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4. In situ three-dimensional visualization of Bursaphelenchus xylophilus inoculated in Pinus thunbergii using X-ray micro-computed tomography.

Author

Nakajima, Gou, Iki, Taiichi, Aikawa, Takuya, Hara, Takumi, Ito, Eisuke, and Nakamura, Katsunori

Subjects
*PINEWOOD nematode, *THREE-dimensional imaging, *CONIFER wilt, *PINE, *TOMOGRAPHY, *X-ray computed microtomography
Abstract

Pine wilt disease, a devastating infectious disease of pine trees, is caused by the pinewood nematode, Bursaphelenchus xylophilus. It is important to understand the spatial dispersal processes of B. xylophilus within host-tree tissues to assess its pathogenic mechanism. However, this is not feasible with conventional microscopy-imaging techniques. In this study, we showed that X-ray micro-computed tomography (micro-CT) imaging can be a powerful tool for visualizing infected nematodes within host-tree tissues. We visualized 161 nematodes and 11 eggs within a Pinus thunbergii stem section, 47.3 mm3 in volume, using an appropriate segmentation of the micro-CT images. Quantitative measurements of the segmented region corresponding to the nematodes allowed for the calculation of the longitudinal length and a-value, which were similar to previous morphological descriptions of B. xylophilus. The technique adopted in this study can aid in understanding the behavior of and obtaining quantitative information on B. xylophilus within tree tissues. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions

Author

Nose Mine, Hanaoka So, Fukatsu Eitaro, Kurita Manabu, Miura Masahiro, Hiraoka Yuichiro, Iki Taiichi, Chigira Osamu, Mishima Kentaro, Takahashi Makoto, Watanabe Atsushi, Nose Mine, Hanaoka So, Fukatsu Eitaro, Kurita Manabu, Miura Masahiro, Hiraoka Yuichiro, Iki Taiichi, Chigira Osamu, Mishima Kentaro, Takahashi Makoto, and Watanabe Atsushi

Published
2023

10. Haplotype-resolved de novogenome assemblies of four coniferous tree species

Author

Shirasawa, Kenta, Mishima, Kentaro, Hirakawa, Hideki, Hirao, Tomonori, Tsubomura, Miyoko, Nagano, Soichiro, Iki, Taiichi, Isobe, Sachiko, and Takahashi, Makoto

Abstract

ABSTRACTConiferous trees in gymnosperm are an important source of wood production. Because of their long lifecycle, the breeding programs of coniferous tree are time- and labor-consuming. Genomics could accelerate the selection of superior trees or clones in the breeding programs; however, the genomes of coniferous trees are generally giant in size and exhibit high heterozygosity. Therefore, the generation of long contiguous genome assemblies of coniferous species has been difficult. In this study, we employed high-fidelity (HiFi) long-read sequencing technology to sequence and assemble the genomes of four coniferous tree species, Larix kaempferi, Chamaecyparis obtusa, Cryptomeria japonica, and Cunninghamia lanceolata. Genome assemblies of the four species totaled 13.5 Gb (L. kaempferi), 8.5 Gb (C. obtusa), 9.2 Gb (C. japonica), and 11.7 Gb (C. lanceolata), which covered 99.6% of the estimated genome sizes on average. The contig N50 value, which indicates assembly contiguity, ranged from 1.2 Mb in C. obtusato 16.0 Mb in L. kaempferi, and the assembled sequences contained, on average, 89.2% of the single-copy orthologs conserved in embryophytes. Assembled sequences representing alternative haplotypes covered 70.3–95.1% of the genomes, suggesting that the four coniferous tree genomes exhibit high heterozygosity levels. The genome sequence information obtained in this study represents a milestone in tree genetics and genomics, and will facilitate gene discovery, allele mining, phylogenetics, and evolutionary studies in coniferous trees, and accelerate forest tree breeding programs.

Published
2024
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11. Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions

Author

Nose, Mine, primary, Hanaoka, So, additional, Fukatsu, Eitaro, additional, Kurita, Manabu, additional, Miura, Masahiro, additional, Hiraoka, Yuichiro, additional, Iki, Taiichi, additional, Chigira, Osamu, additional, Mishima, Kentaro, additional, Takahashi, Makoto, additional, and Watanabe, Atsushi, additional

Published
2023
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15. Additional file 9 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Author

Mishima, Kentaro, Hirakawa, Hideki, Iki, Taiichi, Fukuda, Yoko, Hirao, Tomonori, Tamura, Akira, and Takahashi, Makoto

Abstract

Additional file 9. Alignment of known CONSTANS genes and a set of other angiosperm and gymnosperm sequences. Japanese larch open reading frames are shown in green. Kuril larch open reading frames are shown in blue.

Published
2022
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16. Additional file 8 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Author

Mishima, Kentaro, Hirakawa, Hideki, Iki, Taiichi, Fukuda, Yoko, Hirao, Tomonori, Tamura, Akira, and Takahashi, Makoto

Abstract

Additional file 8. Alignment of known FT/FT-like and MFT genes and a set of other angiosperm and gymnosperm sequences. Japanese larch open reading frames are shown in green. Kuril larch open reading frames are shown in blue.

Published
2022
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17. Additional file 5 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Author

Mishima, Kentaro, Hirakawa, Hideki, Iki, Taiichi, Fukuda, Yoko, Hirao, Tomonori, Tamura, Akira, and Takahashi, Makoto

Abstract

Additional file 5. Number of open reading frames (ORFs) similar to NCBI sequeces and other species according to BLASTp E-value cutoff values. a) ORFs obtained from Japanese larch, b) ORFs obtained from ORF Kuril larch.

Published
2022
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19. Additional file 2 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Author

Mishima, Kentaro, Hirakawa, Hideki, Iki, Taiichi, Fukuda, Yoko, Hirao, Tomonori, Tamura, Akira, and Takahashi, Makoto

Abstract

Additional file 2. Gene ontology (GO) categories in biological process (BP) that encoded proteins with sequence similarity (E-value ≤ 1e-10) in the NCBI database. a) Japanese larch, b) Kuril larch. Gene ontology (GO) categories in cellular component (CC) that encoded proteins with sequence similarity (E-value ≤ 1e-10) in the NCBI database. a) Japanese larch, b) Kuril larch. Gene ontology (GO) categories in molecular function (MF) that encoded proteins with sequence similarity (E-value ≤ 1e-10) in the NCBI database. a) Japanese larch, b) Kuril larch.

Published
2022
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20. Additional file 6 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Author

Mishima, Kentaro, Hirakawa, Hideki, Iki, Taiichi, Fukuda, Yoko, Hirao, Tomonori, Tamura, Akira, and Takahashi, Makoto

Abstract

Additional file 6. Alignment of known MADS-box genes and a set of other angiosperm and gymnosperm sequences. Japanese larch open reading frames are shown in green. Kuril larch open reading frames are shown in blue.

Published
2022
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21. Additional file 7 of Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica)

Author

Mishima, Kentaro, Hirakawa, Hideki, Iki, Taiichi, Fukuda, Yoko, Hirao, Tomonori, Tamura, Akira, and Takahashi, Makoto

Abstract

Additional file 7. Alignment of known LEAFY and NEEDLY genes and a set of other angiosperm and gymnosperm sequences. Japanese larch open reading frames are shown in green. Kuril larch open reading frames are shown in blue.

Published
2022
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24. Inheritance of the wood properties of the Japanese red pine (Pinus densiflora Siebold et Zucc.) from the open-pollinated families selected as resistance to the pine wood nematode

Author

Ishiguri, Futoshi, primary, Nezu, Ikumi, additional, Endo, Ryota, additional, Kobayashi, Saki, additional, Ngadianto, Agus, additional, Narusawa, Daigo, additional, Takahashi, Yusuke, additional, Tanabe, Jun, additional, Iki, Taiichi, additional, Ohshima, Jyunichi, additional, and Yokota, Shinso, additional

Published
2021
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25. Clonal variations and effects of juvenile wood on lumber quality in Japanese larch.

Author

Tumenjargal, Bayasaa, Ishiguri, Futoshi, Iki, Taiichi, Takahashi, Yusuke, Nezu, Ikumi, Otsuka, Kouhei, Ohshima, Jyunichi, and Yokota, Shinso

Subjects
WOOD, LUMBER, ELASTIC modulus, WOOD quality, HARDWOODS, WOOD density, YOUNG'S modulus, FLEXURAL strength
Abstract

Wood properties, including Young's modulus, differ among clones in Larix kaempferi; however, available information is still limited on among-clonal variations of lumber qualities in L. kaempferi. The objectives of this study were to clarify the clonal variations in lumber quality and to identify the effects of juvenile wood on lumber quality in L. kaempferi. A total of 21 logs of 2.5 m in length were obtained from the trees of nine different plus clones of 57-year-old L. kaempferi trees. The logs were sawn into lumber, and the lumber was kiln-dried and planed into 38 × 89 mm in a cross-section. Lumber quality, such as bending properties, was determined. Significant differences were found in wood density, dynamic Young's modulus, modulus of elasticity, and modulus of rupture of the lumber among the nine clones. The highest repeatability was recorded in wood density. The lumber consisting of juvenile wood showed a lower lumber quality compared to the lumber consisting of mature wood. To produce lumber with a high quality from L. kaempferi, the clonal variation of lumber quality and the existence of juvenile wood should be considered. [ABSTRACT FROM AUTHOR]

Published
2022
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27. Do Seedlings Derived from Pinewood Nematode-Resistant Pinus thunbergii Parl. Clones Selected in Southwestern Region Perform Well in Northern Regions in Japan? Inferences from Nursery Inoculation Tests

Author

Matsunaga, Koji, primary, Iki, Taiichi, additional, Hirao, Tomonori, additional, Ohira, Mineko, additional, Yamanobe, Taro, additional, Iwaizumi, Masakazu G., additional, Miura, Masahiro, additional, Isoda, Keiya, additional, Kurita, Manabu, additional, Takahashi, Makoto, additional, and Watanabe, Atsushi, additional

Published
2020
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28. Effects of Temperature Factors on Resistance against Pine Wood Nematodes in Pinus thunbergii, Based on Multiple Location Sites Nematode Inoculation Tests

Author

Iki, Taiichi, primary, Matsunaga, Koji, additional, Hirao, Tomonori, additional, Ohira, Mineko, additional, Yamanobe, Taro, additional, Iwaizumi, Masakazu G, additional, Miura, Masahiro, additional, Isoda, Keiya, additional, Kurita, Manabu, additional, Takahashi, Makoto, additional, and Watanabe, Atsushi, additional

Published
2020
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29. SNP Genotyping with Target Amplicon Sequencing Using a Multiplexed Primer Panel and Its Application to Genomic Prediction in Japanese Cedar, Cryptomeria japonica (L.f.) D.Don

Author

Nagano, Soichiro, primary, Hirao, Tomonori, additional, Takashima, Yuya, additional, Matsushita, Michinari, additional, Mishima, Kentaro, additional, Takahashi, Makoto, additional, Iki, Taiichi, additional, Ishiguri, Futoshi, additional, and Hiraoka, Yuichiro, additional

Published
2020
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32. Effects of day length- and temperature-regulated genes on annual transcriptome dynamics in Japanese cedar (Cryptomeria japonica D. Don), a gymnosperm indeterminate species

Author

Nose, Mine, primary, Kurita, Manabu, additional, Tamura, Miho, additional, Matsushita, Michinari, additional, Hiraoka, Yuichiro, additional, Iki, Taiichi, additional, Hanaoka, So, additional, Mishima, Kentaro, additional, Tsubomura, Miyoko, additional, and Watanabe, Atsushi, additional

Published
2020
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38. Geographical cline and inter‐seaside difference in cone characteristics related to climatic conditions of old planted Pinus thunbergii populations throughout Japan.

Author

Iwaizumi, Masakazu G., Matsunaga, Koji, Iki, Taiichi, Yamanobe, Taro, Hirao, Tomonori, and Watanabe, Atsushi

Subjects
CONES, BIOLOGICAL fitness, PINE, ANALYSIS of covariance, SEED size
Abstract

Although cone morphology has been mainly utilized for taxonomy or forestry purposes, characterization of the environmental factors that influence its variation is still insufficient. Major conifers distributed over diverse climatic conditions like the Japanese archipelago could show cone morphology variation among populations related to large differences in key influential factors such as temperature, snow, irradiance and sunshine. Geographical variation in cone characteristics (cone size, seed production, seed productivity per cone and seed size) was examined across the species distribution in 24 old planted Pinus thunbergii populations (479 trees) along two major seasides in Japan (Pacific Ocean side and Japan Sea side). Variance components of cone characteristics explained by seaside were at similar levels to those for populations nested within seasides. Populations on the Japan Sea side produced cones that had larger size (length and width), higher seed production (number of filled seeds per cone and seed mass per cone) and seed productivity per cone (seed‐to‐ovule ratio). Analysis of covariance showed that significant latitudinal clines observed in cone size and seed productivity per cone were mostly a result of inter‐seaside differences. Linear mixed model analysis detected that geographical variation in cone size, seed production and seed productivity per cone in the populations were affected significantly by low temperature, more snow, less solar irradiance and less sunshine time. Large cone sizes and high seed productivity per cone found in the populations on the Japan Sea side could be explained by a genetic or plastic response to maintain reproductive success. [ABSTRACT FROM AUTHOR]

Published
2021
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39. Inheritance of static bending properties and classification of load-deflection curves in Cryptomeria japonica.

Author

Takahashi, Yusuke, Ishiguri, Futoshi, Aiso, Haruna, Takashima, Yuya, Hiraoka, Yuichiro, Iki, Taiichi, Ohshima, Jyunichi, Iizuka, Kazuya, and Yokota, Shinso

Subjects
CRYPTOMERIA japonica, ELASTICITY, FLEXURAL strength, PRINCIPAL components analysis, ELASTIC modulus
Abstract

To clarify inheritance of static bending properties in relation to elastic and plastic regions, air-dry density, microfibril angle of the S2 layer in latewood tracheid (MFA), and static bending properties (modulus of elasticity [MOE], modulus of rupture [MOR] and bending work) were examined for juvenile wood of 18 full-sib families in 20-year-old Cryptomeria japonica. Heritability of all traits ranged from 0.12 (bending work) to 0.51 (air-dry density). Based on the results from principal component analysis (PCA) and cluster analysis, the families were classified into four groups with different types of load-deflection curves, suggesting that both elastic properties and deflection in plastic region differed among families. Furthermore, families included in a group were produced from specific parents, suggesting that deflection in plastic region as well as elastic property is inheritable. It can be concluded that mating parents may affect elasticity and plasticity of offspring. [ABSTRACT FROM AUTHOR]

Published
2021
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42. Wood properties of Larix sibirica naturally grown in Tosontsengel, Mongolia

Author

Ishiguri, Futoshi, primary, Tumenjargal, Bayasaa, additional, Baasan, Bayartsetseg, additional, Jigjjav, Ayursed, additional, Pertiwi, Yus Andhini Bhekti, additional, Aiso-Sanada, Haruna, additional, Takashima, Yuya, additional, Iki, Taiichi, additional, Ohshima, Jyunichi, additional, Iizuka, Kazuya, additional, and Yokota, Shinso, additional

Published
2018
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43. Inheritance of the wood properties of the Japanese red pine (Pinus densifloraSiebold et Zucc.) from the open-pollinated families selected as resistance to the pine wood nematode

Author

Ishiguri, Futoshi, Nezu, Ikumi, Endo, Ryota, Kobayashi, Saki, Ngadianto, Agus, Narusawa, Daigo, Takahashi, Yusuke, Tanabe, Jun, Iki, Taiichi, Ohshima, Jyunichi, and Yokota, Shinso

Abstract

Pine wilt disease is one of the most serious tree diseases occurring worldwide. Clones of Pinus densifloraSiebold et Zucc with pine wood nematode resistance were selected. In addition to resistance, wood quality is also an important criterion in the breeding program of P. densiflorabecause of its use as construction lumber. However, little information is available on the wood qualities of the progenies of resistant clones. The repeatabilities of the wood properties were investigated for 11 open-pollinated families of P. densifloraselected for their pine wood nematode resistance. Oven-dry density, latewood tracheid length, the microfibril angle (MFA) of the S2 layer in latewood tracheids, modulus of elasticity (MOE), and modulus of rupture (MOR) were measured in the third or fourth annual ring from the pith. No significant correlations were found between the wood properties and the stem diameter or tree height. However, significant correlations were found between oven-dry density and MOE or MOR, which suggests that oven-dry density is a good indicator for selecting wood with higher bending properties. Among the measured wood properties, oven-dry density had the highest repeatability (R=0.47), followed by MOR (R=0.33), tracheid length (R=0.21), and MFA (R=0.14). MOE had the lowest value (R=0.01). The 11 families examined were classified into three groups according to their growth characteristics, wood properties, and resistance to pine wilt disease. On the basis of the results, we conclude that genetic improvement of wood properties especially for wood density and MOR is possible for the resistant P. densiflora.

Published
2021
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48. Spatial and temporal distribution of Bursaphelenchus xylophilusinoculated in grafts of a resistant clone of Pinus thunbergii

Author

Nakajima, Gou, Iki, Taiichi, Yamanobe, Taro, Nakamura, Katsunori, and Aikawa, Takuya

Abstract

ABSTRACTPreventive plantation of resistant Pinus thunbergiiseedlings is anticipated in non-epidemic areas of pine wilt disease (PWD) in Japan. The scions of resistant clones, which are required to establish a seed orchard for the production of resistant seedlings, might harbor Bursaphelenchus xylophilus(a pathogen of PWD), as they are grown in epidemic areas and artificially inoculated with B. xylophilusto verify their resistance. In this study, we analyzed within-tree distribution of B. xylophilusin inoculated grafts of a resistant P. thunbergiiclone, Yuza-155, at two different times, 7 and 19 months after inoculation. Experimental evidence using both direct extraction of nematodes and a DNA-based detection technique demonstrated that the migration and propagation of inoculated nematodes were restricted mostly within the scion stems and rootstocks. In branch samples, nematodes were detected less frequently by the DNA-based method and no live nematodes were extracted at 7 months after inoculation, whereas at 19 months after inoculation, neither of the methods detected any nematodes. Thus, the probability that the current-year shoots of this resistant clone, Yuza-155, which initiated plant growth in the season following inoculation, are infected with B. xylophilusis quite low. Therefore, they may serve as pathogen-free scions for propagation of ramets of resistant P. thunbergiiclones and construction of seed orchards in PWD non-epidemic locations.

Published
2019
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50. Demonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica

Author

Uchiyama, Kentaro, primary, Iwata, Hiroyoshi, additional, Moriguchi, Yoshinari, additional, Ujino-Ihara, Tokuko, additional, Ueno, Saneyoshi, additional, Taguchi, Yuriko, additional, Tsubomura, Miyoko, additional, Mishima, Kentaro, additional, Iki, Taiichi, additional, Watanabe, Atsushi, additional, Futamura, Norihiro, additional, Shinohara, Kenji, additional, and Tsumura, Yoshihiko, additional

Published
2013
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