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Accordingly, a comprehensive study of the compositional diversity and evolutionary patterns of accessory proteins is critical to understanding the host adaptation and epidemic variation of coronaviruses. Here, we developed a standardized genome annotation tool for coronavirus (CoroAnnoter) by combining open reading frame prediction, transcription regulatory sequence recognition and homologous alignment. Using CoroAnnoter, we annotated 39 representative coronavirus strains to form a compositional profile for all of the accessary proteins. Large variations were observed in the number of accessory proteins of 1\u201310 for different coronaviruses, with SARS-CoV-2 and SARS-CoV having the most (9 and 10, respectively). The variation between SARS-CoV and SARS-CoV-2 accessory proteins could be traced back to related coronaviruses in other hosts. The genomic distribution of accessory proteins had significant intra-genus conservation and inter-genus diversity and could be grouped into 1, 4, 2 and 1 types for alpha-, beta-, gamma-, and delta-coronaviruses, respectively. Evolutionary analysis suggested that accessory proteins are more conservative locating before the N-terminal of proteins E and M (E-M), while they are more diverse after these proteins. Furthermore, comparison of virus-host interaction networks of SARS-CoV-2 and SARS-CoV accessory proteins showed that they share multiple antiviral signaling pathways, those involved in the apoptotic process, viral life cycle and response to oxidative stress. In summary, our study provides a tool for coronavirus genome annotation and builds a comprehensive profile for coronavirus accessory proteins covering their composition, classification, evolutionary pattern and host interaction.<\/jats:p>","DOI":"10.1093\/bib\/bbaa262","type":"journal-article","created":{"date-parts":[[2020,9,14]],"date-time":"2020-09-14T19:12:49Z","timestamp":1600110769000},"page":"1267-1278","source":"Crossref","is-referenced-by-count":29,"title":["Compositional diversity and evolutionary pattern of coronavirus accessory proteins"],"prefix":"10.1093","volume":"22","author":[{"given":"Jingzhe","family":"Shang","sequence":"first","affiliation":[{"name":"Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu, Suzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Na","family":"Han","sequence":"additional","affiliation":[{"name":"Suzhou Institute of Systems 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Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu, Suzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengyang","family":"Ji","sequence":"additional","affiliation":[{"name":"Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu, Suzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Meng","sequence":"additional","affiliation":[{"name":"Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu, Suzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taijiao","family":"Jiang","sequence":"additional","affiliation":[{"name":"Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 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