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Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation

Genomics, Proteomics & Bioinformatics 2021年第5期19卷 772-786页

作者： Pengju Zhao Xianrui Zheng Ying Yu Zhuocheng Hou Chenguang Diao Haifei Wang Huimin Kang Chao Ning Junhui Li Wen Feng Wen Wang george eliu Bugao Li Jacqueline Smith Yangzom Chamba Jian-Feng Liu National Engineering Laboratory for Animal Breeding Key Laboratory of Animal GeneticsBreeding and ReproductionMinistry of AgricultureCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China Center for Ecological and Environmental Sciences Northwestern Polytechnical UniversityXi’an 710072China Animal Genomics and Improvement Laboratory Beltsville Agricultural Research CenterU.S.Department of AgricultureBeltsvilleMD 20705USA Department of Animal Sciences and Veterinary Medicine Shanxi Agricultural UniversityTaigu 030801China The Roslin Institute and Royal(Dick)School of Veterinary Studies University of EdinburghEaster BushMidlothian EH259RGUK Tibet Agriculture and Animal Husbandry College Linzhi 860000China

A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical *** this study,we developed a tissue-based proteome map using 34 major normal pig tissues.A total of 5841 unknown protein isoforms were identified and systematically characterized,including 2225 novel protein isoforms,669 protein isoforms from 460 genes symbolized beginning with LOC,and 2947 protein isoforms without clear NCBI annotation in the current pig reference *** newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues,further improving the genome annotation of the corresponding protein-coding *** the well-annotated genes that have parallel expression pattern and subcellular witness,we predicted the tissue-related subcellular locations and potential functions for these unknown ***,we mined 3081 orthologous genes for 52.7% of unknown protein isoforms across multiple species,referring to 68 KEGG pathways as well as 23 disease signaling *** findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology,as well as biomedical model application to human medicine.

关键词： Expression pattern Unknown protein Pig Proteome Subcellular location

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