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Li J, Chen C, Zeng Z, Wu F, Feng J, Liu B, Mai Y, Chu X, Wei W, Li X, Liang Y, Liu Y, Xu J, Xia R. SapBase: A central portal for functional and comparative genomics of Sapindaceae species. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1561-1570. [PMID: 38804840 DOI: 10.1111/jipb.13680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/06/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024]
Abstract
The Sapindaceae family, encompassing a wide range of plant forms such as herbs, vines, shrubs, and trees, is widely distributed across tropical and subtropical regions. This family includes economically important crops like litchi, longan, rambutan, and ackee. With the wide application of genomic technologies in recent years, several Sapindaceae plant genomes have been decoded, leading to an accumulation of substantial omics data in this field. This surge in data highlights the pressing need for a unified genomic data center capable of storing, sharing, and analyzing these data. Here, we introduced SapBase, that is, the Sapindaceae Genome Database. SapBase houses seven published plant genomes alongside their corresponding gene structure and functional annotations, small RNA annotations, gene expression profiles, gene pathways, and synteny block information. It offers user-friendly features for gene information mining, co-expression analysis, and inter-species comparative genomic analysis. Furthermore, we showcased SapBase's extensive capacities through a detailed bioinformatic analysis of a MYB gene in litchi. Thus, SapBase could serve as an integrative genomic resource and analysis platform for the scientific exploration of Sapinaceae species and their comparative studies with other plants.
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Affiliation(s)
- Jiawei Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - Fengqi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - Junting Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - Bo Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - Yingxiao Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - Xinyi Chu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
| | - Wanchun Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - Xin Li
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - Yanyang Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - YuanLong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - Jing Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of Agriculture and Rural Affairs, South China Agricultural University, College of Horticulture, Guangzhou, 510640, China
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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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Zhao Z, Liang C, Zhang W, Yang Y, Bi Q, Yu H, Wang L. Genome-wide association analysis identifies a candidate gene controlling seed size and yield in Xanthoceras sorbifolium Bunge. HORTICULTURE RESEARCH 2024; 11:uhad243. [PMID: 38225982 PMCID: PMC10788774 DOI: 10.1093/hr/uhad243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/17/2023] [Indexed: 01/17/2024]
Abstract
Yellow horn (Xanthoceras sorbifolium Bunge) is a woody oilseed tree species whose seed oil is rich in unsaturated fatty acids and rare neuronic acids, and can be used as a high-grade edible oil or as a feedstock for biodiesel production. However, the genetic mechanisms related to seed yield in yellow horn are not well elucidated. This study identified 2 164 863 SNP loci based on 222 genome-wide resequencing data of yellow horn germplasm. We conducted genome-wide association study (GWAS) analysis on three core traits (hundred-grain weight, single-fruit seed mass, and single-fruit seed number) that influence seed yield for the years 2022 and 2020, and identified 399 significant SNP loci. Among these loci, the Chr10_24013014 and Chr10_24012613 loci caught our attention due to their consistent associations across multiple analyses. Through Sanger sequencing, we validated the genotypes of these two loci across 16 germplasms, confirming their consistency with the GWAS analysis results. Downstream of these two significant loci, we identified a candidate gene encoding an AP2 transcription factor protein, which we named XsAP2. RT-qPCR analysis revealed high expression of the XsAP2 gene in seeds, and a significant negative correlation between its expression levels and seed hundred-grain weight, as well as single-fruit seed mass, suggesting its potential role in the normal seed development process. Transgenic Arabidopsis lines with the overexpressed XsAP2 gene exhibited varying degrees of reduction in seed size, number of seeds per silique, and number of siliques per plant compared with wild-type Arabidopsis. Combining these results, we hypothesize that the XsAP2 gene may have a negative regulatory effect on seed yield of yellow horn. These results provide a reference for the molecular breeding of high-yielding yellow horn.
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Affiliation(s)
- Ziquan Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Chongjun Liang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
- College of Forestry, Hainan University, Haikou 570228, China
| | - Wei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Yingying Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Quanxin Bi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Haiyan Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
- College of Forestry, Hainan University, Haikou 570228, China
- College of Forestry, Northwest A&F University, Yangling 712100, China
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Wang J, Hu H, Liang X, Tahir ul Qamar M, Zhang Y, Zhao J, Ren H, Yan X, Ding B, Guo J. High-quality genome assembly and comparative genomic profiling of yellowhorn ( Xanthoceras sorbifolia) revealed environmental adaptation footprints and seed oil contents variations. FRONTIERS IN PLANT SCIENCE 2023; 14:1147946. [PMID: 37025151 PMCID: PMC10070836 DOI: 10.3389/fpls.2023.1147946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/06/2023] [Indexed: 05/31/2023]
Abstract
Yellowhorn (Xanthoceras sorbifolia) is a species of deciduous tree that is native to Northern and Central China, including Loess Plateau. The yellowhorn tree is a hardy plant, tolerating a wide range of growing conditions, and is often grown for ornamental purposes in parks, gardens, and other landscaped areas. The seeds of yellowhorn are edible and contain rich oil and fatty acid contents, making it an ideal plant for oil production. However, the mechanism of its ability to adapt to extreme environments and the genetic basis of oil synthesis remains to be elucidated. In this study, we reported a high-quality and near gap-less yellowhorn genome assembly, containing the highest genome continuity with a contig N50 of 32.5 Mb. Comparative genomics analysis showed that 1,237 and 231 gene families under expansion and the yellowhorn-specific gene family NB-ARC were enriched in photosynthesis and root cap development, which may contribute to the environmental adaption and abiotic stress resistance of yellowhorn. A 3-ketoacyl-CoA thiolase (KAT) gene (Xso_LG02_00600) was identified under positive selection, which may be associated with variations of seed oil content among different yellowhorn cultivars. This study provided insights into environmental adaptation and seed oil content variations of yellowhorn to accelerate its genetic improvement.
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Affiliation(s)
- Juan Wang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Haifei Hu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xizhen Liang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Muhammad Tahir ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Yunxiang Zhang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Jianguo Zhao
- Engineering Research Center of Coalbased Ecological Carbon Sequestration Technology of the Ministry of Education, Datong University, Taigu, Shanxi, China
| | - Hongqian Ren
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Xingrong Yan
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Baopeng Ding
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Engineering Research Center of Coalbased Ecological Carbon Sequestration Technology of the Ministry of Education, Datong University, Taigu, Shanxi, China
| | - Jinping Guo
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Shanxi Agricultural University, Taigu, Shanxi, China
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Li J, Zhou X, Xiong C, Zhou H, Li H, Ruan C. Yellowhorn Xso-miR5149-XsGTL1 enhances water-use efficiency and drought tolerance by regulating leaf morphology and stomatal density. Int J Biol Macromol 2023; 237:124060. [PMID: 36933587 DOI: 10.1016/j.ijbiomac.2023.124060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023]
Abstract
Yellowhorn (Xanthoceras sorbifolium) is a unique edible woody oil tree species in China. Drought stress is the major yield-limiting factor of yellowhorn. MicroRNAs play an important role in regulating the response of woody plants to drought stress. However, the regulatory function of miRNAs in yellowhorn remains unclear. Here, we first constructed coregulatory networks integrated with miRNAs and their target genes. According to GO function and expression pattern analysis, we selected the Xso-miR5149-XsGTL1 module for further study. Xso-miR5149 is a key regulator of leaf morphology and stomatal density by directly mediating the expression of the transcription factor XsGTL1. Downregulation of XsGTL1 in yellowhorn led to increased leaf area and reduced stomatal density. RNA-seq analysis indicated that downregulation of XsGTL1 increased the expression of genes involved in the negative control of stomatal density, leaf morphology, and drought tolerance. After drought stress treatments, the XsGTL1-RNAi yellowhorn plants were less damaged and had higher water-use efficiency than the WT plants, while destruction of Xso-miR5149 or overexpression of XsGTL1 had the opposite effect. Our findings indicated that the Xso-miR5149-XsGTL1 regulatory module plays a critical role in controlling leaf morphology and stomatal density; hence, it's a potential candidate module for engineering enhanced drought tolerance in yellowhorn.
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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, 116600 Dalian, Liaoning Province, PR China
| | - Xudong Zhou
- College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, 311300 Lin'an, Zhejiang Province, PR China
| | - Chaowei Xiong
- College of Forestry, Northwest Agriculture and Forestry University, 712100 Yangling, Shaanxi Province, PR China
| | - Hui Zhou
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, 116600 Dalian, Liaoning Province, PR China
| | - He Li
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, 116600 Dalian, Liaoning Province, PR China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, 116600 Dalian, Liaoning Province, PR China.
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Cao Y, Li Q, Zhang L. The core triacylglycerol toolbox in woody oil plants reveals targets for oil production bioengineering. FRONTIERS IN PLANT SCIENCE 2023; 14:1170723. [PMID: 37077641 PMCID: PMC10106636 DOI: 10.3389/fpls.2023.1170723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/21/2023] [Indexed: 05/03/2023]
Abstract
Woody oil plants are the most productive oil-bearing species that produce seeds with high levels of valuable triacylglycerols (TAGs). TAGs and their derivatives are the raw materials for many macromolecular bio-based products, such as nylon precursors, and biomass-based diesel. Here, we identified 280 genes encoding seven distinct classes of enzymes (i.e., G3PAT, LPAAT, PAP, DGAT, PDCT, PDAT, and CPT) involved in TAGs-biosynthesis. Several multigene families are expanded by large-scale duplication events, such as G3PATs, and PAPs. RNA-seq was used to survey the expression profiles of these TAG pathway-related genes in different tissues or development, indicating functional redundancy for some duplicated genes originated from the large-scale duplication events, and neo-functionalization or sub-functionalization for some of them. Sixty-two genes showed strong, preferential expression during the period of rapid seed lipid synthesis, suggesting that their might represented the core TAG-toolbox. We also revealed for the first time that there is no PDCT pathway in Vernicia fordii and Xanthoceras sorbifolium. The identification of key genes involved in lipid biosynthesis will be the foundation to plan strategies to develop woody oil plant varieties with enhanced processing properties and high oil content.
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Affiliation(s)
- Yunpeng Cao
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
- *Correspondence: Yunpeng Cao, ; Lin Zhang,
| | - Qiang Li
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China
| | - Lin Zhang
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, China
- *Correspondence: Yunpeng Cao, ; Lin Zhang,
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Liu JN, Fang H, Liang Q, Dong Y, Wang C, Yan L, Ma X, Zhou R, Lang X, Gai S, Wang L, Xu S, Yang KQ, Wu D. Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis. Gigascience 2022; 12:giad053. [PMID: 37494283 PMCID: PMC10370455 DOI: 10.1093/gigascience/giad053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/09/2023] [Accepted: 06/29/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND The woody halophyte Tamarix chinensis is a pioneer tree species in the coastal wetland ecosystem of northern China, exhibiting high resistance to salt stress. However, the genetic information underlying salt tolerance in T. chinensis remains to be seen. Here we present a genomic investigation of T. chinensis to elucidate the underlying mechanism of its high resistance to salinity. RESULTS Using a combination of PacBio and high-throughput chromosome conformation capture data, a chromosome-level T. chinensis genome was assembled with a size of 1.32 Gb and scaffold N50 of 110.03 Mb. Genome evolution analyses revealed that T. chinensis significantly expanded families of HAT and LIMYB genes. Whole-genome and tandem duplications contributed to the expansion of genes associated with the salinity adaptation of T. chinensis. Transcriptome analyses were performed on root and shoot tissues during salt stress and recovery, and several hub genes responding to salt stress were identified. WRKY33/40, MPK3/4, and XBAT31 were critical in responding to salt stress during early exposure, while WRKY40, ZAT10, AHK4, IRX9, and CESA4/8 were involved in responding to salt stress during late stress and recovery. In addition, PER7/27/57/73 encoding class III peroxidase and MCM3/4/5/7 encoding DNA replication licensing factor maintained up/downregulation during salt stress and recovery stages. CONCLUSIONS The results presented here reveal the genetic mechanisms underlying salt adaptation in T. chinensis, thus providing important genomic resources for evolutionary studies on tamarisk and plant salt tolerance genetic improvement.
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Affiliation(s)
- Jian Ning Liu
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Qiang Liang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Liping Yan
- Shandong Provincial Academy of Forestry, Jinan 250014, China
| | - Xinmei Ma
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Rui Zhou
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Xinya Lang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Shasha Gai
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Lichang Wang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Shengyi Xu
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Dejun Wu
- Shandong Provincial Academy of Forestry, Jinan 250014, China
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The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis. Int J Mol Sci 2022; 23:ijms232415932. [PMID: 36555572 PMCID: PMC9781956 DOI: 10.3390/ijms232415932] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.
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10
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Liu F, Wu R, Ma X, Su E. The Advancements and Prospects of Nervonic Acid Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12772-12783. [PMID: 36166330 DOI: 10.1021/acs.jafc.2c05770] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nervonic acid (NA) is a monounsaturated very long-chain fatty acid (VLCFA) and has been identified with critical biological functions in medical and health care for brain development and injury repair. Yet, the approaches to producing NA from the sources of plants or animals continue to pose challenges to meet increasing market demand, as they are generally associated with high costs, a lack of natural resources, a long life cycle, and low production efficiency. The recent technological advance in metabolic engineering allows us to precisely engineer oleaginous microbes to develop high-content NA-producing strains, which has the potential to provide a possible solution to produce NA on a commercial fermentation scale. In this Review, the biosynthetic pathway, natural sources, and metabolic engineering of NA are summarized. The strategies of metabolic engineering that could be adopted to modify oleaginous yeast to produce NA are discussed in detail, providing the prospecting views for the microbial cells producing NA.
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Affiliation(s)
- Feixiang Liu
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
- Department of Biological Science and Food Engineering, Bozhou University, Bozhou 236800, China
| | - Rong Wu
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaoqiang Ma
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Erzheng Su
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
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11
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Guo L, Yao H, Chen W, Wang X, Ye P, Xu Z, Zhang S, Wu H. Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era. HORTICULTURE RESEARCH 2022; 9:uhac223. [PMID: 36479585 PMCID: PMC9720450 DOI: 10.1093/hr/uhac223] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/22/2022] [Indexed: 06/01/2023]
Abstract
Globally, medicinal plant natural products (PNPs) are a major source of substances used in traditional and modern medicine. As we human race face the tremendous public health challenge posed by emerging infectious diseases, antibiotic resistance and surging drug prices etc., harnessing the healing power of medicinal plants gifted from mother nature is more urgent than ever in helping us survive future challenge in a sustainable way. PNP research efforts in the pre-genomic era focus on discovering bioactive molecules with pharmaceutical activities, and identifying individual genes responsible for biosynthesis. Critically, systemic biological, multi- and inter-disciplinary approaches integrating and interrogating all accessible data from genomics, metabolomics, structural biology, and chemical informatics are necessary to accelerate the full characterization of biosynthetic and regulatory circuitry for producing PNPs in medicinal plants. In this review, we attempt to provide a brief update on the current research of PNPs in medicinal plants by focusing on how different state-of-the-art biotechnologies facilitate their discovery, the molecular basis of their biosynthesis, as well as synthetic biology. Finally, we humbly provide a foresight of the research trend for understanding the biology of medicinal plants in the coming decades.
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Affiliation(s)
- Li Guo
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
| | - Hui Yao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Weikai Chen
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
| | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an 710061, China
| | - Peng Ye
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Sisheng Zhang
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hong Wu
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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12
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Liang Q, Liu JN, Fang H, Dong Y, Wang C, Bao Y, Hou W, Zhou R, Ma X, Gai S, Wang L, Li S, Yang KQ, Sang YL. Genomic and transcriptomic analyses provide insights into valuable fatty acid biosynthesis and environmental adaptation of yellowhorn. FRONTIERS IN PLANT SCIENCE 2022; 13:991197. [PMID: 36147226 PMCID: PMC9486082 DOI: 10.3389/fpls.2022.991197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 06/01/2023]
Abstract
Yellowhorn (Xanthoceras sorbifolium) is an oil-bearing tree species growing naturally in poor soil. The kernel of yellowhorn contains valuable fatty acids like nervonic acid. However, the genetic basis underlying the biosynthesis of valued fatty acids and adaptation to harsh environments is mainly unexplored in yellowhorn. Here, we presented a haplotype-resolved chromosome-scale genome assembly of yellowhorn with the size of 490.44 Mb containing scaffold N50 of 34.27 Mb. Comparative genomics, in combination with transcriptome profiling analyses, showed that expansion of gene families like long-chain acyl-CoA synthetase and ankyrins contribute to yellowhorn fatty acid biosynthesis and defense against abiotic stresses, respectively. By integrating genomic and transcriptomic data of yellowhorn, we found that the transcription of 3-ketoacyl-CoA synthase gene XS04G00959 was consistent with the accumulation of nervonic and erucic acid biosynthesis, suggesting its critical regulatory roles in their biosynthesis. Collectively, these results enhance our understanding of the genetic basis underlying the biosynthesis of valuable fatty acids and adaptation to harsh environments in yellowhorn and provide foundations for its genetic improvement.
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Affiliation(s)
- Qiang Liang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Jian Ning Liu
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Yan Bao
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Wenrui Hou
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Rui Zhou
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Xinmei Ma
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Shasha Gai
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Lichang Wang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Shouke Li
- Worth Agricultural Development Co. Ltd., Weifang, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Tai’an, Shandong, China
| | - Ya Lin Sang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Tai’an, Shandong, China
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13
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Bian Z, Wang X, Lu J, Wang D, Zhou Y, Liu Y, Wang S, Yu Z, Xu D, Meng S. The yellowhorn AGL transcription factor gene XsAGL22 contributes to ABA biosynthesis and drought tolerance in poplar. TREE PHYSIOLOGY 2022; 42:1296-1309. [PMID: 34726236 DOI: 10.1093/treephys/tpab140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Regulation of abscisic acid (ABA) biosynthesis helps plants adapt to drought stress, but the underlying molecular mechanisms are largely unclear. Here, a drought-induced transcription factor XsAGL22 was isolated from yellowhorn (Xanthoceras sorbifolium Bunge). Yeast one-hybrid and electrophoretic mobility shift assays indicated that XsAGL22 can physically bind to the promoters of the ABA biosynthesis-related genes XsNCED6 and XsBG1, and a dual-luciferase assay showed that XsAGL22 activates the promoters of the later two genes. Transient overexpression of XsAGL22 in yellowhorn leaves also increased the expression of XsNCED6 and XsBG1 and increased cellular ABA levels. Finally, heterologous overexpression of XsAGL22 in poplar increased ABA content, reduced stomatal aperture and increased drought resistance. Our results suggest that XsAGL22 is a powerful regulator of ABA biosynthesis and plays a critical role in drought resistance in plants.
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Affiliation(s)
- Zhan Bian
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong 510520, China
| | - Xiaoling Wang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi 330096, China
| | - Junkun Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong 510520, China
| | - Dongli Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong 510520, China
| | - Yangyan Zhou
- Salver Academy of Botany, Rizhao, Shandong 262300, China
| | - Yunshan Liu
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, China
| | - Shengkun Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong 510520, China
| | - Zequn Yu
- Shanghai Gardening-Landscaping Construction Co., Ltd, Shanghai 200333, China
| | - Daping Xu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong 510520, China
| | - Sen Meng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong 510520, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, China
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14
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Population Genetics and Development of a Core Collection from Elite Germplasms of Xanthoceras sorbifolium Based on Genome-Wide SNPs. FORESTS 2022. [DOI: 10.3390/f13020338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Xanthoceras sorbifolium is one of the most important species of woody oil. In this study, whole genome re-sequencing of 119 X. sorbifolium germplasms was conducted and, after filtering, 105,685,557 high-quality SNPs were identified, which were used to perform population genetics and core collection development analyses. The results from the phylogenetic, population structure, and principal component analyses showed a high level of agreement, with 119 germplasms being classified into three main groups. The germplasms were not completely classified based on their geographical origins and flower colors; furthermore, the genetic backgrounds of these germplasms were complex and diverse. The average polymorphsim information content (PIC) values for the three inferred groups clustered by structure analysis and the six classified color groups were 0.2445 and 0.2628, respectively, indicating a low to medium informative degree of genetic diversity. Moreover, a core collection containing 29.4% (35) out of the 119 X. sorbifolium germplasms was established. Our results revealed the genetic diversity and structure of X. sorbifolium germplasms, and the development of a core collection will be useful for the efficient improvement of breeding programs and genome-wide association studies.
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15
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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: 5] [Impact Index Per Article: 1.7] [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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16
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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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17
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Feng S, Liu Z, Cheng J, Li Z, Tian L, Liu M, Yang T, Liu Y, Liu Y, Dai H, Yang Z, Zhang Q, Wang G, Zhang J, Jiang H, Wei A. Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome. HORTICULTURE RESEARCH 2021; 8:205. [PMID: 34480029 PMCID: PMC8417289 DOI: 10.1038/s41438-021-00665-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 05/14/2023]
Abstract
Zanthoxylum bungeanum is an important spice and medicinal plant that is unique for its accumulation of abundant secondary metabolites, which create a characteristic aroma and tingling sensation in the mouth. Owing to the high proportion of repetitive sequences, high heterozygosity, and increased chromosome number of Z. bungeanum, the assembly of its chromosomal pseudomolecules is extremely challenging. Here, we present a genome sequence for Z. bungeanum, with a dramatically expanded size of 4.23 Gb, assembled into 68 chromosomes. This genome is approximately tenfold larger than that of its close relative Citrus sinensis. After the divergence of Zanthoxylum and Citrus, the lineage-specific whole-genome duplication event η-WGD approximately 26.8 million years ago (MYA) and the recent transposable element (TE) burst ~6.41 MYA account for the substantial genome expansion in Z. bungeanum. The independent Zanthoxylum-specific WGD event was followed by numerous fusion/fission events that shaped the genomic architecture. Integrative genomic and transcriptomic analyses suggested that prominent species-specific gene family expansions and changes in gene expression have shaped the biosynthesis of sanshools, terpenoids, and anthocyanins, which contribute to the special flavor and appearance of Z. bungeanum. In summary, the reference genome provides a valuable model for studying the impact of WGDs with recent TE activity on gene gain and loss and genome reconstruction and provides resources to accelerate Zanthoxylum improvement.
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Affiliation(s)
- Shijing Feng
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Zhenshan Liu
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Jian Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zihe Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shanxi, China
| | - Lu Tian
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Tuxi Yang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Yulin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Yonghong Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, China
| | - Zujun Yang
- Center for Information in Biology, College of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gang Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China.
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Yanhe Lang. Genome-Wide Identification and Characterization of Yellow Horn (Xanthoceras sorbifolia Bunge) NAC Transcription Factor Gene Family against Diverse Abiotic Stresses. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421040062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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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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20
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Liu F, Wang P, Xiong X, Zeng X, Zhang X, Wu G. A Review of Nervonic Acid Production in Plants: Prospects for the Genetic Engineering of High Nervonic Acid Cultivars Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:626625. [PMID: 33747006 PMCID: PMC7973461 DOI: 10.3389/fpls.2021.626625] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/29/2021] [Indexed: 05/15/2023]
Abstract
Nervonic acid (NA) is a very-long-chain monounsaturated fatty acid that plays crucial roles in brain development and has attracted widespread research interest. The markets encouraged the development of a refined, NA-enriched plant oil as feedstocks for the needed further studies of NA biological functions to the end commercial application. Plant seed oils offer a renewable and environmentally friendly source of NA, but their industrial production is presently hindered by various factors. This review focuses on the NA biosynthesis and assembly, NA resources from plants, and the genetic engineering of NA biosynthesis in oil crops, discusses the factors that affect NA production in genetically engineered oil crops, and provides prospects for the application of NA and prospective trends in the engineering of NA. This review emphasizes the progress made toward various NA-related topics and explores the limitations and trends, thereby providing integrated and comprehensive insight into the nature of NA production mechanisms during genetic engineering. Furthermore, this report supports further work involving the manipulation of NA production through transgenic technologies and molecular breeding for the enhancement of crop nutritional quality or creation of plant biochemical factories to produce NA for use in nutraceutical, pharmaceutical, and chemical industries.
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Affiliation(s)
- Fang Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Pandi Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojuan Xiong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xinhua Zeng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaobo Zhang
- Life Science and Technology Center, China National Seed Group Co. Ltd., Wuhan, China
| | - Gang Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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21
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Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, Zhou H. Review on the Development and Applications of Medicinal Plant Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:791219. [PMID: 35003182 PMCID: PMC8732986 DOI: 10.3389/fpls.2021.791219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.
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Affiliation(s)
- Qi-Qing Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yue Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zi-Yu Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chi-Chou Lao
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yan-Yu Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chun-Song Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, The Ministry of Education of the People’s Republic of China, Macau University of Science and Technology, Taipa, Macao SAR, China
- *Correspondence: Hua Zhou,
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22
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Ma Q, Sun T, Li S, Wen J, Zhu L, Yin T, Yan K, Xu X, Li S, Mao J, Wang Y, Jin S, Zhao X, Li Q. The Acer truncatum genome provides insights into nervonic acid biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:662-678. [PMID: 32772482 PMCID: PMC7702125 DOI: 10.1111/tpj.14954] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 07/08/2020] [Accepted: 07/21/2020] [Indexed: 05/10/2023]
Abstract
Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high-quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 kb; scaffold N50 = 46.36 Mb) with at least 28 438 predicted genes. The genome underwent an ancient triplication, similar to the core eudicots, but there have been no recent whole-genome duplication events. Acer yangbiense and A. truncatum are estimated to have diverged about 9.4 million years ago. A combined genomic, transcriptomic, metabonomic, and cell ultrastructural analysis provided new insights into the biosynthesis of very long-chain monounsaturated fatty acids. In addition, three KCS genes were found that may contribute to regulating nervonic acid biosynthesis. The KCS paralogous gene family expanded to 28 members, with 10 genes clustered together and distributed in the 0.27-Mb region of pseudochromosome 4. Our chromosome-scale genomic characterization may facilitate the discovery of agronomically important genes and stimulate functional genetic research on A. truncatum. Furthermore, the data presented also offer important foundations from which to study the molecular mechanisms influencing the production of nervonic acids.
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Affiliation(s)
- Qiuyue Ma
- Institute of Leisure AgricultureJiangsu Academy of Agricultural SciencesJiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing210014China
| | - Tianlin Sun
- Novogene Bioinformatics InstituteBeijing100083China
| | - Shushun Li
- Institute of Leisure AgricultureJiangsu Academy of Agricultural SciencesJiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing210014China
| | - Jing Wen
- Institute of Leisure AgricultureJiangsu Academy of Agricultural SciencesJiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing210014China
| | - Lu Zhu
- Institute of Leisure AgricultureJiangsu Academy of Agricultural SciencesJiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing210014China
| | - Tongming Yin
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of ForestryNanjing Forestry UniversityNanjing210037China
| | - Kunyuan Yan
- Institute of Leisure AgricultureJiangsu Academy of Agricultural SciencesJiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing210014China
| | - Xiao Xu
- Novogene Bioinformatics InstituteBeijing100083China
| | - Shuxian Li
- The Southern Modern Forestry Collaborative Innovation CenterNanjing Forestry UniversityNanjing210037China
| | - Jianfeng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing100083China
| | - Ya‐nan Wang
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of ForestryNanjing Forestry UniversityNanjing210037China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Xing Zhao
- Novogene Bioinformatics InstituteBeijing100083China
| | - Qianzhong Li
- Institute of Leisure AgricultureJiangsu Academy of Agricultural SciencesJiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing210014China
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Construction of Pseudomolecules for the Chinese Chestnut ( Castanea mollissima) Genome. G3-GENES GENOMES GENETICS 2020; 10:3565-3574. [PMID: 32847817 PMCID: PMC7534444 DOI: 10.1534/g3.120.401532] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Chinese chestnut (Castanea mollissima Bl.) is a woody nut crop with a high ecological value. Although many cultivars have been selected from natural seedlings, elite lines with comprehensive agronomic traits and characters remain rare. To explore genetic resources with aid of whole genome sequence will play important roles in modern breeding programs for chestnut. In this study, we generated a high-quality C. mollissima genome assembly by combining 90× Pacific Biosciences long read and 170× high-throughput chromosome conformation capture data. The assembly was 688.93 Mb in total, with a contig N50 of 2.83 Mb. Most of the assembled sequences (99.75%) were anchored onto 12 chromosomes, and 97.07% of the assemblies were accurately anchored and oriented. A total of 33,638 protein-coding genes were predicted in the C. mollissima genome. Comparative genomic and transcriptomic analyses provided insights into the genes expressed in specific tissues, as well as those associated with burr development in the Chinese chestnut. This highly contiguous assembly of the C. mollissima genome provides a valuable resource for studies aiming at identifying and characterizing agronomical-important traits, and will aid the design of breeding strategies to develop more focused, faster, and predictable improvement programs.
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Lang Y, Liu Z. Basic Helix-Loop-Helix (bHLH) transcription factor family in Yellow horn (Xanthoceras sorbifolia Bunge): Genome-wide characterization, chromosome location, phylogeny, structures and expression patterns. Int J Biol Macromol 2020; 160:711-723. [DOI: 10.1016/j.ijbiomac.2020.05.253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 11/27/2022]
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25
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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: 25] [Impact Index Per Article: 6.3] [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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26
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Wang J, Guo J, Zhang Y, Yan X. Integrated transcriptomic and metabolomic analyses of yellow horn (Xanthoceras sorbifolia) in response to cold stress. PLoS One 2020; 15:e0236588. [PMID: 32706804 PMCID: PMC7380624 DOI: 10.1371/journal.pone.0236588] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/08/2020] [Indexed: 01/10/2023] Open
Abstract
Xanthoceras sorbifolia, a medicinal and oil-rich woody plant, has great potential for biodiesel production. However, little study explores the link between gene expression level and metabolite accumulation of X. sorbifolia in response to cold stress. Herein, we performed both transcriptomic and metabolomic analyses of X. sorbifolia seedlings to investigate the regulatory mechanism of resistance to low temperature (4 °C) based on physiological profile analyses. Cold stress resulted in a significant increase in the malondialdehyde content, electrolyte leakage and activity of antioxidant enzymes. A total of 1,527 common differentially expressed genes (DEGs) were identified, of which 895 were upregulated and 632 were downregulated. Annotation of DEGs revealed that amino acid metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, galactose metabolism, fructose and mannose metabolism, and the citrate cycle (TCA) were strongly affected by cold stress. In addition, DEGs within the plant mitogen-activated protein kinase (MAPK) signaling pathway and TF families of ERF, WRKY, NAC, MYB, and bHLH were transcriptionally activated. Through metabolomic analysis, we found 51 significantly changed metabolites, particularly with the analysis of primary metabolites, such as sugars, amino acids, and organic acids. Moreover, there is an overlap between transcript and metabolite profiles. Association analysis between key genes and altered metabolites indicated that amino acid metabolism and sugar metabolism were enhanced. A large number of specific cold-responsive genes and metabolites highlight a comprehensive regulatory mechanism, which will contribute to a deeper understanding of the highly complex regulatory program under cold stress in X. sorbifolia.
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Affiliation(s)
- Juan Wang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
| | - Jinping Guo
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
| | - Yunxiang Zhang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
| | - Xingrong Yan
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, Shanxi, China
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27
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Lang Y, Liu Z, Zheng Z. Retracted Article: Investigation of yellow horn ( Xanthoceras sorbifolia Bunge) transcriptome in response to different abiotic stresses: a comparative RNA-Seq study. RSC Adv 2020; 10:6512-6519. [PMID: 35496033 PMCID: PMC9049705 DOI: 10.1039/c9ra09535g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/05/2020] [Indexed: 01/23/2023] Open
Abstract
Yellow horn (Xanthoceras sorbifolia Bunge) is a well-known oil-rich seed shrub which can grow well in barren and arid environments in the northern part of China. Yellow horn has received worldwide attention because of its excellent economic and environmental value. However, because of its limited genetic data, little information can be found regarding the molecular defense mechanisms of yellow horn exposed to various abiotic stresses. In view of this, the current study aims to investigate the impact of different abiotic stresses (i.e. NaCl, ABA and low temperature) on the transcriptome of yellow horn using RNA-Seq. Based on the transcriptome sequencing data, approximately 27% to 45% of stress-responsive genes were found highly expressed after stress treatment for 24 h. In addition, these genes were found to be still expressed after stress treatment for 48 h. However, many additional genes were stress-regulated after 48 h treatment compared with the 24 h treatment. GO enrichment analysis revealed that the expression patterns of the stress-responsive, type-specific terms were generally down-regulated. Most shared GO terms were primarily involved in protein folding, unfolding protein binding, protein transport and protein modification. Further, transcription factors (TFs), such as ERFs, bHLH, GRAS and NAC, were found to be enriched only in the low temperature treatment group, particularly the ERF TFs families. These combined results suggested that yellow horn may have developed specific molecular defense systems against diverse abiotic stresses.
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Affiliation(s)
- Yanhe Lang
- State Key Laboratory of Tree Genetics and Breeding Laboratory, Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), College of Life Science, Northeast Forestry University Harbin Heilongjiang Province China +86-151-0453-8096
| | - Zhi Liu
- State Key Laboratory of Tree Genetics and Breeding Laboratory, Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), College of Life Science, Northeast Forestry University Harbin Heilongjiang Province China +86-151-0453-8096
| | - Zhimin Zheng
- State Key Laboratory of Tree Genetics and Breeding Laboratory, Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), College of Life Science, Northeast Forestry University Harbin Heilongjiang Province China +86-151-0453-8096
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28
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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: 35] [Impact Index Per Article: 7.0] [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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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: 29] [Impact Index Per Article: 5.8] [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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