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Abstract Background The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms. Results The C. japonica cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (trnI-CAU, trnQ-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the C. japonica cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as Cycas and Gingko, and additionally has completely lost its trnR-CCG, partially lost its trnT-GGU, and shows diversification of accD. The genomic structure of the C. japonica cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the Pinus thunbergii cp genome into that of C. japonica. In the C. japonica cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements. Conclusion The observed differences in genomic structure between C. japonica and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the C. japonica cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome.

Key message: Complete differentiation of the first earlywood vessels occurred earlier in upper regions of stems than in middle and lower regions when buds swelling in a ring-porous hardwood Quercus serrata seedlings.Abstract: In deciduous ring-porous hardwoods, the timing of the onset of conduction of water via the networks of the current year’s earlywood vessels is very important for the growth of buds and shoots because the main pathways for conduction of water are the networks of the current year’s earlywood vessels. The purpose of this study was to visualize the formation of the networks of first earlywood vessels in the current year’s xylem of seedlings of the deciduous ring-porous hardwood Quercus serrata. We monitored the distribution of water in the current and the previous year’s secondary xylem at the cellular level in upper, middle and lower regions of stems during the formation of earlywood vessels by cryo-scanning electron microscopy after freeze-etching. We also examined how changes in water distribution were correlated with leaf phenology. The contents of the first vessel elements in the upper region of the stem changed from cytoplasm-rich to water earlier than those in middle and lower regions of the stem when buds were increasing in size. At bud break, vessel elements were filled with water throughout the entire stem. When the cambium was dormant and during formation of earlywood vessels, the previous year’s latewood vessels were filled with water. Our results showed that complete differentiation of vessel elements occurred earlier in upper regions of stems than in middle and lower regions. Moreover, the functional networks of the previous year’s latewood vessels appeared to be involved in supplying water to new networks of earlywood vessels in the current year’s xylem. [ABSTRACT FROM AUTHOR]

Background: The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms. Results: The C. japonica cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (trnI-CAU, trnQ-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the C. japonica cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as Cycas and Gingko, and additionally has completely lost its trnR-CCG, partially lost its trnT-GGU, and shows diversification of accD. The genomic structure of the C. japonica cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the Pinus thunbergii cp genome into that of C. japonica. In the C. japonica cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements. Conclusion: The observed differences in genomic structure between C. japonica and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the C. japonica cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome. [ABSTRACT FROM AUTHOR]

Microsatellite markers were isolated from Robinia pseudoacacia L. using an enrichment method. Eleven of the 23 primer pairs designed successfully amplified unambiguous and polymorphic single loci among 39 individual R. pseudoacacia L. from northeastern Japan. The observed and expected heterozygosities of the 11 microsatellite markers ranged from 0.333 to 0.821 and from 0.489 to 0.867, respectively. The polymorphisms observed at the 11 microsatellite loci are useful genetic data for forest ecological studies involving R. pseudoacacia L. [ABSTRACT FROM AUTHOR]

Managing uncertainty is the way to secure stability of the supply chain. Uncertainty within chipping operation and chip transportation causes production loss. In the wood chip supply chain for bioenergy, operational uncertainty mainly appears in the moisture content of the material, chipping productivity, and the interval of truck arrival. This study theoretically quantified the loss in wood chip production by applying queuing theory and stochastic modelling. As well as the loss in production, the inefficiency was identified as the idling time of chipper and the queuing time of trucks. The aim of this study is to quantify the influence of three uncertainties on wood chip production. This study simulated the daily chip production using a mobile chipper by applying queuing theory and stochastic modelling of three uncertainties. The result was compared with the result of deterministic simulation which did not consider uncertainty. Uncertainty reduced the production by 14% to 27% compared to the production of deterministic simulation. There were trucks scheduled but not used. The cases using small trucks show the largest daily production amount, but their lead time was the longest. The large truck was sensitive to the moisture content of material because of the balance between payload and volumetric capacity. This simulation method can present a possible loss in production amount and enables to evaluate some ways for the loss compensation quantitatively such as outsourcing or storing buffer. For further development, the data about the interval of truck arrival should be collected from fields and analyzed. We must include the other uncertainties causing technical and operator delays. [ABSTRACT FROM AUTHOR]