QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics
文献类型：期刊论文
| 作者 | Chen, Guisen5; Du, Hehe5; Cao, Zhenjie5; Wu, Ying5; Zhang, Chen5; Zhou, Yongcan5; Ao, Jingqun4; Sun, Yun2,3,5; Yuan, Zihao1 |
| 刊名 | MOLECULAR ECOLOGY RESOURCES
 |
| 出版日期 | 2026-01-12 |
| 卷号 | 26期号:2页码:12 |
| 关键词 | comparative genomics Epinephelinae gene prediction Rutaceae Xenopus |
| ISSN号 | 1755-098X |
| DOI | 10.1111/1755-0998.70097 |
| 通讯作者 | Sun, Yun(syshui207@126.com) ; Yuan, Zihao(yuanzihao@qdio.ac.cn) |
| 英文摘要 | The rapid growth of genome sequencing has outpaced the development of efficient annotation tools, especially for species lacking transcriptome data. To address this challenge, we present QuickProt, a fast, accurate and user-friendly homology-based protein annotation tool. QuickProt constructs a non-redundant gene model by aligning homologous proteins from closely related species, offering an accurate and cost-effective solution suitable for large-scale comparative genomic studies. Benchmarking against BRAKER2 and GALBA across reference genomes demonstrated that QuickProt offers high specificity and dramatically improved runtime, while maintaining competitive annotation accuracy. To demonstrate its utility, we applied QuickProt to diverse genomes, including a non-model teleost (Epinephelus bruneus), two tetraploid Xenopus species and 11 Rutaceae plants. Across these datasets, QuickProt supported robust phylogenetic reconstruction, identification of conserved orthologs and detection of biologically functional genes, pathways, and chromosomal evolution mechanisms, regardless of genome ploidy. Notably, it revealed a potential horizontal gene transfer event between groupers and Vibrio, and uncovered conserved modules involved in volatile oil biosynthesis and oil gland development in citrus. With its scalability and minimal computational demands, QuickProt provides a powerful platform for genome annotation and evolutionary inference. As the number of sequenced genomes continues to expand, QuickProt is a useful tool for accelerating comparative genomics and functional exploration across the tree of life. |
| WOS关键词 | RNA-SEQ ; EVOLUTION ; PREDICTION |
| 资助项目 | National Natural Science Foundation of China[U22A20534] ; Innovational Fund for Scientific and Technological Personnel of Hainan Province[KJRC2023C38] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:001659161700001 |
| 出版者 | WILEY |
| 源URL | [http://ir.qdio.ac.cn/handle/337002/204550]  |
| 专题 | 海洋研究所_实验海洋生物学重点实验室 |
| 通讯作者 | Sun, Yun; Yuan, Zihao |
| 作者单位 | 1.Chinese Acad Sci, Inst Oceanol, CAS Ctr Ocean Mega Sci, CAS & Shandong Prov Key Lab Expt Marine Biol, Qingdao, Peoples R China 2.Int Joint Res Ctr Hainan Prov Blue Carbon & Coasta, Haikou, Peoples R China 3.Engn Res Ctr Hainan Prov Blue Carbon & Coastal Wet, Haikou, Peoples R China 4.Fujian Agr & Forestry Univ, Coll Marine Sci, Coll Life Sci, Fuzhou, Peoples R China 5.Hainan Univ, Sanya Inst Breeding & Multiplicat, Collaborat Innovat Ctr Marine Sci & Technol, Sch Marine Biol & Fisheries, Haikou, Hainan, Peoples R China |
| 推荐引用方式 GB/T 7714 | Chen, Guisen,Du, Hehe,Cao, Zhenjie,et al. QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics[J]. MOLECULAR ECOLOGY RESOURCES,2026,26(2):12. |
| APA | Chen, Guisen.,Du, Hehe.,Cao, Zhenjie.,Wu, Ying.,Zhang, Chen.,...&Yuan, Zihao.(2026).QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics.MOLECULAR ECOLOGY RESOURCES,26(2),12. |
| MLA | Chen, Guisen,et al."QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics".MOLECULAR ECOLOGY RESOURCES 26.2(2026):12. |
入库方式： OAI收割
来源：海洋研究所
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