De novo genome assembly and functional insights of the first commercial pink Auricularia cornea

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Genomics Pub Date : 2024-07-23 DOI:10.1016/j.ygeno.2024.110902

Lei Ye , Lingzi Zhang , Xin Li , Yu Huang , Bo Zhang , Xuezhen Yang , Wei Tan , Xiaolin Li , Xiaoping Zhang

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Abstract

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.

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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。

2022年首次商业化栽培的粉红角杯藻（Auricularia cornea）先锋品种缺乏基因组数据，阻碍了遗传育种、基因发现和产品开发方面的研究。在此，我们报告了粉红角杯藻 Fen-A1 基因组的全新组装，并提供了详细的功能注释。该基因组大小为 73.17 Mb，包含 86 个支架（N50 ~ 5.49 Mb），GC 含量为 59.09%，编码 19120 个预测基因，BUSCO 完整性为 92.60%。比较基因组分析揭示了 Fen-A1 的系统发育相关性和显著的基因家族动态。发现的推定基因与 3 个抗生素相关基因、36 个光依赖基因和 25 个萜烯代谢物相关。此外，还对 789 个 CAZymes 基因进行了分类，揭示了采后冷藏导致品质损失的动态变化。总之，我们的工作是对粉红角鲨属基因组的首次报道，并提供了对其复杂功能的全面了解。

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来源期刊

Genomics 生物-生物工程与应用微生物

CiteScore

9.60

自引率

2.30%

发文量

260

审稿时长

60 days

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.