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Yin X, Yang D, Zhao Y, Yang X, Zhou Z, Sun X, Kong X, Li X, Wang G, Duan Y, Yang Y, Yang Y. Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies. PLANT COMMUNICATIONS 2023; 4:100427. [PMID: 36056558 PMCID: PMC9860189 DOI: 10.1016/j.xplc.2022.100427] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 07/30/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Pseudogenes are important resources for investigation of genome evolution and genomic diversity because they are nonfunctional but have regulatory effects that influence plant adaptation and diversification. However, few systematic comparative analyses of pseudogenes in closely related species have been conducted. Here, we present a turnip (Brassica rapa ssp. rapa) genome sequence and characterize pseudogenes among diploid Brassica species/subspecies. The results revealed that the number of pseudogenes was greatest in Brassica oleracea (CC genome), followed by B. rapa (AA genome) and then Brassica nigra (BB genome), implying that pseudogene differences emerged after species differentiation. In Brassica AA genomes, pseudogenes were distributed asymmetrically on chromosomes because of numerous chromosomal insertions/rearrangements, which contributed to the diversity among subspecies. Pseudogene differences among subspecies were reflected in the flavor-related glucosinolate (GSL) pathway. Specifically, turnip had the highest content of pungent substances, probably because of expansion of the methylthioalkylmalate synthase-encoding gene family in turnips; these genes were converted into pseudogenes in B. rapa ssp. pekinensis (Chiifu). RNA interference-based silencing of the gene encoding 2-oxoglutarate-dependent dioxygenase 2, which is also associated with flavor and anticancer substances in the GSL pathway, resulted in increased abundance of anticancer compounds and decreased pungency of turnip and Chiifu. These findings revealed that pseudogene differences between turnip and Chiifu influenced the evolution of flavor-associated GSL metabolism-related genes, ultimately resulting in the different flavors of turnip and Chiifu.
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Affiliation(s)
- Xin Yin
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Danni Yang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youjie Zhao
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, Yunnan, China
| | - Xingyu Yang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhili Zhou
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xudong Sun
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiangxiang Kong
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiong Li
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Guangyan Wang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yuanwen Duan
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yunqiang Yang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Yongping Yang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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Alrifai O, Mats L, Liu R, Hao X, Marcone MF, Tsao R. Effect of combined light-emitting diodes on the accumulation of glucosinolates in Brassica microgreens. FOOD PRODUCTION, PROCESSING AND NUTRITION 2021. [DOI: 10.1186/s43014-021-00072-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
AbstractAs of recent, microgreen vegetable production in controlled environments are being investigated for their bioactive properties. Phytochemicals like glucosinolates (GLS) are highly sensitive to varying spectral qualities of light, especially in leafy greens of Brassica where the responses are highly species-dependent. The accumulation of bioactive GLS were studied under 8 different treatments of combined amber (590 nm), blue (455 nm), and red (655 nm) light-emitting diodes (rbaLED). A semi-targeted metabolomics approach was carried out to profile common intact-GLS in microgreen extracts of Brassica by means of LC-HRMS/MS. Thirteen GLS were identified, among them were 8 aliphatic, 4 indolic and 1 aromatic GLS. Mass spectrometry data showed sinigrin had the highest average concentration and was highest in B. juncea, progoitrin was highest in B. rapa and glucobrassicin in R. sativus. The individual and total GLS in the microgreens of the present study were largely different under rbaLED; B. rapa microgreens contained the highest profile of total GLS, followed by R. sativus and B. juncea. Sinigrin was increased and gluconasturtiin was decreased under rbaLED lighting in most microgreens, glucoalyssin uniquely increased in R. sativus and decreased in B. rapa and glucobrassicin uniquely decreased in both B. rapa and B. juncea. The present study showed that rbaLED contributed to the altered profiles of GLS resulting in their significant modulation. Optimizing the light spectrum for improved GLS biosynthesis could lead to production of microgreens with targeted health-promoting properties.
Graphical Abstract
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Improvement of glucosinolates by metabolic engineering in Brassica crops. ABIOTECH 2021; 2:314-329. [PMID: 36303883 PMCID: PMC9590530 DOI: 10.1007/s42994-021-00057-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/07/2021] [Indexed: 02/08/2023]
Abstract
Glucosinolates (GSLs) are a class of sulfur- and nitrogen-containing, and amino acid-derived important secondary metabolites, which mainly present in plants of Brassicaceae family, including Brassica crops, such as broccoli, cabbage, and oilseed rape. The bioactive GSL metabolites confer benefits to plant defense, human health, and the unique flavor of some Brassica crops. However, certain GSL profiles have adverse effects and are known as anti-nutritional factors. This has attracted mounting attempts to increase beneficial GSLs and reduce detrimental ones in the most commonly consumed Brassica crops. We provide a comprehensive overview of metabolic engineering applied in Brassica crops to achieve this purpose, including modulation of GSL biosynthesis, ablation of GSL hydrolysis, inhibition of GSL transport processes, and redirection of metabolic flux to GSL. Moreover, advances in omics approaches, i.e., genomics, transcriptome, and metabolome, applied in the elucidation of GSL metabolism in Brassica crops, as well as promising and potential genome-editing technologies are also discussed.
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Zhao Y, Chen Z, Chen J, Chen B, Tang W, Chen X, Lai Z, Guo R. Comparative transcriptomic analyses of glucosinolate metabolic genes during the formation of Chinese kale seeds. BMC PLANT BIOLOGY 2021; 21:394. [PMID: 34418959 PMCID: PMC8380351 DOI: 10.1186/s12870-021-03168-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/10/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND To understand the mechanism of glucosinolates (GSs) accumulation in the specific organs, combined analysis of physiological change and transcriptome sequencing were applied in the current study. Taking Chinese kale as material, seeds and silique walls were divided into different stages based on the development of the embryo in seeds and then subjected to GS analysis and transcriptome sequencing. RESULTS The main GS in seeds of Chinese kale were glucoiberin and gluconapin and their content changed with the development of the seed. During the transition of the embryo from torpedo- to the early cotyledonary-embryo stage, the accumulation of GS in the seed was accompanied by the salient decline of GS in the corresponding silique wall. Thus, the seed and corresponding silique wall at these two stages were subjected to transcriptomic sequencing analysis. 135 genes related to GS metabolism were identified, of which 24 genes were transcription factors, 81 genes were related to biosynthetic pathway, 25 genes encoded catabolic enzymes, and 5 genes matched with transporters. The expression of GS biosynthetic genes was detected both in seeds and silique walls. The high expression of FMOGS-OX and AOP2, which is related to the production of gluconapin by side modification, was noted in seeds at both stages. Interestingly, the expression of GS biosynthetic genes was higher in the silique wall compared with that in the seed albeit lower content of GS existed in the silique wall than in the seed. Combined with the higher expression of transporter genes GTRs in silique walls than in seeds, it was proposed that the transportation of GS from the silique wall to the seed is an important source for seed GS accumulation. In addition, genes related to GS degradation expressed abundantly in the seed at the early cotyledonary-embryo stage indicating its potential role in balancing seed GS content. CONCLUSIONS Two stages including the torpedo-embryo and the early cotyledonary-embryo stage were identified as crucial in GS accumulation during seed development. Moreover, we confirmed the transportation of GS from the silique wall to the seed and proposed possible sidechain modification of GS biosynthesis may exist during seed formation.
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Affiliation(s)
- Yijiao Zhao
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zeyuan Chen
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jiaxuan Chen
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Bingxing Chen
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weiling Tang
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaodong Chen
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhongxiong Lai
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Rongfang Guo
- College of Horticulture, Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Song X, Wei Y, Xiao D, Gong K, Sun P, Ren Y, Yuan J, Wu T, Yang Q, Li X, Nie F, Li N, Feng S, Pei Q, Yu T, Zhang C, Liu T, Wang X, Yang J. Brassica carinata genome characterization clarifies U's triangle model of evolution and polyploidy in Brassica. PLANT PHYSIOLOGY 2021; 186:388-406. [PMID: 33599732 PMCID: PMC8154070 DOI: 10.1093/plphys/kiab048] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/12/2021] [Indexed: 05/03/2023]
Abstract
Ethiopian mustard (Brassica carinata) in the Brassicaceae family possesses many excellent agronomic traits. Here, the high-quality genome sequence of B. carinata is reported. Characterization revealed a genome anchored to 17 chromosomes with a total length of 1.087 Gb and an N50 scaffold length of 60 Mb. Repetitive sequences account for approximately 634 Mb or 58.34% of the B. carinata genome. Notably, 51.91% of 97,149 genes are confined to the terminal 20% of chromosomes as a result of the expansion of repeats in pericentromeric regions. Brassica carinata shares one whole-genome triplication event with the five other species in U's triangle, a classic model of evolution and polyploidy in Brassica. Brassica carinata was deduced to have formed ∼0.047 Mya, which is slightly earlier than B. napus but later than B. juncea. Our analysis indicated that the relationship between the two subgenomes (BcaB and BcaC) is greater than that between other two tetraploid subgenomes (BjuB and BnaC) and their respective diploid parents. RNA-seq datasets and comparative genomic analysis were used to identify several key genes in pathways regulating disease resistance and glucosinolate metabolism. Further analyses revealed that genome triplication and tandem duplication played important roles in the expansion of those genes in Brassica species. With the genome sequencing of B. carinata completed, the genomes of all six Brassica species in U's triangle are now resolved. The data obtained from genome sequencing, transcriptome analysis, and comparative genomic efforts in this study provide valuable insights into the genome evolution of the six Brassica species in U's triangle.
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Affiliation(s)
- Xiaoming Song
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
- Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE 68526, USA
- School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yanping Wei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ke Gong
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Pengchuan Sun
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yiming Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaqing Yuan
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tong Wu
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Qihang Yang
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Xinyu Li
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fulei Nie
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Nan Li
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Shuyan Feng
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Qiaoying Pei
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tong Yu
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
- Author for communication:
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiyin Wang
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
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