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Cloning and sequence analysis of nine novel MYB genes in Taxodiaceae plants

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Journal of Forestry Research 2014年第4期25卷 795-804页

作者： Yong-quan LU Qing JIA Zai-kang TONG The nurturing station for the state key laboratory of subtropical silviculture Zhejiang Agriculture and Forestry University

Myeloblastosis （MYB） is one of the largest transcribed factor families in plants. To gain an overall picture of the evolution of MYB genes in relict plants, we cloned nine novel MYB genes in Taxodiaceae plants （ Taxodium distichum, Taxodium ascendens, Cryptomeria japonica var. Sinensis, Cryptomeria japonica cv. Araucarioides, Cryptomer Ja- ponica, Metasequoia glyptostroboides, Cunninghamia lanceolata, Tai- wania cryptomerioides and Glyptostrobus pensilis）. The deduced amino acid sequences for MYBs showed that the nine MYB proteins contained two DNA binding domains. The first domain is from amino acid position 29 to 78, wherein three tryptophanes at 33, 53 and 73 were separated by 19 amino acids, respectively. The second domain is from amino acid position 82 to 127, wherein three tryptophanes at 86, 105 and 124 were separated by 18 amino acids, respectively, whereas the first tryptophane at amino acid position 86 is replaced by a phenylalanine. The characteri- zation of these conserved domains at nine MYBs indicated that they all belong to the R2R3-MYB group. The secondary structure analysis showed that a-helix and 13-turn are the major motifs of the predicted secondary structure of MYBs. The three dimensional model of each MYB protein showed that the structure is like clip, making it more flexi- ble and mobile. The similarities between the nine MYB proteins in Taxodiaceae were calculated. The highest identical value of 99% is be- tween CjsMYB, CjMYB and CjaMYB, whereas the lowest value of 82% is between TaMYB and C1MYB. According to the phylogenetic tree, the distances between different genera were relatively large whereas those within genera were relatively small. As expected, accessions of the same genus formed a subgroup before being grouped with other genera.

关键词： Myeloblastosis Taxodiaceae clone analysis R2R3-MYB group

Development of amplified consensus genetic markers in Taxodiaceae based on Cryptomeria japonica ESTs data

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Journal of Forestry Research 2013年第3期24卷 503-508页

作者： LU Yong-quan JIA Qing TONG Zai-kang The nurturing station for the state key laboratory of subtropical silviculture Zhejiang Agriculture and Forestry University

Amplified consensus genetic marker （ACGM） is a PCR-based marker technique that uses primers designed within conserved regions of coding sequences. After a comparison of Cryptomeria japonica and Arabidopsis ESTs to search for conserved sequences, 237 single e-PCR products were obtained. We randomly selected 110 candidate ACGM markers to test. Of the 110 candidate ACGM markers tested, 106 yielded stable and clear PCR products in C. japonica. We then tested the utility of these 106 primer pairs in 10 species, representing 7 genera of Taxodi- aceae. The number of specific amplification primer pairs among those 10 species varied from 49 to 103 （or 46.2±97.2%）. The 106 primer pairs （ACGM loci） were high transferable to Cryptomeria fortunei Hooibrenk （97.2%） but were low in Metasequoia glyptostroboides （46.2%）. The number of PCR bands per primer pair ranged from 1.06 to 1.15, which means that most of the ACGM primers can obtain a single band within these 10 Taxodiaceae species. In summary, our study shows that ACGM is a technique applicable for marker development even in species with limited sequence data.

关键词： ACGM Taxodiaceae Cryptomeriajaponica EST database

Canopy structural heterogeneity drives α and β species-genetic diversity correlations in a Chinese subtropical forest

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Plant Diversity 2025年第1期47卷 106-114页

作者： Zhiliang Yao Xia Pan Xin Yang Xiaona Shao Bin Wang Yun Deng Zhiming Zhang Qiaoming Li Luxiang Lin CAS key laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesKunming 650223YunnanChina University of Chinese Academy of Sciences Beijing 100049China School of Ecology and Environment Hainan UniversityHaikou 570228HainanChina state Forestry and Grassland Administration key laboratory of silviculture in Downstream Areas of the Yellow River Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland AdministrationForestry College of Shandong Agricultural UniversityTai'an 271018ShandongChina School of Ecology and Environmental Sciences&Yunnan key laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments Yunnan UniversityKunming 650500YunnanChina National Forest Ecosystem Research station at Xishuangbanna Mengla 666303YunnanChina

Patterns and drivers of species–genetic diversity correlations(SGDCs)have been broadly examined across taxa and ecosystems and greatly deepen our understanding of how biodiversity is ***,few studies have examined the role of canopy structural heterogeneity,which is a defining feature of forests,in shaping ***,we determine what factors contribute toα-andβ-species–genetic diversity correlations(i.e.,α-andβ-SGDCs)in a Chinese subtropical *** this purpose,we used neutral molecular markers to assess genetic variation in almost all adult individuals of the dominant tree species,Lithocarpus xylocarpus,across plots in the Ailaoshan National Natural *** also quantified microhabitat variation by quantifying canopy structure heterogeneity with airborne laser scanning on 201-ha subtropical forest *** found that speciesα-diversity was negatively correlated with geneticα-*** structural heterogeneity was positively correlated with speciesα-diversity but negatively correlated with geneticα-*** contrasting effects contributed to the formation of a negativeα-***,we found that canopy structural heterogeneity increases speciesα-diversity and decreases geneticα-diversity by reducing the population size of target ***β-diversity,in contrast,was positively correlated with geneticβ-*** in canopy structural heterogeneity between plots had non-linear parallel effects on the two levels ofβ-diversity,while geographic distance had a relatively weak effect onβ-*** study indicates that canopy structural heterogeneity simultaneously affects plot-level community species diversity and population genetic diversity,and species and genetic turnover across plots,thus drivingα-andβ-SGDCs.

关键词： Dominant species Forest structure LiDAR Lithocarpus xylocarpus Speciesegenetic diversity correlation subtropical evergreen broad-leaved forest

Rising frequency of ozone-favorable synoptic weather patterns contributes to 2015-2022 ozone increase in Guangzhou

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Journal of Environmental Sciences 2025年第2期148卷 502-514页

作者： Nanxi Liu Guowen He Haolin Wang Cheng He Haofan Wang Chenxi Liu Yiming Wang Haichao Wang Lei Li Xiao Lu Shaojia Fan School of Atmospheric Sciences Sun Yat-sen Universityand Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)Zhuhai 519082China Guangdong Provincial Observation and Research station for Climate Environment and Air Quality Change in the Pearl River Estuary Key Laboratory of Tropical Atmosphere-Ocean System(Sun Yat-sen University)Ministry of EducationZhuhai 519082China

Objective weather classification methods have been extensively applied to identify dominant ozone-favorable synoptic weather patterns(SWPs),however,the consistency of different classification methods is rarely *** this study,we apply two widely-used objective methods,the self-organizing map(SOM)and K-means clustering analysis,to derive ozone-favorable SWPs at four Chinese megacities in *** find that the two algorithms are largely consistent in recognizing dominant ozone-favorable SWPs for four Chinese *** the case of classifying six SWPs,the derived circulation fields are highly similar with a spatial correlation of 0.99 between the two methods,and the difference in themean frequency of each SWP is less than 7%.The six dominant ozone-favorable SWPs in Guangzhou are all characterized by anomaly higher radiation and temperature,lower cloud cover,relative humidity,and wind speed,and stronger subsidence compared to climatology *** find that during 2015-2022,the occurrence of ozone-favorable SWPs days increases significantly at a rate of 3.2 days/year,faster than the increases in the ozone exceedance days(3.0 days/year).The interannual variability between the occurrence of ozone-favorable SWPs and ozone exceedance days are generally consistent with a temporal correlation coefficient of *** particular,the significant increase in ozone-favorable SWPs in 2022,especially the subtropical High type which typically occurs in September,is consistent with a long-lasting ozone pollution episode in Guangzhou during September *** results thus reveal that enhanced frequency of ozone-favorable SWPs plays an important role in the observed 2015-2022 ozone increase in Guangzhou.

关键词： Ozone(O3) Objective weather classification methods Synoptic weather patterns Trends Guangzhou

Exploring the spatiotemporal heterogeneity of vegetation changes in subtropical humid karst region under CO_(2)fertilization

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Journal of Geographical Sciences 2025年第1期35卷 65-87页

作者： CHEN Meng ZHOU Qiuwen PENG Dawei YAN Weihong School of Geography and Environmental Science Guizhou Normal UniversityGuiyang550001China Huanjiang Observation and Research station for Karst Ecosystem Guangxi Key Laboratory of Karst Ecological Processes and ServicesInstitute of Subtropical AgricultureCASChangsha410125China University of Chinese Academy of Sciences Beijing100049China Faculty of Geographical Science Beijing Normal UniversityBeijing100875China Forestry Bureau of Shibing County 556000GuizhouQiandongnan PrefectureChina

Terrestrial ecosystems heavily depend on vegetation,which responds to carbon dioxide(CO_(2))fertilization in hot and humid *** subtropical humid karst region is a hot and humid region;whether and to what extent CO_(2)fertilization affects vegetation changes in such regions remains *** this study,we investigated the degree to which CO_(2)fertilization influences vegetation changes,along with their spatial and temporal differences,in the subtropical humid karst region using time-lag effect analysis,a random forest model,and multiple regression *** showed that CO_(2)fertilization plays an important role in vegetation changes,exhibiting clear spatial variations across different geomorphological zones,with its degree of influence ranging mainly between 11%and 25%.The highest contribution of CO_(2)fertilization was observed in the karst basin and non-karstic region,whereas the lowest contribution was found in the karst plateau *** studies have primarily attributed vegetation changes in subtropical humid karst region to ecological engineering,leading to an overestimation of its contribution to these *** findings of this study enhance the understanding of the mechanism of vegetation changes in humid karst region and provide theoretical and practical insights for ecological and environmental protection in these regions.

关键词： karst vegetation changes NDVI driving factors carbon dioxide fertilization

Response of Chinese fir seedlings to low phosphorus stress and analysis of gene expression differences

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Journal of Forestry Research 2019年第1期30卷 183-192页

作者： Jianhui Li Dingwei Luo Guifang Ma Licui Jia Jinliang Xu Huahong Huang Zaikang Tong Yong-Quan Lu nurturing station for the state key laboratory of subtropical silviculture Zhejiang Agriculture and Forestry University Northeast Forestry University Kaihua Forestry Farm

Chinese fir(Cunninghamia lanceolata) is an excellent fast-growing timber species occurring in southern China and has significant value in the forestry industry. In order to enhance the phosphorus utilization efficiency in Chinese fir, four clones named X6, S3, S39 and FK were used, and low phosphorus(LP) stress experiments were performed to analyze the response of different clones to phosphorus deficiency. According to the results on seedling height, maximum root length, leaf blade aspect ratio, root ratio, malondialdehyde content, acid phosphates activity,proline content, soluble protein level, and chlorophyll a and b levels of the tested clones, compared to the control groups(CK), the phosphorus high efficiency clone X6 was screen out for transcriptome sequencing experiments. De novo RNA-seq was then used to sequence the root transcriptomes of X6 under LP stress and CK, and we then compared the gene expression differences under the two conditions. A total of 3416 SDEGs were obtained by comparing the LP and CK groups, among which 1742 were up-regulated and 1682 were down-regulated. All SDEGs obtained from the LP and CK treated samples were subjected to KEGG annotation and classification. Through classification statistical analysis using WEGO software,607 SDEGs obtained KEGG pathway annotations, which were related to 206 metabolic pathways. In Chinese fir subjected to LP stress, 53 SDEGs related with phosphorus metabolism, and phosphate uptake and transport were obtained from our transcriptome data. Based on the phosphorus metabolism pathway obtained by KEGG classification, combined with previously report on gene annotation related with phosphorus metabolism, the enzymes encoded by SDEG related with phosphorus metabolism and their expression pattern were mapped onto phosphorus metabolism pathway.

关键词： Chinese fir Low phosphorus stress Root transcriptomes SDEG Phosphorus metabolism

Identification and evaluation of reference genes for normalization in quantitative real-time PCR analysis in the premodel tree Betula luminifera

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Journal of Forestry Research 2017年第2期28卷 273-282页

作者： Jun Wu Junhong Zhang Ying Pan Huahong Huang Xiongzhen Lou Zaikang Tong nurturing station for the state key laboratory of subtropical silviculture Zhejiang Agriculture and Forestry UniversityLin'anHangzhou 311300ZhejiangPeople's Republic of China

Betula luminifera is a commercial tree species that is emerging as a new model system for tree genomics research. A draft genomic sequence is expected to be publicly available in the near future, which means that an explosion of gene expression studies awaits. Thus, the work of selecting appropriate reference genes for q PCR normalization in different tissues or under various experimental conditions is extremely valuable. In this study, ten candidate genes were analyzed in B. luminifera subjected to different abiotic stresses and at various flowering *** expression stability of these genes was evaluated using three distinct algorithms implemented using ge Norm,Norm Finder and Best Keeper. The best-ranked reference genes varied across different sample sets, though RPL39,MDH and EF1 a were determined as the most stable by the three programs among all tested samples. RPL39 and EF1 a should be appropriate for normalization in N-starved roots,while the combination of RPL39 and MDH should be appropriate for N-starved stems and EF1 a and MDH should be appropriate in N-starved leaves. In PEG-treated（osmotic） roots, MDH was the most suitable, whereas EF1 a was suitable for PEG-treated stems and leaves. TUA was also stably expressed levels in PEG-treated plants. The combination of RPL39 and TUB should be appropriate for heat-stressed leaves and flowering stage. For reference gene validation, the expression levels of SOD and NFYA-3were investigated. This work will be beneficial to future studies on gene expression under different abiotic stress conditions and flowering status in B. luminifera.

关键词： flowering abiotic Betula normalization osmotic varied roots programs valuable stressed

Exploit SSR in Cryptromeria fortunei and application in genetic diversity analysis

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Journal of Forestry Research 2015年第4期26卷 963-969页

作者： Yongquan Lu Jingli Zhang Zaikang Tong A nurturing station for the state key laboratory of Subtropitical silviculture Zhejiang Agriculture and Forestry University

Cryptromeria fortunei is one of the main forest plantation species in the subtropical high altitude areas in China. In this paper we collected 49 C. fortunei germplasm resources and provides a study of the utility of freely available C. japonica EST resources for the development of markers necessary for genetic diversity analyses of C. fortunei. By screening 24,299 EST sequences from C. japonica with SSR Finder, we identified 2384 ESTs car- rying 2783 SSR motifs. We successfully obtained 364 （15 %） primers from 2419 putative SSR loci. Of the 80 candidate SSR markers tested, 70 （87.5 %） yielded stable and clear PCR products. With those primers, the genetic diversity of 49 C. fortunei we collected was studied. The results showed that 18 primers yield polymorphism within these accessions. These 18 primers generated 48 scorable SSR loci and the average number of polymorphic SSR loci per primer was 2.7. The PIC value varied from 0.375 to 0.8101, with the average of 0.4780. The Shannon index is 0.5718, and the value of the observed number of alleles and effective number of alleles are 1.9167 and 1.7289, respectively. The genetic coefficient of these 49 accessions varied from 0.28 to 0.87. According to the genetic dis- tances, a cluster tree was constructed. At genetic coefficient of 0.60, these 49 accessions can group into 3： group I contains only FJ-laizhou accession, and group II contains 2accessions from FJ-layang, and the other one group con- tains mixed accessions. At genetic coefficient of 0.68, the former group II was constructed into 7 subgroups, with the first 3 subgroups contain 16 accessions in which 11 （69 %） are from Fujian province, and the later 4 subgroup contain 31 accessions in which 20 （65 %） were from Zhejiang province.

关键词： Cryptromeria fortunei EST–SSR Germplasm collection Genetic diversity

DNA methylation in tissues of Chamaedorea elegans

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Journal of Forestry Research 2012年第3期23卷 425-428页

作者： LU Yongquan QING Jia LI Haiying TONG Zaikang The nurturing station for the state key laboratory of subtropical silviculture Zhejiang Agriculture and Forestry UniversityLin'an 311300China.

DNA methylation plays a crucial role in regulating plant development and tissue differentiation. In this study, we compared the methylation levels in leaf, root, and stem in Chamaedorea elegans by using the technique of methylation-sensitive amplified fragment length polymorphism AFLP. Over 19% （42/220） bases were uniformly methy- lated in these tissues. The percentages of polymorphism resulting from varied methylation in mature leaf （L1）, young leaf （L2）, baby leaf （L3）, stem （S）, young root （R1） and lignified root （R2） were 29.5%, 29.0%, 27.1%, 30.7%, 63.0% and 28.3%, respectively. The numbers of poly- morphic loci detected in the leaves of three developmental stages were similar, ranging from 20 to 30. In contrast, roots at the two developmental stages differed greatly, with 145 polymorphic loci detected in R1 and 27 in R2. Our results suggest that the methylation level in leaves slightly increases with aging, while that in roots decreases dramatically with aging.

关键词： DNA Methylation Chamaedorea elegans tissue root leaf stem