Lei Ye , Lingzi Zhang , Xin Li , Yu Huang , Bo Zhang , Xuezhen Yang , Wei Tan , Xiaolin Li , Xiaoping Zhang
{"title":"首个商业化粉红耳廓藻角膜的全新基因组组装和功能研究。","authors":"Lei Ye , Lingzi Zhang , Xin Li , Yu Huang , Bo Zhang , Xuezhen Yang , Wei Tan , Xiaolin Li , Xiaoping Zhang","doi":"10.1016/j.ygeno.2024.110902","DOIUrl":null,"url":null,"abstract":"<div><p>A pioneering pink cultivar of <em>Auricularia cornea</em>, first commercially cultivated in 2022, lacks genomic data, hindering research in genetic breeding, gene discovery, and product development. Here, we report the de novo assembly of the pink <em>A. cornea</em> Fen-A1 genome and provide a detailed functional annotation. The genome is 73.17 Mb in size, contains 86 scaffolds (N50 ∼ 5.49 Mb), 59.09% GC content and encodes 19,120 predicted genes with a BUSCO completeness of 92.60%. Comparative genomic analysis reveals the phylogenetic relatedness of Fen-A1 and remarkable gene family dynamics. Putative genes were found mapped to 3 antibiotic-related, 36 light-dependent and 25 terpene metabolites. In addition, 789 CAZymes genes were classified, revealing the dynamics of quality loss due to postharvest refrigeration. Overall, our work is the first report on a pink <em>A. cornea</em> genome and provides a comprehensive insight into its complex functions.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110902"},"PeriodicalIF":3.4000,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S088875432400123X/pdfft?md5=e29e1581ba4c1349c90bca58b752a31d&pid=1-s2.0-S088875432400123X-main.pdf","citationCount":"0","resultStr":"{\"title\":\"De novo genome assembly and functional insights of the first commercial pink Auricularia cornea\",\"authors\":\"Lei Ye , Lingzi Zhang , Xin Li , Yu Huang , Bo Zhang , Xuezhen Yang , Wei Tan , Xiaolin Li , Xiaoping Zhang\",\"doi\":\"10.1016/j.ygeno.2024.110902\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>A pioneering pink cultivar of <em>Auricularia cornea</em>, first commercially cultivated in 2022, lacks genomic data, hindering research in genetic breeding, gene discovery, and product development. Here, we report the de novo assembly of the pink <em>A. cornea</em> Fen-A1 genome and provide a detailed functional annotation. The genome is 73.17 Mb in size, contains 86 scaffolds (N50 ∼ 5.49 Mb), 59.09% GC content and encodes 19,120 predicted genes with a BUSCO completeness of 92.60%. Comparative genomic analysis reveals the phylogenetic relatedness of Fen-A1 and remarkable gene family dynamics. Putative genes were found mapped to 3 antibiotic-related, 36 light-dependent and 25 terpene metabolites. In addition, 789 CAZymes genes were classified, revealing the dynamics of quality loss due to postharvest refrigeration. Overall, our work is the first report on a pink <em>A. cornea</em> genome and provides a comprehensive insight into its complex functions.</p></div>\",\"PeriodicalId\":12521,\"journal\":{\"name\":\"Genomics\",\"volume\":\"116 5\",\"pages\":\"Article 110902\"},\"PeriodicalIF\":3.4000,\"publicationDate\":\"2024-07-23\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S088875432400123X/pdfft?md5=e29e1581ba4c1349c90bca58b752a31d&pid=1-s2.0-S088875432400123X-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genomics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S088875432400123X\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genomics","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S088875432400123X","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
De novo genome assembly and functional insights of the first commercial pink Auricularia cornea
A pioneering pink cultivar of Auricularia cornea, first commercially cultivated in 2022, lacks genomic data, hindering research in genetic breeding, gene discovery, and product development. Here, we report the de novo assembly of the pink A. cornea Fen-A1 genome and provide a detailed functional annotation. The genome is 73.17 Mb in size, contains 86 scaffolds (N50 ∼ 5.49 Mb), 59.09% GC content and encodes 19,120 predicted genes with a BUSCO completeness of 92.60%. Comparative genomic analysis reveals the phylogenetic relatedness of Fen-A1 and remarkable gene family dynamics. Putative genes were found mapped to 3 antibiotic-related, 36 light-dependent and 25 terpene metabolites. In addition, 789 CAZymes genes were classified, revealing the dynamics of quality loss due to postharvest refrigeration. Overall, our work is the first report on a pink A. cornea genome and provides a comprehensive insight into its complex functions.
期刊介绍：
Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation.
As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope.
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