollip. Quantitative real-time PCR was used to investigate the expression profiles of PyTollip in different developmental stages, healthy adult tissues, and in hemolymph after Micrococcus luteus and Vibrio anguillarum bacterial infection. Real-time PCR analysis demonstrated differential expression of PyTollip at the acute phase (3 h) after infection with Gram-negative (V. anguillarum) and Gram-positive (M. luteus) bacteria. A second strong response of PyTollip expression was observed 24 h after challenge with V. anguillarum. Collectively, these results provide novel insights into the specific role and response of Tollip and TLR signaling pathways in host immune responses against different bacterial pathogens in bivalves.

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Extracytoplasmic function (ECF) σ factors respond to environmental stresses and regulate numerous genes required for adaptation. Under normal growth conditions, the ECF σ factors are sequestered by transmembrane anti-σ factor proteins, from which they are released under stress conditions. In Bacillus subtilis ugtP null mutant cells, which lack glucolipids, three of the seven ECF σ factors, σ^M, σ^V and σ^X, are activated. The Escherichia coli cell membrane does not contain glucolipids. When the genes for these three ECF σ and anti-σ factors were introduced into E. coli cells, expression of lacZ fused to the ECF σ factor-regulated promoters indicated ECF σ factor activity. Additional expression of the ugtP gene in these E. coli cells led to the synthesis of small amounts of glucolipids, and the activities of σ^M and σ^V were repressed, but the activity of σ^X was unaffected. It is likely that glucolipids directly influence anti-σ^M and anti-σ^V factors by stabilizing conformations that sequester the respective ECF σ factors.

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Introgression between related species with different ploidy levels has played important roles in wheat subspecies differentiation. Persian wheat, a cultivated tetraploid wheat subspecies (Triticum turgidum subsp. carthlicum), is postulated to have evolved through interploidy hybridization between tetraploid and hexaploid wheats. Here, we report evidence for the origin of subsp. carthlicum based on the discovery of a new allele for the 5th-to-6th exon region of the Wknox1bKNOTTED1-type homeobox gene in a common wheat subspecies (T. aestivum subsp. carthlicoides). In this Wknox1b region, subsp. carthlicoides contains an inverted duplication mutation in the 3’ flanking region of a 157-bp MITE insertion site. This structural mutation resulted in the suppression of Wknox1b expression in subsp. carthlicoides, but no structural mutation was observed in the same region of subsp. carthlicum. In addition, the carthlicum allele for the Wknox1b 5th-to-6th exon region exhibited the same sequence as that in the wild emmer wheat subsp. dicoccoides. These observations support an alternative hypothesis that subsp. carthlicum evolved by interploidy hybridization between subsp. carthlicoides and tetraploid wheat.

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