1.Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation
Zhao PENGJU ; Zheng XIANRUI ; Yu YING ; Hou ZHUOCHENG ; Diao CHENGUANG ; Wang HAIFEI ; Kang HUIMIN ; Ning CHAO ; Li JUNHUI ; Feng WEN ; Wang WEN ; E.Liu GEORGE ; Li BUGAO ; Smith JACQUELINE ; Chamba YANGZOM ; Liu JIAN-FENG
Genomics, Proteomics & Bioinformatics 2021;19(5):772-786
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 model.In this study,we developed a tissue-based proteome map using 34 major normal pig tissues.A total of 5841 unknown protein iso-forms were identified and systematically characterized,including 2225 novel protein isoforms,669 protein isoforms from 460 genes symbolized beginning with LOC,and 2947 protein isoforms with-out clear NCBI annotation in the current pig reference genome.These newly identified protein iso-forms 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 corre-sponding protein-coding genes.Combining 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 proteins.Finally,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 pathways.These 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.
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