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1.  Isolation and characterization of 22 EST-SSR markers for the genus Thujopsis (Cupressaceae)1 
Applications in Plant Sciences  2015;3(2):apps.1400101.
• 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.
PMCID: PMC4332144
Cupressaceae; expressed sequence tag; microsatellite; next-generation sequencing; Thujopsis
2.  Anatomical features that facilitate radial flow across growth rings and from xylem to cambium in Cryptomeria japonica 
Annals of Botany  2009;103(7):1145-1157.
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.
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 µm2 and their total volume was 0·06 % of that of the xylem and 2·07 % of the volume of rays.
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.
PMCID: PMC2707907  PMID: 19258338
Cryptomeria japonica; bordered pit; intercellular spaces; lateral transport; tracheid network; water conduction; xylem permeability
3.  A frameshift mutation of the chloroplast matK coding region is associated with chlorophyll deficiency in the Cryptomeria japonica virescent mutant Wogon-Sugi 
Current Genetics  2009;55(3):311-321.
Wogon-Sugi has been reported as a cytoplasmically inherited virescent mutant selected from a horticultural variety of Cryptomeria japonica. Although previous studies of plastid structure and inheritance indicated that at least some mutations are encoded by the chloroplast genome, the causative gene responsible for the primary chlorophyll deficiency in Wogon-Sugi, has not been identified. In this study, we identified this gene by genomic sequencing of chloroplast DNA and genetic analysis. Chloroplast DNA sequencing of 16 wild-type and 16 Wogon-Sugi plants showed a 19-bp insertional sequence in the matK coding region in the Wogon-Sugi. This insertion disrupted the matK reading frame. Although an indel mutation in the ycf1 and ycf2 coding region was detected in Wogon-Sugi, sequence variations similar to that of Wogon-Sugi were also detected in several wild-type lines, and they maintained the reading frame. Genetic analysis of the 19 bp insertional mutation in the matK coding region showed that it was found only in the chlorophyll-deficient sector of 125 full-sibling seedlings. Therefore, the 19-bp insertion in the matK coding region is the most likely candidate at present for a mutation underlying the Wogon-Sugi phenotype.
Electronic supplementary material
The online version of this article (doi:10.1007/s00294-009-0247-9) contains supplementary material, which is available to authorized users.
PMCID: PMC2691868  PMID: 19449186
Cryptomeria japonica; Wogon-Sugi; Virescent mutant; matK gene; Frameshift mutation
4.  Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species 
BMC Plant Biology  2008;8:70.
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.
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.
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.
PMCID: PMC2443145  PMID: 18570682

Results 1-4 (4)