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Jiao X, Li X, Zhang N, Zhang W, Yan B, Huang J, Zhao J, Zhang H, Chen W, Fan D. Postmortem Muscle Proteome Characteristics of Silver Carp ( Hypophthalmichthys molitrix): Insights from Full-Length Transcriptome and Deep 4D Label-Free Proteomic. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1376-1390. [PMID: 38165648 DOI: 10.1021/acs.jafc.3c06902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
The coverage of the protein database directly determines the results of shotgun proteomics. In this study, PacBio single-molecule real-time sequencing technology was performed on postmortem silver carp muscle transcripts. A total of 42.43 Gb clean data, 35,834 nonredundant transcripts, and 15,413 unigenes were obtained. In total, 99.32% of the unigenes were successfully annotated and assigned specific functions. PacBio long-read isoform sequencing (Iso-Seq) analysis can provide more accurate protein information with a higher proportion of complete coding sequences and longer lengths. Subsequently, 2671 proteins were identified in deep 4D proteomics informed by a full-length transcriptomics technique, which has been shown to improve the identification of low-abundance muscle proteins and potential protein isoforms. The feature of the sarcomeric protein profile and information on more than 30 major proteins in the white dorsal muscle of silver carp were reported here for the first time. Overall, this study provides valuable transcriptome data resources and the comprehensive muscle protein information detected to date for further study into the processing characteristic of early postmortem fish muscle, as well as a spectral library for data-independent acquisition and data processing. This batch of muscle-specific dependent acquisition data is available via PRIDE with identifier PXD043702.
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Affiliation(s)
- Xidong Jiao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xingying Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Nana Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Ministry of Agriculture and Rural Affairs, Xiamen 361022, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wenhai Zhang
- Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Ministry of Agriculture and Rural Affairs, Xiamen 361022, China
- Fujian Provincial Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Xiamen 361022, China
- Anjoy Foods Group Co., Ltd., Xiamen 361022, China
| | - Bowen Yan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Ministry of Agriculture and Rural Affairs, Xiamen 361022, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianlian Huang
- Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Ministry of Agriculture and Rural Affairs, Xiamen 361022, China
- Fujian Provincial Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Xiamen 361022, China
- Anjoy Foods Group Co., Ltd., Xiamen 361022, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Daming Fan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Ministry of Agriculture and Rural Affairs, Xiamen 361022, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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