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Wang M, Chen Y, Li S, Yu J, Yang L, Hong L. Widely Targeted Metabolomic Analysis Provides New Insights into the Effect of Rootstocks on Citrus Fruit Quality. Metabolites 2024; 14:242. [PMID: 38668370 PMCID: PMC11052146 DOI: 10.3390/metabo14040242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
The use of different rootstocks has a significant effect on the content of flavor components and overall fruit quality. However, little information is available about the metabolic basis of the nutritional value of citrus plants. In this study, UPLC-MS/MS (ultra-performance liquid chromatography-tandem mass spectrometry) was performed to analyze the metabolites of three late-maturing hybrid mandarin varieties ('Gold Nugget', 'Tango' and 'Orah') grafted on four rootstocks ('Trifoliate orange', 'Carrizo citrange', 'Red tangerine' and 'Ziyang Xiangcheng'). A total of 1006 metabolites were identified through OPLS-DA (Orthogonal Partial Least Squares-Discriminant Analysis) analysis. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed the most critical pathways among the different pathways associated with genes grafted on the four rootstocks that were differentially activated, including tryptophan metabolism and sphingolipid metabolism in 'Gold Nugget'; tryptophan metabolism, phenylpropanoid biosynthesis and sphingolipid metabolism in 'Tango'; and pantothenate and CoA biosynthesis- and photosynthesis-related biosynthesis in 'Orah'. A considerable difference between the different rootstocks was also observed in the accumulation of lipids, phenolic acids and flavonoids; further analysis revealed that the rootstocks regulated specific metabolites, including deacetylnomylinic acid, sudachinoid A, amoenin evodol, rutaevin, cyclo (phenylalanine-glutamic acid), cyclo (proline-phenylalanine), 2-hydroxyisocaproic acid, and 2-hydroxy-3-phenylpropanoic acid. The results of this study provide a useful foundation for further investigation of rootstock selection for late-maturation hybrid mandarin varieties.
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Affiliation(s)
- Min Wang
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (M.W.); (S.L.); (J.Y.)
- Key Laboratory of Evaluation and Utilization for Special Crops Germplasm Resource in the Southwest Mountains, Ministry of Agriculture and Rural Affairs, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China;
| | - Yang Chen
- Key Laboratory of Evaluation and Utilization for Special Crops Germplasm Resource in the Southwest Mountains, Ministry of Agriculture and Rural Affairs, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China;
- Biotechnology Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Shuang Li
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (M.W.); (S.L.); (J.Y.)
- Key Laboratory of Evaluation and Utilization for Special Crops Germplasm Resource in the Southwest Mountains, Ministry of Agriculture and Rural Affairs, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China;
| | - Jianjun Yu
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (M.W.); (S.L.); (J.Y.)
- Key Laboratory of Evaluation and Utilization for Special Crops Germplasm Resource in the Southwest Mountains, Ministry of Agriculture and Rural Affairs, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China;
| | - Lei Yang
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (M.W.); (S.L.); (J.Y.)
- Key Laboratory of Evaluation and Utilization for Special Crops Germplasm Resource in the Southwest Mountains, Ministry of Agriculture and Rural Affairs, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China;
| | - Lin Hong
- Fruit Tree Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China; (M.W.); (S.L.); (J.Y.)
- Key Laboratory of Evaluation and Utilization for Special Crops Germplasm Resource in the Southwest Mountains, Ministry of Agriculture and Rural Affairs, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China;
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He S, Dong W, Chen J, Zhang J, Lin W, Yang S, Xu D, Zhou Y, Miao B, Wang W, Chen F. DataColor: unveiling biological data relationships through distinctive color mapping. Hortic Res 2024; 11:uhad273. [PMID: 38333729 PMCID: PMC10852383 DOI: 10.1093/hr/uhad273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/06/2023] [Indexed: 02/10/2024]
Abstract
In the era of rapid advancements in high-throughput omics technologies, the visualization of diverse data types with varying orders of magnitude presents a pressing challenge. To bridge this gap, we introduce DataColor, an all-encompassing software solution meticulously crafted to address this challenge. Our aim is to empower users with the ability to handle a wide array of data types through an assortment of tools, while simultaneously streamlining parameter selection for rapid insights and detailed enhancements. DataColor stands as a robust toolkit, encompassing 23 distinct tools coupled with over 600 parameters. The defining characteristic of this toolkit is its adept utilization of the color spectrum, allowing for the representation of data spanning diverse types and magnitudes. Through the integration of advanced algorithms encompassing data clustering, normalization, squarified layouts, and customizable parameters, DataColor unveils an abundance of insights that lay hidden within the intricate relationships embedded in the data. Whether you find yourself navigating the analysis of expansive datasets or embarking on the quest to visualize intricate patterns, DataColor stands as the comprehensive and potent solution. We extend the availability of DataColor to all users at no cost, accessible through the following link: https://github.com/frankgenome/DataColor.
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Affiliation(s)
- Shuang He
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Wei Dong
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou 510055, China
| | - Junhao Chen
- Department of Biology, Saint Louis University, St Louis, MO 63103, USA
| | - Junyu Zhang
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Weiwei Lin
- Merkle Business Information Consultancy (Nanjing) Co., Ltd, Nanjing 210032, China
| | - Shuting Yang
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Dong Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yuhan Zhou
- State Key Laboratory of Rice Biology & Breeding, Zhejiang Provincial Key Laboratory of Crop Germplasm, The Advanced Seed Institute, Zhejiang University, Hangzhou 310058, China
| | - Benben Miao
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Wenquan Wang
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Fei Chen
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
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Zhang K, Du M, Zhang H, Zhang X, Cao S, Wang X, Wang W, Guan X, Zhou P, Li J, Jiang W, Tang M, Zheng Q, Cao M, Zhou Y, Chen K, Liu Z, Fang Y. The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes. Hortic Res 2023; 10:uhad205. [PMID: 38046853 PMCID: PMC10689054 DOI: 10.1093/hr/uhad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/01/2023] [Indexed: 12/05/2023]
Abstract
Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin, flesh, and vegetative tissues, endowing them with high utility value in red wine blending and nutrient-enriched foods developing. However, due to the lack of genome information, the mechanism involved in regulating teinturier grape coloring has not yet been elucidated and their genetic utilization research is still insufficient. Here, the cultivar 'Yan73' was used for assembling the telomere-to-telomere (T2T) genome of teinturier grapes by combining the High Fidelity (HiFi), Hi-C and ultralong Oxford Nanopore Technologies (ONT) reads. Two haplotype genomes were assembled, at the sizes of 501.68 Mb and 493.38 Mb, respectively. In the haplotype 1 genome, the transposable elements (TEs) contained 32.77% of long terminal repeats (LTRs), while in the haplotype 2 genome, 31.53% of LTRs were detected in TEs. Furthermore, obvious inversions were identified in chromosome 18 between the two haplotypes. Transcriptome profiling suggested that the gene expression patterns in 'Cabernet Sauvignon' and 'Yan73' were diverse depending on tissues, developmental stages, and varieties. The transcription program of genes in the anthocyanins biosynthesis pathway between the two cultivars exhibited high similarity in different tissues and developmental stages, whereas the expression levels of numerous genes showed significant differences. Compared with other genes, the expression levels of VvMYBA1 and VvUFGT4 in all samples, VvCHS2 except in young shoots and VvPAL9 except in the E-L23 stage of 'Yan73' were higher than those of 'Cabernet Sauvignon'. Further sequence alignments revealed potential variant gene loci and structure variations of anthocyanins biosynthesis related genes and a 816 bp sequence insertion was found in the promoter of VvMYBA1 of 'Yan73' haplotype 2 genome. The 'Yan73' T2T genome assembly and comparative analysis provided valuable foundations for further revealing the coloring mechanism of teinturier grapes and the genetic improvement of grape coloring traits.
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Affiliation(s)
- Kekun Zhang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Mengrui Du
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Hongyan Zhang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Xiaoqian Zhang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wenrui Wang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Xueqiang Guan
- Shandong Grape Research Institute, Shanda South Road, Jinan 250199, China
| | - Penghui Zhou
- Shandong Technology Innovation Center of Wine Grape and Wine, COFCO Great Wall Wine (Penglai) Co., Ltd., Yantai 265600, China
| | - Jin Li
- Shandong Technology Innovation Center of Wine Grape and Wine, COFCO Great Wall Wine (Penglai) Co., Ltd., Yantai 265600, China
| | | | - Meiling Tang
- Yantai Academy of Agricultural Sciences, Gangcheng West Street, Yantai 264000, China
| | - Qiuling Zheng
- Yantai Academy of Agricultural Sciences, Gangcheng West Street, Yantai 264000, China
| | - Muming Cao
- Viticulture and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 570100, China
| | - Keqin Chen
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yulin Fang
- College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling 712100, China
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4
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Monje-Rueda MD, Pal'ove-Balang P, Trush K, Márquez AJ, Betti M, García-Calderón M. Mutation of MYB36 affects isoflavonoid metabolism, growth, and stress responses in Lotus japonicus. Physiol Plant 2023; 175:e14084. [PMID: 38148200 DOI: 10.1111/ppl.14084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/11/2023] [Accepted: 10/29/2023] [Indexed: 12/28/2023]
Abstract
Isoflavonoids are mostly produced by legumes although little is known about why and how legumes are able to regulate the biosynthesis of these particular compounds. Understanding the role of potential regulatory genes of the isoflavonoid biosynthetic pathway constitutes an important topic of research. The LORE1 mutation of the gene encoding the transcription factor MYB36 allowed the identification of this gene as a regulator of isoflavonoid biosynthesis in Lotus japonicus plants. The levels of several isoflavonoid compounds were considerably lower in two lines of Ljmyb36 mutant plants compared to the WT. In addition, we found that Ljmyb36 mutant plants were significantly smaller and showed a substantial decrease in the chlorophyll levels under normal growth conditions. The analysis of plants subjected to different types of abiotic stress conditions further revealed that mutant plants presented a higher sensitivity than WT plants, indicating that the MYB36 transcription factor is also involved in the stress response in L. japonicus plants.
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Affiliation(s)
- María Dolores Monje-Rueda
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Sevilla, Spain
| | - Peter Pal'ove-Balang
- Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University in Košice, Košice, Slovakia
| | - Kristina Trush
- Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University in Košice, Košice, Slovakia
| | - Antonio J Márquez
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Sevilla, Spain
| | - Marco Betti
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Sevilla, Spain
| | - Margarita García-Calderón
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Sevilla, Spain
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5
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Zhong H, Yadav V, Wen Z, Zhou X, Wang M, Han S, Pan M, Zhang C, Zhang F, Wu X. Comprehensive metabolomics-based analysis of sugar composition and content in berries of 18 grape varieties. Front Plant Sci 2023; 14:1200071. [PMID: 37360706 PMCID: PMC10288860 DOI: 10.3389/fpls.2023.1200071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023]
Abstract
Xinjiang is the largest grape-producing region in China and the main grape cultivation area in the world. The Eurasian grape resources grown in Xinjiang are very rich in diversity. The sugar composition and content are the main factors that determine the quality of berries. However, there are currently no systematic reports on the types and contents of sugars in grapes grown in Xinjiang region. In this research, we evaluated the appearance and fruit maturity indicators of 18 grape varieties during fruit ripening and determined their sugar content using GC-MS. All cultivars primarily contained glucose, D-fructose, and sucrose. The glucose content in varieties varied from 42.13% to 46.80% of the total sugar, whereas the fructose and sucrose contents varied from 42.68% to 50.95% and 6.17% to 12.69%, respectively. The content of trace sugar identified in grape varieties varied from 0.6 to 2.3 mg/g. The comprehensive assessment by principal component analysis revealed strong positive correlations between some sugar components. A comprehensive study on the content and types of sugar will provide the foundation to determine the quality of grape cultivars and effective ways to utilize resources to improve sugar content through breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xinyu Wu
- *Correspondence: Fuchun Zhang, ; Xinyu Wu,
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Liu Z, Zhu C, Sun J, Zhang Z, Zhao S, Shi W, Wang W, Zhao B. Influence of rootstock on endogenous hormones and color change in Cabernet Sauvignon grapes. Sci Rep 2023; 13:6608. [PMID: 37095085 PMCID: PMC10125983 DOI: 10.1038/s41598-023-33089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
Different rootstocks for grapes can significantly affect fruit color and quality, possibly by affecting hormone contents, related genetic pathways, and fruit coloring mechanisms in skin. 'Cabernet Sauvignon' was grafted to '5BB', 'SO4', '140R', 'CS', '3309M' and 'Vitis riparia' rootstocks, with self-rooting seedlings as the control (CS/CS), and sampled from the early stage of veraison to the ripening stage. The effects of rootstock on the contents of gibberellin (GA3), auxin (IAA), and abscisic acid (ABA) in grape skin were determined alongside the expression levels of eight anthocyanin synthesis related genes using real-time fluorescence quantitative PCR methods. The rootstock cultivars exhibited accelerated fruit color change, and the CS/140R combination resulted in grapes with more color than the control group in the same period. With the development of fruit, the IAA and GA3 contents in the skin of different rootstock combinations showed trends of increasing initially, then decreasing, while the ABA content decreased initially and then increased. During the verasion (28 July), the various 'Cabernet Sauvignon' rootstock combinations exhibited varying degrees of increases in GA3, ABA, and IAA contents; correlation analysis showed that, at the start of veraison, the expression levels of the anthocyanin synthesis-related genes VvCHS, VvDFR, and VvUFGT had strong positive correlations with hormone contents, which indicated they are key genes involved in the endogenous hormone responsive anthocyanin biosynthesis pathway. The results of this study showed that rootstock regulates the fruit coloring process by influencing the metabolism level of peel hormones in the 'Cabernet Sauvignon' grape.
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Affiliation(s)
- Zhiyu Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China
| | - Chunmei Zhu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China
| | - Junli Sun
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China
| | - Zhijun Zhang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China
| | - Shucheng Zhao
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
| | - Wenchao Shi
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China
| | - Wei Wang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
| | - Baolong Zhao
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China.
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China.
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Li F, Xu S, Xiao Z, Wang J, Mei Y, Hu H, Li J, Liu J, Hou Z, Zhao J, Yang S, Wang J. Gap-free genome assembly and comparative analysis reveal the evolution and anthocyanin accumulation mechanism of Rhodomyrtus tomentosa. Hortic Res 2023; 10:uhad005. [PMID: 36938565 PMCID: PMC10022486 DOI: 10.1093/hr/uhad005] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/08/2021] [Indexed: 06/18/2023]
Abstract
Rhodomyrtus tomentosa is an important fleshy-fruited tree and a well-known medicinal plant of the Myrtaceae family that is widely cultivated in tropical and subtropical areas of the world. However, studies on the evolution and genomic breeding of R. tomentosa were hindered by the lack of a reference genome. Here, we presented a chromosome-level gap-free T2T genome assembly of R. tomentosa using PacBio and ONT long read sequencing. We assembled the genome with size of 470.35 Mb and contig N50 of ~43.80 Mb with 11 pseudochromosomes. A total of 33 382 genes and 239.31 Mb of repetitive sequences were annotated in this genome. Phylogenetic analysis elucidated the independent evolution of R. tomentosa starting from 14.37MYA and shared a recent WGD event with other Myrtaceae species. We identified four major compounds of anthocyanins and their synthetic pathways in R. tomentosa. Comparative genomic and gene expression analysis suggested the coloring and high anthocyanin accumulation in R. tomentosa tends to be determined by the activation of anthocyanin synthesis pathway. The positive selection and up-regulation of MYB transcription factors were the implicit factors in this process. The copy number increase of downstream anthocyanin transport-related OMT and GST gene were also detected in R. tomentosa. Expression analysis and pathway identification enriched the importance of starch degradation, response to stimuli, effect of hormones, and cell wall metabolism during the fleshy fruit development in Myrtaceae. Our genome assembly provided a foundation for investigating the origins and differentiation of Myrtaceae species and accelerated the genetic improvement of R. tomentosa.
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Affiliation(s)
| | | | | | - Jingming Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Yu Mei
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China
| | - Haifei Hu
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jingyu Li
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China
| | - Jieying Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Zhuangwei Hou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Junliang Zhao
- Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shaohai Yang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China
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Li Q, Gao Y, Wang K, Feng J, Sun S, Lu X, Liu Z, Zhao D, Li L, Wang D. Transcriptome Analysis of the Effects of Grafting Interstocks on Apple Rootstocks and Scions. Int J Mol Sci 2023; 24:ijms24010807. [PMID: 36614250 PMCID: PMC9821396 DOI: 10.3390/ijms24010807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/08/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
Apples are a major horticultural crop worldwide. Grafting techniques are widely utilized in apple production to keep the varieties pure. Interstocks are frequently used in Northern China to achieve intensive apple dwarfing cultivation. High-throughput sequencing was used to investigate differentially expressed genes in the phloem tissues of two different xenograft systems, M ('Gala'/'Mac 9'/Malus baccata (L.) Borkh.) and B ('Gala'/Malus baccata (L.) Borkh.). The results showed that dwarfing interstocks could significantly reduce the height and diameters of apple trees while have few effects on the growth of annual branches. The interstocks were found to regulate the expression of genes related to hormone metabolism and tree body control (GH3.9, PIN1, CKI1, ARP1, GA2ox1 and GA20ox1), these effects may attribute the dwarf characters for apple trees with interstocks. Besides, the interstocks reduce photosynthesis-related genes (MADH-ME4 and GAPC), promote carbon (C) metabolism gene expression (AATP1, GDH and PFK3), promote the expression of nitrogen (N)-metabolism-related genes (NRT2.7, NADH and GDH) in rootstocks, and improve the expression of genes related to secondary metabolism in scions (DX5, FPS1, TPS21 and SRG1). We also concluded that the interstocks acquired early blooming traits due to promotion of the expression of flowering genes in the scion (MOF1, FTIP7, AGL12 and AGL24). This study is a valuable resource regarding the molecular mechanisms of dwarf interstocks' influence on various biological processes and transplantation systems in both scions and rootstocks.
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Affiliation(s)
- Qingshan Li
- Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture and Rural Affairs of the People’s Republic of China, No. 98 Xinghai South Street, Xingcheng 125100, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China
| | - Yuan Gao
- Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture and Rural Affairs of the People’s Republic of China, No. 98 Xinghai South Street, Xingcheng 125100, China
| | - Kun Wang
- Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture and Rural Affairs of the People’s Republic of China, No. 98 Xinghai South Street, Xingcheng 125100, China
| | - Jianrong Feng
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China
| | - Simiao Sun
- Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture and Rural Affairs of the People’s Republic of China, No. 98 Xinghai South Street, Xingcheng 125100, China
| | - Xiang Lu
- Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture and Rural Affairs of the People’s Republic of China, No. 98 Xinghai South Street, Xingcheng 125100, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China
| | - Zhao Liu
- Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture and Rural Affairs of the People’s Republic of China, No. 98 Xinghai South Street, Xingcheng 125100, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China
| | - Deying Zhao
- Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture and Rural Affairs of the People’s Republic of China, No. 98 Xinghai South Street, Xingcheng 125100, China
| | - Lianwen Li
- Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture and Rural Affairs of the People’s Republic of China, No. 98 Xinghai South Street, Xingcheng 125100, China
| | - Dajiang Wang
- Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture and Rural Affairs of the People’s Republic of China, No. 98 Xinghai South Street, Xingcheng 125100, China
- Correspondence: ; Tel.: +86-429-359-8120
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