Leaf phenology and properties are the vital traits of productivity and fitness of individual trees. Understanding the climatic conditions associated with the trait variation is essential for evalua...
{"title":"Climate-related variation in leaf size and phenology of Betula ermanii in multiple common gardens","authors":"Takaki Aihara, Kyoko Araki, Ragini Sarmah, Yihan Cai, Aye Myat Myat Paing, Susumu Goto, Yoko Hisamoto, Haruhiko Taneda, Nobuhiro Tomaru, Kosuke Homma, Masahiro Takagi, Toshiya Yoshida, Atsuhiro Iio, Dai Nagamatsu, Hajime Kobayashi, Mitsuru Hirota, Yoshihiko Tsumura","doi":"10.1080/13416979.2023.2289731","DOIUrl":"https://doi.org/10.1080/13416979.2023.2289731","url":null,"abstract":"Leaf phenology and properties are the vital traits of productivity and fitness of individual trees. Understanding the climatic conditions associated with the trait variation is essential for evalua...","PeriodicalId":15839,"journal":{"name":"Journal of Forest Research","volume":"28 8","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138509998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Scolytus esuriens is a vector of Dutch elm disease (DED) in Japan. However, small holes that were presumed to be irruption or flight holes of bark beetle species other than S. esuriens were observe...
荷兰榆树病(Dutch elm disease, DED)是日本的一种病媒。然而，观察到的小洞被认为是除s.s esuriens以外的树皮甲虫种类的入侵或飞行孔。
{"title":"New vectors: Scolytus chikisanii and S. japonicus (Scolytidae) associated with Dutch elm disease in Hokkaido, Japan","authors":"Takatoshi Yamaki, Toshizumi Miyamoto, Hayato Masuya, Satoshi Urabe, Hideyuki Saito, Masato Shibuya","doi":"10.1080/13416979.2023.2286040","DOIUrl":"https://doi.org/10.1080/13416979.2023.2286040","url":null,"abstract":"Scolytus esuriens is a vector of Dutch elm disease (DED) in Japan. However, small holes that were presumed to be irruption or flight holes of bark beetle species other than S. esuriens were observe...","PeriodicalId":15839,"journal":{"name":"Journal of Forest Research","volume":"42 21","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138509975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ozone is an atmospheric pollutant that adversely affects woody species, causing impaired stomatal control known as stomatal sluggishness. Stomatal sluggishness may affect stomatal ozone uptake beca...
{"title":"Effects of ozone on stomatal ozone uptake in leaves of Fagus crenata seedlings grown under different CO2 concentrations","authors":"Yuqing Lyu, Ryo Ariura, Jing Li, Misako Matsumoto, Takuro Aoki, Yoshiyuki Kinose, Masahiro Yamaguchi, Takeshi Izuta, Makoto Watanabe","doi":"10.1080/13416979.2023.2283981","DOIUrl":"https://doi.org/10.1080/13416979.2023.2283981","url":null,"abstract":"Ozone is an atmospheric pollutant that adversely affects woody species, causing impaired stomatal control known as stomatal sluggishness. Stomatal sluggishness may affect stomatal ozone uptake beca...","PeriodicalId":15839,"journal":{"name":"Journal of Forest Research","volume":"13 2","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138509989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-20DOI: 10.1080/13416979.2023.2272451
Published in Journal of Forest Research (Vol. 28, No. 6, 2023)
发表于《森林研究》2023年第28卷第6期
{"title":"List of Reviewers","authors":"","doi":"10.1080/13416979.2023.2272451","DOIUrl":"https://doi.org/10.1080/13416979.2023.2272451","url":null,"abstract":"Published in Journal of Forest Research (Vol. 28, No. 6, 2023)","PeriodicalId":15839,"journal":{"name":"Journal of Forest Research","volume":"42 12","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138509976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Since most leaf defense traits are derived from photosynthates, the increase of feeding damage in woody plants can be partially attributed to the recent increase in ground-surface O3 (elevated O3; ...
{"title":"Leaf defense traits of birch, beech, and oak saplings grown under two types of soil in a free-air ozone exposure system","authors":"Cong Shi, Noburu Masui, Takayoshi Koike, Chisato Terada, Masahiro Nakamura, Toshihiro Watanabe","doi":"10.1080/13416979.2023.2280730","DOIUrl":"https://doi.org/10.1080/13416979.2023.2280730","url":null,"abstract":"Since most leaf defense traits are derived from photosynthates, the increase of feeding damage in woody plants can be partially attributed to the recent increase in ground-surface O3 (elevated O3; ...","PeriodicalId":15839,"journal":{"name":"Journal of Forest Research","volume":"28 16","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138509997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ABSTRACTLeaf herbivory potentially affects carbon (C) and nutrient cycling in forest ecosystems. It is especially critical to study the leaf herbivory rates in mangroves to understand the pattern of resource changes from the detrital pathway to the grazing pathway. However, determinants of leaf herbivory rates in mangroves are poorly understood. We examined the differences in leaf herbivory rates among leaf phenotypes (sun or shade leaves), leaf ages (young or old leaves), and season (summer or winter) and investigated the relationships between the leaf herbivory rates and 12 leaf traits (including chemical, physiological, and physical/mechanical traits) in each of six communities from the seaward fringe to the inland of subtropical mangroves on Iriomote Island, southern Japan. The herbivory rates decreased from seaward to landward mangrove species, excluding one species in the landward mangroves. The herbivory rates also decreased as the concentration of condensed tannins or the tannins:nitrogen ratio increased but did not correlate with the other leaf traits. Overall, season, leaf phenotype, and leaf age had no effect on the herbivory rate. However, in the two seaward and one rhizophoraceous species, the herbivory rates were higher in summer than in winter and were affected by the leaf phenotypes. The concentration of leaf condensed tannins moderately influenced leaf herbivory, fluctuating from seaward to landward; therefore, it was one of the factors driving the grazing pathway in mangroves. Understanding these mechanisms is critical for a comprehensive appreciation of the high productivity of and nutrient cycling in mangrove forest ecosystems.KEYWORDS: Leaf herbivoryleaf traitsmangrovecondensed tanninsplant–herbivore interaction AcknowledgementsWe thank the Ministry of the Environment, Japan, for permission to conduct the field survey on Iriomote Island (number OKINAWA 558); M. Iwao for the chemical analyses; K. Oshima and J. Yokoi for the leaf image analyses; S. Katagiri and M. Tamamoto for the field survey; K. Yabe for levelling; S. Watanabe for helpful discussions; and Y. Nemoto for statistical analyses.Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementThe datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.Supplementary dataSupplemental data for this article can be accessed online at https://doi.org/10.1080/13416979.2023.2279003Additional informationFundingThis study was supported by JST SPRING under grant JPMJSP2122 to YH and by JSPS KAKENHI under grant 22H02390 to NI.
{"title":"Relationship between herbivory and leaf traits in mangroves on Iriomote Island, southern Japan","authors":"Yu Hirano, Motoki Marui, Shuhei Tachikake, Taku Kato, Nobuo Imai","doi":"10.1080/13416979.2023.2279003","DOIUrl":"https://doi.org/10.1080/13416979.2023.2279003","url":null,"abstract":"ABSTRACTLeaf herbivory potentially affects carbon (C) and nutrient cycling in forest ecosystems. It is especially critical to study the leaf herbivory rates in mangroves to understand the pattern of resource changes from the detrital pathway to the grazing pathway. However, determinants of leaf herbivory rates in mangroves are poorly understood. We examined the differences in leaf herbivory rates among leaf phenotypes (sun or shade leaves), leaf ages (young or old leaves), and season (summer or winter) and investigated the relationships between the leaf herbivory rates and 12 leaf traits (including chemical, physiological, and physical/mechanical traits) in each of six communities from the seaward fringe to the inland of subtropical mangroves on Iriomote Island, southern Japan. The herbivory rates decreased from seaward to landward mangrove species, excluding one species in the landward mangroves. The herbivory rates also decreased as the concentration of condensed tannins or the tannins:nitrogen ratio increased but did not correlate with the other leaf traits. Overall, season, leaf phenotype, and leaf age had no effect on the herbivory rate. However, in the two seaward and one rhizophoraceous species, the herbivory rates were higher in summer than in winter and were affected by the leaf phenotypes. The concentration of leaf condensed tannins moderately influenced leaf herbivory, fluctuating from seaward to landward; therefore, it was one of the factors driving the grazing pathway in mangroves. Understanding these mechanisms is critical for a comprehensive appreciation of the high productivity of and nutrient cycling in mangrove forest ecosystems.KEYWORDS: Leaf herbivoryleaf traitsmangrovecondensed tanninsplant–herbivore interaction AcknowledgementsWe thank the Ministry of the Environment, Japan, for permission to conduct the field survey on Iriomote Island (number OKINAWA 558); M. Iwao for the chemical analyses; K. Oshima and J. Yokoi for the leaf image analyses; S. Katagiri and M. Tamamoto for the field survey; K. Yabe for levelling; S. Watanabe for helpful discussions; and Y. Nemoto for statistical analyses.Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementThe datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.Supplementary dataSupplemental data for this article can be accessed online at https://doi.org/10.1080/13416979.2023.2279003Additional informationFundingThis study was supported by JST SPRING under grant JPMJSP2122 to YH and by JSPS KAKENHI under grant 22H02390 to NI.","PeriodicalId":15839,"journal":{"name":"Journal of Forest Research","volume":"16 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135038841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ABSTRACTScientific Forestry Management (SciFM), an advanced silvicultural practice, was implemented from 2014 in the protection-oriented community forests (CFs) of Nepal, to advance national prosperity. However, in 2021, deforestation and rampant corruption led to criticism and the program was suspended. New policy formulations and discussions are developing among different actors in forest management. We, therefore, conducted a study to determine how CF users perceived the economic, social, and environmental aspects of SciFM and how it affects their livelihoods. We surveyed 290 households, interviewed key informants and conducted group discussions in the Terai and Hilly regions, where SciFM was implemented in CFs. All the users disagreed with the cessation of SciFM. Implementation of SciFM in CFs with sufficient reserve funds had a positive impact on income. However, those with fewer reserve funds incurred losses due to the initial investment required. 80% of CF users supported SciFM due to its economic benefits; 17% agreed on both economic and social benefits, while a mere 3% valued it for all three merits including resource conservation. SciFM was driven by the desire for financial upliftment, unaware of the corruption involved in its implementation. Policymakers emphasize the importance of addressing corruption issues and providing government support to implement advanced silviculture practices that are easily comprehensible to local forest users. The study’s findings underscore the need for policymakers to regain trust and gain public acceptance and support for regulations and management initiatives. This can be achieved by fostering transparent communication, consistent reliable actions, and active listening to stakeholders’ concerns and feedback.KEYWORDS: Community forestsScientific forest managementforest-dependent userslivelihoodsNepal AcknowledgementsThe authors gratefully acknowledge the support from the community forest user group members of studied community forests. We would like to thank Arvinda Panthee for his valuable comments on the manuscript.Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementData are not publicly available, though the data may be made available upon request from the corresponding author.Supplementary dataSupplemental data for this article can be accessed online at https://doi.org/10.1080/13416979.2023.2275901Additional informationFundingThis research was supported by Kakubun Suzuki Foundation for Environmental Conservation (No. R3-1-04).
{"title":"Scientific forest management practices in Nepal: perceptions of forest users and the impact on their livelihoods","authors":"Sudha Adhikari, Kazuhiro Harada, Nabin Kumar Dahal, Ratan Gurung","doi":"10.1080/13416979.2023.2275901","DOIUrl":"https://doi.org/10.1080/13416979.2023.2275901","url":null,"abstract":"ABSTRACTScientific Forestry Management (SciFM), an advanced silvicultural practice, was implemented from 2014 in the protection-oriented community forests (CFs) of Nepal, to advance national prosperity. However, in 2021, deforestation and rampant corruption led to criticism and the program was suspended. New policy formulations and discussions are developing among different actors in forest management. We, therefore, conducted a study to determine how CF users perceived the economic, social, and environmental aspects of SciFM and how it affects their livelihoods. We surveyed 290 households, interviewed key informants and conducted group discussions in the Terai and Hilly regions, where SciFM was implemented in CFs. All the users disagreed with the cessation of SciFM. Implementation of SciFM in CFs with sufficient reserve funds had a positive impact on income. However, those with fewer reserve funds incurred losses due to the initial investment required. 80% of CF users supported SciFM due to its economic benefits; 17% agreed on both economic and social benefits, while a mere 3% valued it for all three merits including resource conservation. SciFM was driven by the desire for financial upliftment, unaware of the corruption involved in its implementation. Policymakers emphasize the importance of addressing corruption issues and providing government support to implement advanced silviculture practices that are easily comprehensible to local forest users. The study’s findings underscore the need for policymakers to regain trust and gain public acceptance and support for regulations and management initiatives. This can be achieved by fostering transparent communication, consistent reliable actions, and active listening to stakeholders’ concerns and feedback.KEYWORDS: Community forestsScientific forest managementforest-dependent userslivelihoodsNepal AcknowledgementsThe authors gratefully acknowledge the support from the community forest user group members of studied community forests. We would like to thank Arvinda Panthee for his valuable comments on the manuscript.Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementData are not publicly available, though the data may be made available upon request from the corresponding author.Supplementary dataSupplemental data for this article can be accessed online at https://doi.org/10.1080/13416979.2023.2275901Additional informationFundingThis research was supported by Kakubun Suzuki Foundation for Environmental Conservation (No. R3-1-04).","PeriodicalId":15839,"journal":{"name":"Journal of Forest Research","volume":"26 26","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135390311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-16DOI: 10.1080/13416979.2023.2266618
Zane C. Smith, Grace M. Pietsch, Casey Richards, Meher Ony, Clayton Hale, Joshua J. Granger, William E. Klingeman, Matthew Huff, Denita Hadziabdic
ABSTRACTMountain stewartia [Stewartia ovata (Cav.) Weatherby] is a rare, endemic understory tree native to the southeastern U.S.A. While found only in microsites across southeastern Appalachia, the species distribution spans from northern Alabama and Georgia to southern Kentucky and Virginia. However, most occurrences have been recorded in Tennessee. While recent distribution surveys and habitat suitability modeling conducted for this species have improved our understanding of the environmental parameters that constitute its fundamental niche, the ecological profile of S. ovata remains poorly understood. Consequently, its rarity has raised concerns as to the long-term resilience of this species in the wild. Faced with these challenges, the assessment of existing genetic diversity in S. ovata through genetically informative molecular resources is critical to understanding the adaptive potential and ecological resilience of the species. Microsatellites are cost-efficient molecular tools capable of addressing these concerns by elucidating trends in population structure, population demography, and inbreeding. To increase the available genetic resources for S. ovata, we screened 105 microsatellite loci for their suitability to assess these population features using capillary gel electrophoresis. The utility of these markers was evaluated by assessing polymorphism information content (PIC) and population statistics, which yielded 14 highly polymorphic microsatellite markers. These markers displayed an average PIC of 0.695 (PIC range of 0.538–0.851), which supports their ability to capture fine-scale genetic diversity within the species. We also report a low average observed heterozygosity of 0.375 (versus an expected heterozygosity of 0.645) among screened loci, which reinforces the need for broader genetic diversity assessments within this species.Keywords: Mountain StewartiaStewartia ovatamicrosatellite markersAppalachian-endemic treeU.S. native tree Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was supported, in part, by the United States Department of Agriculture (USDA; Grant 58‐6062‐6) and the University of Tennessee, Department of Entomology and Plant Pathology and the Office of Undergraduate Research. Partial funding and support for student efforts were provided by the USDA National Institute of Food and Agriculture Crop Protection and Pest Management (CPPM) Grant #13131957 and #7002511 (TEN00600) and #7004409 Hatch Projects (IPM and Sustainable Strategies for Arthropod Pests and Plant Diseases in Nurseries, Managed Landscapes and Urban Forests and Forest Health and Resilience, respectively). Special thanks to the University of Tennessee Open Publishing Support Fund for providing publication resources.
{"title":"Characterization and development of 14 microsatellite markers for mountain stewartia ( <i>Stewartia ovata</i> ): an uncommon, Appalachian-endemic member of the tea family","authors":"Zane C. Smith, Grace M. Pietsch, Casey Richards, Meher Ony, Clayton Hale, Joshua J. Granger, William E. Klingeman, Matthew Huff, Denita Hadziabdic","doi":"10.1080/13416979.2023.2266618","DOIUrl":"https://doi.org/10.1080/13416979.2023.2266618","url":null,"abstract":"ABSTRACTMountain stewartia [Stewartia ovata (Cav.) Weatherby] is a rare, endemic understory tree native to the southeastern U.S.A. While found only in microsites across southeastern Appalachia, the species distribution spans from northern Alabama and Georgia to southern Kentucky and Virginia. However, most occurrences have been recorded in Tennessee. While recent distribution surveys and habitat suitability modeling conducted for this species have improved our understanding of the environmental parameters that constitute its fundamental niche, the ecological profile of S. ovata remains poorly understood. Consequently, its rarity has raised concerns as to the long-term resilience of this species in the wild. Faced with these challenges, the assessment of existing genetic diversity in S. ovata through genetically informative molecular resources is critical to understanding the adaptive potential and ecological resilience of the species. Microsatellites are cost-efficient molecular tools capable of addressing these concerns by elucidating trends in population structure, population demography, and inbreeding. To increase the available genetic resources for S. ovata, we screened 105 microsatellite loci for their suitability to assess these population features using capillary gel electrophoresis. The utility of these markers was evaluated by assessing polymorphism information content (PIC) and population statistics, which yielded 14 highly polymorphic microsatellite markers. These markers displayed an average PIC of 0.695 (PIC range of 0.538–0.851), which supports their ability to capture fine-scale genetic diversity within the species. We also report a low average observed heterozygosity of 0.375 (versus an expected heterozygosity of 0.645) among screened loci, which reinforces the need for broader genetic diversity assessments within this species.Keywords: Mountain StewartiaStewartia ovatamicrosatellite markersAppalachian-endemic treeU.S. native tree Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was supported, in part, by the United States Department of Agriculture (USDA; Grant 58‐6062‐6) and the University of Tennessee, Department of Entomology and Plant Pathology and the Office of Undergraduate Research. Partial funding and support for student efforts were provided by the USDA National Institute of Food and Agriculture Crop Protection and Pest Management (CPPM) Grant #13131957 and #7002511 (TEN00600) and #7004409 Hatch Projects (IPM and Sustainable Strategies for Arthropod Pests and Plant Diseases in Nurseries, Managed Landscapes and Urban Forests and Forest Health and Resilience, respectively). Special thanks to the University of Tennessee Open Publishing Support Fund for providing publication resources.","PeriodicalId":15839,"journal":{"name":"Journal of Forest Research","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136112928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Coniferous 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. obtusa to 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.
{"title":"Haplotype-resolved <i>de novo</i> genome assemblies of four coniferous tree species","authors":"Kenta Shirasawa, Kentaro Mishima, Hideki Hirakawa, Tomonori Hirao, Miyoko Tsubomura, Soichiro Nagano, Taiichi Iki, Sachiko Isobe, Makoto Takahashi","doi":"10.1080/13416979.2023.2267304","DOIUrl":"https://doi.org/10.1080/13416979.2023.2267304","url":null,"abstract":"Coniferous 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. obtusa to 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.","PeriodicalId":15839,"journal":{"name":"Journal of Forest Research","volume":"76 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136114160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ABSTRACTAquatic hyphomycetes are key decomposers of plant-litter in freshwater environments. Previous studies have shown that conifer needles are colonized less frequently by aquatic hyphomycetes than broad-leaf species. Sakhalin fir (Abies sachalinensis) is the most common coniferous tree species planted for timber production in Hokkaido, Japan. Herein, we investigated aquatic hyphomycete assemblages involving Sakhalin fir needle litter and compared them with those of broad-leaf tree species, including Japanese oak (Quercus crispula) and Japanese linden (Tilia japonica), during immersion in a stream. Seventy percent of the total fungal species observed in fir needles were also observed in broad-leaf litter. However, the structure of the aquatic hyphomycete assemblages differed between the fir and two broad-leaf species, especially in the middle to late stages of the immersion period. The increase in species number and conidia number in fir needles was slower than that in oak leaves in the early stages of the immersion period. However, they continued to increase rapidly relative to the broad-leaf tree litter during the middle stages of the immersion period. These results suggest that fir needle litter was not difficult for aquatic hyphomycetes to colonize in the middle to late stages of the immersion period.KEYWORDS: Aquatic fungiconifer litterSakhalin firfreshwaterfungal assemblage Disclosure statementNo potential conflict of interest was reported by the author(s).Supplementary materialSupplemental data for this article can be accessed online at https://doi.org/10.1080/13416979.2023.2265113Additional informationFundingThis work was supported by the Mitsui & Co., Ltd. Environment Fund, and JSPS KAKENHI Grant Number JP25252030.
{"title":"Aquatic hyphomycete assemblages of <i>Abies sachalinensis</i> leaf litter immersed in a stream in Hokkaido, Japan","authors":"Kohhei Yamamoto, Toshizumi Miyamoto, Akiko Nagasaka, Yu Nagasaka, Yutaka Tamai, Takashi Yajima","doi":"10.1080/13416979.2023.2265113","DOIUrl":"https://doi.org/10.1080/13416979.2023.2265113","url":null,"abstract":"ABSTRACTAquatic hyphomycetes are key decomposers of plant-litter in freshwater environments. Previous studies have shown that conifer needles are colonized less frequently by aquatic hyphomycetes than broad-leaf species. Sakhalin fir (Abies sachalinensis) is the most common coniferous tree species planted for timber production in Hokkaido, Japan. Herein, we investigated aquatic hyphomycete assemblages involving Sakhalin fir needle litter and compared them with those of broad-leaf tree species, including Japanese oak (Quercus crispula) and Japanese linden (Tilia japonica), during immersion in a stream. Seventy percent of the total fungal species observed in fir needles were also observed in broad-leaf litter. However, the structure of the aquatic hyphomycete assemblages differed between the fir and two broad-leaf species, especially in the middle to late stages of the immersion period. The increase in species number and conidia number in fir needles was slower than that in oak leaves in the early stages of the immersion period. However, they continued to increase rapidly relative to the broad-leaf tree litter during the middle stages of the immersion period. These results suggest that fir needle litter was not difficult for aquatic hyphomycetes to colonize in the middle to late stages of the immersion period.KEYWORDS: Aquatic fungiconifer litterSakhalin firfreshwaterfungal assemblage Disclosure statementNo potential conflict of interest was reported by the author(s).Supplementary materialSupplemental data for this article can be accessed online at https://doi.org/10.1080/13416979.2023.2265113Additional informationFundingThis work was supported by the Mitsui & Co., Ltd. Environment Fund, and JSPS KAKENHI Grant Number JP25252030.","PeriodicalId":15839,"journal":{"name":"Journal of Forest Research","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136014448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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