Katsuhiko Takata

Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species

BackgroundThe 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.ResultsThe 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.ConclusionThe 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.

Anatomical features that facilitate radial flow across growth rings and from xylem to cambium in Cryptomeria japonica

BACKGROUND AND AIMS Although the lateral movement of water and gas in tree stems is an important issue for understanding tree physiology, as well as for the development of wood preservation technologies, little is known about the vascular pathways for radial flow. The aim of the current study was to understand the occurrence and the structure of anatomical features of sugi (Cryptomeria japonica) wood including the tracheid networks, and area fractions of intertracheary pits, tangential walls of ray cells and radial intercellular spaces that may be related to the radial permeability (conductivity) of the xylem. METHODS Wood structure was investigated by light microscopy and scanning electron microscopy of traditional wood anatomical preparations and by a new method of exposed tangential faces of growth-ring boundaries. KEY RESULTS Radial wall pitting and radial grain in earlywood and tangential wall pitting in latewood provide a direct connection between subsequent tangential layers of tracheids. Bordered pit pairs occur frequently between earlywood and latewood tracheids on both sides of a growth-ring boundary. In the tangential face of the xylem at the interface with the cambium, the area fraction of intertracheary pit membranes is similar to that of rays (2.8 % and 2.9 %, respectively). The intercellular spaces of rays are continuous across growth-ring boundaries. In the samples, the mean cross-sectional area of individual radial intercellular spaces was 1.2 microm(2) and their total volume was 0.06 % of that of the xylem and 2.07 % of the volume of rays. CONCLUSIONS A tracheid network can provide lateral apoplastic transport of substances in the secondary xylem of sugi. The intertracheid pits in growth-ring boundaries can be considered an important pathway, distinct from that of the rays, for transport of water across growth rings and from xylem to cambium.

Growth and wood quality of sugi (Cryptomeria japonica) planted in Akita prefecture (II). Juvenile/mature wood determination of aged trees

Variations of certain anatomical and mechanical indices within tree stems of aged sugi (Cryptomeria japonica) trees planted in Akita prefecture were studied. The determination of the juvenile/mature wood boundary was also discussed, and the effects of wood structure on mechanical properties were investigated. On the basis of radial and vertical variation of the anatomical and mechanical indices, modulus of elasticity (MOE)/ shear modulus (G) was chosen as the index for determining the juvenile/mature wood boundary. The increase rates of MOE/G at the points of 1%, 2%, and 3% were discussed. It was found that for aged trees, all three points were thought to be effective for dividing juvenile and mature wood. However, for younger trees, the point of 2% was recommended, which was mostly consistent with the result obtained by the increase rate of 1% for tracheid length (TL). Among mechanical properties, the MOE showed more significant juvenile/mature wood differences than did modulus of rupture (MOR) and σ. By correlation analysis, it was suggested that microfibril angle largely contributed to the indices of MOE and G, and specific gravity largely contributed to the indices of MOR and σ.

ANATOMICAL CHARACTERISTICS AND MECHANICAL PROPERTIES OF LARIX SIBIRICA GROWN IN SOUTH-CENTRAL SIBERIA

Tracheid length, microfibril angle, spiral grain, wood density, MOE, MOR, compressive strength, modulus of rigidity and their inter-relationships were investigated for fifty Siberian larch trees (Larix sibirica) collected from five natural stands. No inter-stand variation in tracheid length, microfibril angle and spiral grain was observed. No effect of tracheid length and microfibril angle on the mechanical properties was observed. Inter-stand variation in wood density was significant, especially for mature wood. The wood from the Baikal site in the eastern range of the natural distribution had a very high density. The wood from the Altai site in the mountain range had a low density, especially within the latewood. Minimum density within a ring seemed to be the major source of variation for average density within the heartwood, whereas the effect of maximum density on average density was greater within the sapwood. Wood density, which was much higher for a given ring width than in plantation-grown Japanese larch (Larix kaempferi), had a major effect on the mechanical properties.

Detection of intra- and interspecific variation of the dry rot fungus Serpula lacrymans by PCR-RFLP and RAPD analysis

We investigated a genotype-based assay to discriminate the dry rot fungi Serpula lacrymans. DNAs were extracted from 74 isolates from the northern half of Japan, and internal transcribed spacers (ITS) were amplified by polymerase chain reaction. Genotypes of isolates were checked by restriction fragment length polymorphism (RFLP) using two enzymes, Taq I and Hha I. Among the 74 isolates identified as S. lacrymans in terms of morphologic features, 5 isolates were shown to have been misidentified. Random amplified polymorphic DNA (RAPD) analysis was conducted in order to detect the intraspecific diversity of S. lacrymans isolated in Japan. Because no relation between geographical origin and genetic distances was observed, the intraspecific diversity of S. lacrymans is suggested to be small.

Isolation and characterization of microsatellite markers from Robinia pseudoacacia L.

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.

Quantitative comparisons of antitermite extractives in heartwood from the same clones of Cryptomeria japonica planted at two different sites

The quantities of some extractives in the heartwood of 25 plus tree clones of Japanese cedar (Cryptomeria japonica) from two different sites were investigated to clarify the differences in antitermite properties in relation to clones and environmental factors. The measured compounds were cubebol, epicubebol, sandaracopimarinol, and ferruginol. The total amounts of extractives were calculated from gas chromatogram peak areas. The heartwoods from Tano (Tano Forest Research Station, Miyazaki University; 31° N, 131° E, 130 m asl) tended to contain more of the individual extractives and total extractives than those from Komenono (Komenono Forest Research Station, Ehime University; 33° N, 132° E, 700 m asl). There was a significant difference (calculated by analysis of variance) at the 1% level among clones at both sites in quantities of total and individual extractives. This result suggests that the qualities and quantities of heartwood extractives are largely affected by genetic factors. Spearman’s rank correlation with the average of the extractive quantities at the sites was investigated. The correlation coefficients of total extractives, cubebol, epicubebol, sandaracopimarinol, and ferruginol were 0.61, 0.85, 0.76, 0.67, and 0.74, respectively. This result means that the order of the amounts of these compounds among the cultivars could be maintained at different sites. It is apparent that both environmental and genetic factors affected the quantities of these extractives in the heartwoods of Japanese cedar.

Effects of Competitive and Cooperative Interaction among Neighboring Trees on Tree Growth in a Naturally Regenerated Even-aged Larix sibirica Stand in Considering Height Stratification

This study attempted to explain the variation in growth of individual trees in a naturally regenerated, even-agedLarix sibirica stand using indices that represented the competitive and cooperative interactions among neighboring trees. These interaction indices and DBH were used in stepwise multiple regression procedures to model the growth of individual trees. However, when the data from all trees were used, DBH was the only factor accepted in the growth model. Since DBH can be influenced by the cumulative effect of past interaction and other environmental factors, we stratified the stand into three height strata and repeated the stepwise procedure for each stratum to remove the cumulative effect represented by DBH. Several competition and/or cooperation indices were accepted in growth models of the lower, middle and upper strata. In each stratum, the residual mean square of the growth model was smaller than that of all strata. These facts suggested that height stratification was generally successful in reducing the cumulative effect of past interaction and other factors. The cooperation indices that suggested protection from wind stress by neighboring trees was a significant variable in the growth models of all three strata. This demonstrated that cooperative interaction should be considered in the explanation of variation in tree growth in dry and windy climates such as the present study region.

Application of the Fourier analysis to determine the demarcation between juvenile and mature wood

Juvenile wood produced in the crown has features that distinguish it from the older, more mature wood of the bole. Juvenile wood has important wood quality attributes because, depending on the species, it can have lower density and has shorter tracheids, thin-walled cells, larger fibrial angles, high – more than 10% – lignin and hemicellulose content, and a slightly lower cellulose content than mature wood. Wood juvenility can be established by examining a number of different physical or chemical properties. Juvenile wood is not desirable for solid wood products because of warpage during drying, low strength properties, and other factors considered critical for producing high-stiffness veneer. Fourier transformation is an extremely useful mathematical tool that has been applied in the quantitative analysis of many physical processes. Fourier transformation can be represented as a series of sine and cosine functions. Density spectra derived from X-ray imaging provide new information in the nondestructive testing of wood. Until recently, testing for wood juvenility required wood samples to be milled, dissolved in acids, and painstakingly analyzed for certain anatomical features. The new method proposed in this report opens a new possibility for minimizing the time required to analyze wood formation. The main purpose of this report is thus to demonstrate how to distinguish juvenile wood from mature wood by Fourier analysis of density distribution curves. It is also the first study to employ Fourier analysis-assisted assays of the boundary line between juvenile and mature wood.

Isolation and Characterization of 22 EST-SSR Markers for the Genus Thujopsis (Cupressaceae)

Premise of the study: Expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed from Thujopsis dolabrata var. hondae (Cupressaceae) using Illumina sequencing to investigate the genetic diversity and population structure of the genus Thujopsis. Methods and Results: Twenty-two primer pairs were developed from ESTs of T. dolabrata var. hondae. The primers amplified di- and trinucleotide repeat-containing sequences. Polymorphisms were assessed in 81 individuals from two T. dolabrata var. hondae populations and one T. dolabrata population. The number of alleles ranged from one to 17 per locus. The observed and expected heterozygosities ranged from 0.000 to 1.000 and from 0.000 to 0.926, respectively. Conclusions: These new EST-SSR markers will be useful in analyses of the genetic diversity and population structure of the genus Thujopsis.