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Wang C, Peng D, Zhu J, Zhao D, Shi Y, Zhang S, Ma K, Wu J, Huang L. Transcriptome analysis of Polygonatum cyrtonema Hua: identification of genes involved in polysaccharide biosynthesis. PLANT METHODS 2019; 15:65. [PMID: 31289459 PMCID: PMC6593569 DOI: 10.1186/s13007-019-0441-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 05/17/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Polygonatum cyrtonema Hua (P. cyrtonema) is one of the most important herbs in traditional Chinese medicine. Polysaccharides in P. cyrtonema plants comprise a class of important secondary metabolites and exhibit a broad range of pharmacological functions. RESULTS In order to identify genes involved in polysaccharide biosynthesis, we performed RNA sequencing analysis of leaf, root, and rhizome tissues of P. cyrtonema. A total of 164,573 unigenes were obtained by assembling transcripts from all three tissues and 86,063 of these were annotated in public databases. Differentially expressed genes (DEGs) were determined based on expression profile analysis, and DEG levels in rhizome tissues were then compared with their counterparts in leaf and root tissues. This analysis revealed numerous genes that were either up-regulated or uniquely expressed in the rhizome. Multiple genes encoding important enzymes, such as UDP glycosyltransferases (UGTs), or transcription factors involved in polysaccharide biosynthesis were identified and further analyzed, while a few genes encoding key enzymes were experimentally validated using quantitative real-time PCR. CONCLUSION Our results substantially expand the public transcriptome dataset of P. cyrtonema and provide valuable clues for the identification of candidate genes involved in metabolic pathways.
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Affiliation(s)
- Chenkai Wang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038 China
| | - Daiyin Peng
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230012 China
| | - Jinhang Zhu
- Anhui Medical University, Hefei, 230032 China
| | - Derui Zhao
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038 China
| | - Yuanyuan Shi
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038 China
| | - Shengxiang Zhang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038 China
| | - Kelong Ma
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Clinical College of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Jiawen Wu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038 China
- Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230012 China
| | - Luqi Huang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038 China
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Zhang Z, Zhang K, Chen S, Zhang Z, Zhang J, You X, Bian C, Xu J, Jia C, Qiang J, Zhu F, Li H, Liu H, Shen D, Ren Z, Chen J, Li J, Gao T, Gu R, Xu J, Shi Q, Xu P. Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii. Gigascience 2018; 7:1-7. [PMID: 29659813 PMCID: PMC5893958 DOI: 10.1093/gigascience/giy012] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/12/2018] [Indexed: 01/08/2023] Open
Abstract
Background As one of the most popular and valuable commercial marine fishes in China and East Asian countries, the Chinese black porgy (Acanthopagrus schlegelii), also known as the blackhead seabream, has some attractive characteristics such as fast growth rate, good meat quality, resistance to diseases, and excellent adaptability to various environments. Furthermore, the black porgy is a good model for investigating sex changes in fish due to its protandrous hermaphroditism. Here, we obtained a high-quality genome assembly of this interesting teleost species and performed a genomic survey on potential genes associated with the sex-change phenomenon. Findings We generated 175.4 gigabases (Gb) of clean sequence reads using a whole-genome shotgun sequencing strategy. The final genome assembly is approximately 688.1 megabases (Mb), accounting for 93% of the estimated genome size (739.6 Mb). The achieved scaffold N50 is 7.6 Mb, reaching a relatively high level among sequenced fish species. We identified 19 465 protein-coding genes, which had an average transcript length of 17.3 kb. By performing a comparative genomic analysis, we found 3 types of genes potentially associated with sex change, which are useful for studying the genetic basis of the protandrous hermaphroditism. Conclusions We provide a draft genome assembly of the Chinese black porgy and discuss the potential genetic mechanisms of sex change. These data are also an important resource for studying the biology and for facilitating breeding of this economically important fish.
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Affiliation(s)
- Zhiyong Zhang
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Kai Zhang
- Freshwater Fishery Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Shuyin Chen
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Zhiwei Zhang
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Jinyong Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430000, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China
| | - Jin Xu
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Chaofeng Jia
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Jun Qiang
- Freshwater Fishery Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Fei Zhu
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Hongxia Li
- Freshwater Fishery Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Hailin Liu
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Dehua Shen
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Zhonghong Ren
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Jieming Chen
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Tianheng Gao
- College of Oceanography, Hohhai University, Nanjing, Jiangsu 210098, China
| | - Ruobo Gu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China.,BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, Jiangsu 212000, China
| | - Pao Xu
- Freshwater Fishery Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
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Zhang K, Xu J, Zhang Z, Huang Y, Ruan Z, Chen S, Zhu F, You X, Jia C, Meng Q, Gu R, Lin X, Xu J, Xu P, Zhang Z, Shi Q. A comparative transcriptomic study on developmental gonads provides novel insights into sex change in the protandrous black porgy (Acanthopagrus schlegelii). Genomics 2018; 111:277-283. [PMID: 30439483 DOI: 10.1016/j.ygeno.2018.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 10/31/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
Abstract
Protandrous black porgy (Acanthopagrus schlegelii) is a popular and valuable commercial marine fish in China and East Asian countries. Controlling and managing its breeding has been an imperative step towards obtaining a sustainable supply of this fish in aquaculture production systems. Therefore, study on the molecular mechanisms of sex change in black porgy has both scientific and commercial importance. Previously, we identified some candidate genes related to sex determination and differentiation from a high-quality genome assembly of the black porgy. In the present study, transcriptome sequencing of developmental gonads (including testis, ovotestis and ovary) of black porgy was performed to further investigate the sex-change mechanisms. Our results showed that the highly expressed male-related genes (dmrt1, piwi1, piwi2, sox9, sox30 and amh) at the male phase were significantly down-regulated to a substantial degree at the intersexual stage, and the female-related genes (jnk1, vasa, wnt4, figla and foxl2) were distinctly up-regulated when the fish grows into a female adult, suggesting the potential roles of these genes in sex change of the black porgy. These data also support a previous hypothesis that the femaleness will be switched on when the testis is entering the degenerated stage through the diminished dmrt1 expression. Our transcriptome data provide a very useful genomic resource for future studies on sex change and practical aquaculture in the black porgy.
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Affiliation(s)
- Kai Zhang
- School of Animal and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Jin Xu
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Zhiwei Zhang
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Zhiqiang Ruan
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Shuyin Chen
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Fei Zhu
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Chaofeng Jia
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Qian Meng
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China
| | - Ruobo Gu
- BGI-Zhenjiang Institute of Hydrobiology, BGI Marine, Zhenjiang 212000, China.
| | - Xueqiang Lin
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China; Hainan BGI Marine Science and Technology Co. Ltd., BGI Marine, Wenchang 571327, China.
| | - Junmin Xu
- BGI-Zhenjiang Institute of Hydrobiology, BGI Marine, Zhenjiang 212000, China; School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan.
| | - Pao Xu
- Freshwater Fishery Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China.
| | - Zhiyong Zhang
- Jiangsu Marine Fishery Research Institute, Nantong, Jiangsu 226007, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China; BGI-Zhenjiang Institute of Hydrobiology, BGI Marine, Zhenjiang 212000, China.
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