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Liu G, Liu F, Pan L, Wang H, Lu Y, Liu C, Yu S, Hu X. Agronomic, physiological and transcriptional characteristics provide insights into fatty acid biosynthesis in yellowhorn ( Xanthoceras sorbifolium Bunge) during fruit ripening. Front Genet 2024; 15:1325484. [PMID: 38356698 PMCID: PMC10864670 DOI: 10.3389/fgene.2024.1325484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Yellowhorn (Xanthoceras sorbifolium Bunge) is an oil-bearing tree species in northern China. In this study, we used yellowhorn from Heilongjiang to analyze the morphological and physiological changes of fruit development and conducted transcriptome sequencing. The results showed that the fruit experienced relatively slow growth from fertilization to DAF20 (20 days after flowering). From DAF40 to DAF60, the fruit entered an accelerated development stage, with a rapid increase in both transverse and longitudinal diameters, and the kernel contour developed completely at DAF40. From DAF60 to DAF80, the transverse and vertical diameters of the fruit developed slowly, and the overall measures remained stable until maturity. The soluble sugar, starch, and anthocyanin content gradually accumulated until reaching a peak at DAF80 and then rapidly decreased. RNA-seq analysis revealed differentially expressed genes (DEGs) in the seed coat and kernel, implying that seed components have different metabolite accumulation mechanisms. During the stages of seed kernel development, k-means clustering separated the DEGs into eight sub-classes, indicating gene expression shifts during the fruit ripening process. In subclass 8, the fatty acid biosynthesis pathway was enriched, suggesting that this class was responsible for lipid accumulation in the kernel. WGCNA revealed ten tissue-specific modules for the 12 samples among 20 modules. We identified 54 fatty acid biosynthesis pathway genes across the genome, of which 14 was quantified and confirmed by RT-qPCR. Most genes in the plastid synthesis stage showed high expression during the DAF40-DAF60 period, while genes in the endoplasmic reticulum synthesis stage showed diverse expression patterns. EVM0012847 (KCS) and EVM0002968 (HCD) showed similar high expression in the early stages and low expression in the late stages. EVM0022385 (HCD) exhibited decreased expression from DAF40 to DAF60 and then increased from DAF60 to DAF100. EVM0000575 (KCS) was increasingly expressed from DAF40 to DAF60 and then decreased from DAF60 to DAF100. Finally, we identified transcription factors (TFs) (HB-other, bHLH and ARF) that were predicted to bind to fatty acid biosynthesis pathway genes with significant correlations. These results are conducive to promoting the transcriptional regulation of lipid metabolism and the genetic improvement in terms of high lipid content of yellowhorn.
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Affiliation(s)
- Guan Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Fengjiao Liu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Lin Pan
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Hanhui Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Yanan Lu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Changhua Liu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Song Yu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Xiaohang Hu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
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Wang W, Hu C, Chang Y, Wang L, Bi Q, Lu X, Zheng Z, Zheng X, Wu D, Niu B. Differentiated responses of the phyllosphere bacterial community of the yellowhorn tree to precipitation and temperature regimes across Northern China. FRONTIERS IN PLANT SCIENCE 2023; 14:1265362. [PMID: 37954985 PMCID: PMC10634255 DOI: 10.3389/fpls.2023.1265362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023]
Abstract
Introduction As an ephemeral and oligotrophic environment, the phyllosphere harbors many highly diverse microorganisms. Importantly, it is known that their colonization of plant leaf surfaces is considerably influenced by a few abiotic factors related to climatic conditions. Yet how the dynamics of phyllosphere bacterial community assembly are shaped by detailed climatological elements, such as various bioclimatic variables, remains poorly understood. Methods Using high-throughput 16S rRNA gene amplicon sequencing technology, we analyzed the bacterial communities inhabiting the leaf surfaces of an oilseed tree, yellowhorn (Xanthoceras sorbifolium), grown at four sites (Yinchuan, Otogqianqi, Tongliao, and Zhangwu) whose climatic status differs in northern China. Results and Discussion We found that the yellowhorn phyllosphere's bacterial community was generally dominated by four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Nevertheless, bacterial community composition differed significantly among the four sampled site regions, indicating the possible impact of climatological factors upon the phyllosphere microbiome. Interestingly, we also noted that the α-diversities of phyllosphere microbiota showed strong positive or negative correlation with 13 bioclimatic factors (including 7 precipitation factors and 6 temperature factors). Furthermore, the relative abundances of 55 amplicon sequence variants (ASVs), including three ASVs representing two keystone taxa (the genera Curtobacterium and Streptomyces), exhibited significant yet contrary responses to the precipitation and temperature climatic variables. That pattern was consistent with all ASVs' trends of possessing opposite correlations to those two parameter classes. In addition, the total number of links and nodes, which conveys community network complexity, increased with rising values of most temperature variables. Besides that, remarkably positive relevance was found between average clustering coefficient and most precipitation variables. Altogether, these results suggest the yellowhorn phyllosphere bacterial community is capable of responding to variation in rainfall and temperature regimes in distinctive ways.
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Affiliation(s)
- Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Congcong Hu
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Yu Chang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Quanxin Bi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xin Lu
- Chifeng Research Institute of Forestry Science, Chifeng, China
- National Forestry and Grassland Shiny-Leaved Yellowhorn Engineering and Technology Research Center, Chifeng, China
| | - Zhimin Zheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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Liu H, Yan XM, Wang XR, Zhang DX, Zhou Q, Shi TL, Jia KH, Tian XC, Zhou SS, Zhang RG, Yun QZ, Wang Q, Xiang Q, Mannapperuma C, Van Zalen E, Street NR, Porth I, El-Kassaby YA, Zhao W, Wang XR, Guan W, Mao JF. Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn ( Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:766389. [PMID: 34880890 PMCID: PMC8647845 DOI: 10.3389/fpls.2021.766389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/18/2021] [Indexed: 05/17/2023]
Abstract
In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
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Affiliation(s)
- Hui Liu
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Mei Yan
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xin-rui Wang
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Dong-Xu Zhang
- Protected Agricultural Technology, R&D Center, Shanxi Datong University, Datong, China
| | - Qingyuan Zhou
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Tian-Le Shi
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kai-Hua Jia
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Chan Tian
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shan-Shan Zhou
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ren-Gang Zhang
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang, China
| | - Quan-Zheng Yun
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang, China
| | - Qing Wang
- Key Laboratory of Forest Ecology and Environment of the National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Qiuhong Xiang
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Chanaka Mannapperuma
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Elena Van Zalen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Nathaniel R. Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et de Géomatique, Université Laval Québec, Quebec City, QC, Canada
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Wei Zhao
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Xiao-Ru Wang
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Wenbin Guan
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jian-Feng Mao
- National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Wang L, Ruan C, Bao A, Li H. Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn. BMC PLANT BIOLOGY 2021; 21:464. [PMID: 34641783 PMCID: PMC8513341 DOI: 10.1186/s12870-021-03239-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 09/29/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Yellowhorn (Xanthoceras sorbifolium), an endemic woody oil-bearing tree, has become economically important and is widely cultivated in northern China for bioactive oil production. However, the regulatory mechanisms of seed development and lipid biosynthesis affecting oil production in yellowhorn are still elusive. MicroRNAs (miRNAs) play crucial roles in diverse aspects of biological and metabolic processes in seeds, especially in seed development and lipid metabolism. It is still unknown how the miRNAs regulate the seed development and lipid biosynthesis in yellowhorn. RESULTS Here, based on investigations of differences in the seed growth tendency and embryo oil content between high-oil-content and low-oil-content lines, we constructed small RNA libraries from yellowhorn embryos at four seed development stages of the two lines and then profiled small RNA expression using high-throughput sequencing. A total of 249 known miRNAs from 46 families and 88 novel miRNAs were identified. Furthermore, by pairwise comparisons among the four seed development stages in each line, we found that 64 miRNAs (53 known and 11 novel miRNAs) were differentially expressed in the two lines. Across the two lines, 15, 11, 10, and 7 differentially expressed miRNAs were detected at 40, 54, 68, and 81 days after anthesis, respectively. Bioinformatic analysis was used to predict a total of 2654 target genes for 141 differentially expressed miRNAs (120 known and 21 novel miRNAs). Most of these genes were involved in the fatty acid biosynthetic process, regulation of transcription, nucleus, and response to auxin. Using quantitative real-time PCR and an integrated analysis of miRNA and mRNA expression, miRNA-target regulatory modules that may be involved in yellowhorn seed size, weight, and lipid biosynthesis were identified, such as miR172b-ARF2 (auxin response factor 2), miR7760-p3_1-AGL61 (AGAMOUS-LIKE 61), miR319p_1-FAD2-2 (omega-6 fatty acid desaturase 2-2), miR5647-p3_1-DGAT1 (diacylglycerol acyltransferase 1), and miR7760-p5_1-MED15A (Mediator subunit 15a). CONCLUSIONS This study provides new insights into the important regulatory roles of miRNAs in the seed development and lipid biosynthesis in yellowhorn. Our results will be valuable for dissecting the post-transcriptional and transcriptional regulation of seed development and lipid biosynthesis, as well as improving yellowhorn in northern China.
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Affiliation(s)
- Li Wang
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, College of Marine Life Science, Ocean University of China, Qingdao, 266100, China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China.
| | - Aomin Bao
- Institute of Economic Forest, Tongliao Academy of Forestry Science and Technology, Tongliao, 028000, China
| | - He Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
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Liang Q, Fang H, Liu J, Zhang B, Bao Y, Hou W, Yang KQ. Analysis of the nutritional components in the kernels of yellowhorn (Xanthoceras sorbifolium Bunge) accessions. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Li J, Zhao S, Yu X, Du W, Li H, Sun Y, Sun H, Ruan C. Role of Xanthoceras sorbifolium MYB44 in tolerance to combined drought and heat stress via modulation of stomatal closure and ROS homeostasis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:410-420. [PMID: 33740680 DOI: 10.1016/j.plaphy.2021.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Yellowhorn (Xanthoceras sorbifolium) is an important edible woody oil tree species that is endemic to China. Drought and heat stresses are factors severely limiting the high-quality development of the yellowhorn industry. Transcription factors (TFs) play critical roles in regulating the response of woody plant species to water deficit or high temperature. However, the MYB TFs that respond to combined drought and heat stress in yellowhorn remain unclear. Here, we first investigated the physiological changes in 5 yellowhorn varieties in response to combined stress treatments. We observed significant changes in antioxidant enzyme activities and photosynthesis. The Maigaiti variety yielded the best results and was selected for subsequent experiments. An R2R3-type MYB TF, designated XsMYB44, was isolated from the leaves of yellowhorn. XsMYB44 expression was strongly induced by combined stress. Suppression of XsMYB44 expression via virus-induced gene silencing weakened yellowhorn tolerance to both individual and combined drought and heat stress, and the increased susceptibility was coupled with decreased plant height, fresh weight and relative water content and inhibited stomatal closure. Moreover, compared with the individual stresses, the combined stress caused increased reactive oxygen species levels and decreased antioxidant enzyme activities and proline content in XsMYB44-silenced plants. Furthermore, the expression levels of several defense-related genes were reduced in the XsMYB44-silenced plants. Overall, we studied the physiological characteristics of 5 yellowhorn varieties, and the results demonstrated that XsMYB44 acts as a positive regulator in the yellowhorn response to combined stress by triggering stomatal closure to maintain water levels and by modulating ROS homeostasis.
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Affiliation(s)
- Jingbin Li
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China; Divisions of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Shang Zhao
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China
| | - Xue Yu
- Divisions of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Wei Du
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China
| | - He Li
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China
| | - Ying Sun
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China
| | - Hao Sun
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China.
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Xiong C, Zhao S, Yu X, Sun Y, Li H, Ruan C, Li J. Yellowhorn drought-induced transcription factor XsWRKY20 acts as a positive regulator in drought stress through ROS homeostasis and ABA signaling pathway. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:187-195. [PMID: 32771930 DOI: 10.1016/j.plaphy.2020.06.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/05/2020] [Accepted: 06/22/2020] [Indexed: 05/11/2023]
Abstract
Yellowhorn (Xanthoceras sorbifolium) is a peculiar woody edible oil-bearing tree in China. WRKY transcription factors have specific roles in plant multiple abiotic stress responses. However, it is still not clear that the molecular mechanisms of WRKYs involve in drought tolerance in yellowhorn. In this study, we isolated a drought-induced group I WRKY gene from yellowhorn, designated as XsWRKY20. Expression of XsWRKY20 was strongly induced by PEG6000, NaCl, ABA and SA. Virus-induced gene silencing (VIGS) of XsWRKY20 reduced tolerance to drought stress in yellowhorn, as determined through physiological analyses of POD activity, SOD activity and proline content. This susceptibility was coupled with decreased expression of stress-related genes. In contrast, overexpression of XsWRKY20 in tobacco notably improved drought tolerance. Compared with the WT plants, the XsWRKY20-transgenic lines exhibited lower ROS and MDA content and higher antioxidant enzyme activity and proline content after drought treatment. Moreover, overexpression of XsWRKY20 enhanced the expression of several genes associated with encoding these antioxidant enzymes, proline biosynthesis and ABA signaling pathway. Taken together, XsWRKY20 functions as a positive regulator contributing to drought stress tolerance through either ROS homeostasis by antioxidant systems or ABA-dependent/independent gene expression pathway.
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Affiliation(s)
- Chaowei Xiong
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China
| | - Shang Zhao
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China
| | - Xue Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Ying Sun
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China
| | - He Li
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China
| | - Jingbin Li
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, PR China; Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.
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Transcriptome and Co-Expression Network Analyses Identify the Molecular Signatures Underlying Drought Resistance in Yellowhorn. FORESTS 2020. [DOI: 10.3390/f11080840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Drought is a key factor that limits plant growth and yield. Yellowhorn is an important and vigorously promoted oil tree in China. It can survive under certain drought conditions, but a lack of water severely restricts its growth and results in yield losses in arid and semi-arid areas. Therefore, it is important to identify the key pathways and genes to understand the mechanisms of its drought resistance. In this study, we evaluated drought resistance in four types of yellowhorn, and obtained 2669 and 2451 differentially expressed genes (DEGs) via the transcriptome analysis of the comparison of water-saving/water-consuming and fast-growing/slow-growing yellowhorn, respectively, under long-term drought conditions. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of DEGs showed the key biological processes and metabolic pathways involved in drought resistance, which demonstrated that there are both the same and different biological processes involved in regulating water use efficiency (WUE) and growth in response to drought stress. Furthermore, the network analysis indicated hub genes (especially seven protein kinases) and potential co-expressed gene clusters in a greenyellow module associated with WUE and a blue module associated with growth. These identified hub genes and key biological processes can significantly enhance our knowledge about the molecular mechanisms of drought resistance in yellowhorn.
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Bi Q, Zhao Y, Du W, Lu Y, Gui L, Zheng Z, Yu H, Cui Y, Liu Z, Cui T, Cui D, Liu X, Li Y, Fan S, Hu X, Fu G, Ding J, Ruan C, Wang L. Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome. Gigascience 2019; 8:giz070. [PMID: 31241154 PMCID: PMC6593361 DOI: 10.1093/gigascience/giz070] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 03/02/2019] [Accepted: 05/22/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Yellowhorn (Xanthoceras sorbifolium) is a species of the Sapindaceae family native to China and is an oil tree that can withstand cold and drought conditions. A pseudomolecule-level genome assembly for this species will not only contribute to understanding the evolution of its genes and chromosomes but also bring yellowhorn breeding into the genomic era. FINDINGS Here, we generated 15 pseudomolecules of yellowhorn chromosomes, on which 97.04% of scaffolds were anchored, using the combined Illumina HiSeq, Pacific Biosciences Sequel, and Hi-C technologies. The length of the final yellowhorn genome assembly was 504.2 Mb with a contig N50 size of 1.04 Mb and a scaffold N50 size of 32.17 Mb. Genome annotation revealed that 68.67% of the yellowhorn genome was composed of repetitive elements. Gene modelling predicted 24,672 protein-coding genes. By comparing orthologous genes, the divergence time of yellowhorn and its close sister species longan (Dimocarpus longan) was estimated at ∼33.07 million years ago. Gene cluster and chromosome synteny analysis demonstrated that the yellowhorn genome shared a conserved genome structure with its ancestor in some chromosomes. CONCLUSIONS This genome assembly represents a high-quality reference genome for yellowhorn. Integrated genome annotations provide a valuable dataset for genetic and molecular research in this species. We did not detect whole-genome duplication in the genome. The yellowhorn genome carries syntenic blocks from ancient chromosomes. These data sources will enable this genome to serve as an initial platform for breeding better yellowhorn cultivars.
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Affiliation(s)
- Quanxin Bi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Key Laboratory of Biotechnology and Bioresources Utilization, State Ethnic Affairs Commission & Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Yang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Wei Du
- Key Laboratory of Biotechnology and Bioresources Utilization, State Ethnic Affairs Commission & Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Ying Lu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai 201306, China
| | - Lang Gui
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai 201306, China
| | - Zhimin Zheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin 150040, China
| | - Haiyan Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Beijing ABT Biotechnology Co., Ltd., Beijing 102200, China
| | - Yifan Cui
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhi Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin 150040, China
| | - Tianpeng Cui
- Zhangwu Deya yellowhorn Professional Cooperatives, Zhangwu 123200, China
| | - Deshi Cui
- Zhangwu Deya yellowhorn Professional Cooperatives, Zhangwu 123200, China
| | - Xiaojuan Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yingchao Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Siqi Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Xiaoyu Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Guanghui Fu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jian Ding
- Key Laboratory of Biotechnology and Bioresources Utilization, State Ethnic Affairs Commission & Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, State Ethnic Affairs Commission & Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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10
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Liang Q, Li H, Li S, Yuan F, Sun J, Duan Q, Li Q, Zhang R, Sang YL, Wang N, Hou X, Yang KQ, Liu JN, Yang L. The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge). Gigascience 2019; 8:giz071. [PMID: 31241155 PMCID: PMC6593362 DOI: 10.1093/gigascience/giz071] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/06/2019] [Accepted: 05/22/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Yellowhorn (Xanthoceras sorbifolium Bunge), a deciduous shrub or small tree native to north China, is of great economic value. Seeds of yellowhorn are rich in oil containing unsaturated long-chain fatty acids that have been used for producing edible oil and nervonic acid capsules. However, the lack of a high-quality genome sequence hampers the understanding of its evolution and gene functions. FINDINGS In this study, a whole genome of yellowhorn was sequenced and assembled by integration of Illumina sequencing, Pacific Biosciences single-molecule real-time sequencing, 10X Genomics linked reads, Bionano optical maps, and Hi-C. The yellowhorn genome assembly was 439.97 Mb, which comprised 15 pseudo-chromosomes covering 95.42% (419.84 Mb) of the assembled genome. The repetitive fractions accounted for 56.39% of the yellowhorn genome. The genome contained 21,059 protein-coding genes. Of them, 18,503 (87.86%) genes were found to be functionally annotated with ≥1 "annotation" term by searching against other databases. Transcriptomic analysis showed that 341, 135, 125, 113, and 100 genes were specifically expressed in hermaphrodite flower, staminate flower, young fruit, leaf, and shoot, respectively. Phylogenetic analysis suggested that yellowhorn and Dimocarpus longan diverged from their most recent common ancestor ∼46 million years ago. CONCLUSIONS The availability and subsequent annotation of the yellowhorn genome, as well as the identification of tissue-specific functional genes, provides a valuable reference for plant comparative genomics, evolutionary studies, and molecular design breeding.
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Affiliation(s)
- Qiang Liang
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Huayang Li
- College of Plant Protection, Shandong Agricultural University, Daizong Road No.61, Tai'an 271018, China
| | - Shouke Li
- Worth Agricultural Development Co. Ltd.,Taishanxi Road No. 17, Anqiu city, Weifang 262100, China
| | - Fuling Yuan
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Jingfeng Sun
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Qicheng Duan
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Qingyun Li
- College of Plant Protection, Shandong Agricultural University, Daizong Road No.61, Tai'an 271018, China
| | - Rui Zhang
- College of Plant Protection, Shandong Agricultural University, Daizong Road No.61, Tai'an 271018, China
| | - Ya Lin Sang
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Nian Wang
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Xiangwen Hou
- KeGene Science & Technology Co. Ltd., Nantianmen Middle Road, Tai'an 271018, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Daizong Road No.61,Tai'an 271018, China
| | - Jian Ning Liu
- KeGene Science & Technology Co. Ltd., Nantianmen Middle Road, Tai'an 271018, China
| | - Long Yang
- College of Plant Protection, Shandong Agricultural University, Daizong Road No.61, Tai'an 271018, China
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11
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Zhu R, Wang Q, Guan W, Mao Y, Tian B, Cheng J, El‐Kassaby YA. Conservation of genetic diversity hotspots of the high-valued relic yellowhorn ( Xanthoceras sorbifolium) considering climate change predictions. Ecol Evol 2019; 9:3251-3263. [PMID: 30962890 PMCID: PMC6434555 DOI: 10.1002/ece3.4944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/22/2018] [Accepted: 01/07/2019] [Indexed: 11/25/2022] Open
Abstract
Genetic structure and major climate factors may contribute to the distribution of genetic diversity of a highly valued oil tree species Xanthoceras sorbifolium (yellowhorn). Long-term over utilization along with climate change is affecting the viability of yellowhorn wild populations. To preserve the species known and unknown valuable gene pools, the identification of genetic diversity "hotspots" is a prerequisite for their consideration as in situ conservation high priority. Chloroplast DNA (cpDNA) diversity was high among 38 natural populations (H d = 0.717, K = 4.616, Tajmas' D = -0.22) and characterized by high genetic divergence (F ST = 0.765) and relatively low gene flow (N m = 0.03), indicating populations isolation reflecting the species' habitat fragmentation and inbreeding depression. Six out of the studied 38 populations are defined as genetic diversity "hotspots." The number and geographic direction of cpDNA mutation steps supported the species southwest to northeast migration history. Climatic factors such as extreme minimum temperature over 30 years indicated that the identified genetic "hotspots" are expected to experience 5°C temperature increase in next following 50 years. The results identified vulnerable genetic diversity "hotspots" and provided fundamental information for the species' future conservation and breeding activities under the anticipated climate change. More specifically, the role of breeding as a component of a gene resource management strategy aimed at fulfilling both utilization and conservation goals.
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Affiliation(s)
- Ren‐Bin Zhu
- Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglunChina
- College of Resource and EnvironmentNorthwest A&F UniversityYanglingChina
| | - Qing Wang
- School of Nature ConservationBeijing Forestry UniversityBeijingChina
- Department of Forest and Conservation Sciences, Faculty of ForestryThe University of British ColumbiaVancouverBritish ColumbiaCanada
| | - Wen‐Bin Guan
- School of Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Yanjia Mao
- Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglunChina
| | - Bin Tian
- Key Laboratory of Biodiversity Conservation in Southwest ChinaState Forestry Administration, Southwest Forestry UniversityKunmingChina
| | - Ji‐Min Cheng
- College of Resource and EnvironmentNorthwest A&F UniversityYanglingChina
- Institute of Soil and Water ConservationChinese Academy of Sciences and Ministry of Water resourcesYanglingChina
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences, Faculty of ForestryThe University of British ColumbiaVancouverBritish ColumbiaCanada
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