| 薏苡黑粉菌基因组测序揭示其物种分类及适应性进化 |
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| 引用本文： | 李祥栋,郑传奇,陆秀娟,潘虹,魏心元,石明,付瑜华,陆平,高爱农,周美亮.薏苡黑粉菌基因组测序揭示其物种分类及适应性进化[J].菌物学报,2022,41(12):1960-1970. |
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| 作者姓名： | 李祥栋 郑传奇 陆秀娟 潘虹 魏心元 石明 付瑜华 陆平 高爱农 周美亮 |
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| 作者单位： | 1 黔西南州农业林业科学研究院，贵州 兴义 5624002 贵州省薏苡工程技术研究中心，贵州 兴义 5624003 贵州省亚热带作物研究所，贵州 兴义 5624004 中国农业科学院作物科学研究所，北京 100081 |
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| 基金项目： | 第三次全国作物种质资源普查收集——杂粮种质资源繁殖编目入库(19210866);贵州省现代农业产业体系([2019]15);黔西南州科技计划项目(2020-1-03) |
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| 摘 要： | 以薏苡黑粉菌病瘿为研究对象，采用固体和液体培养方法对薏苡黑粉菌进行分离纯化培养和形态观察；利用Illumina、Pacbio测序和Hi-C辅助基因组组装技术对黑粉菌进行测序、组装和注释，分析其基因组结构和组成特征。通过与其他6个黑粉菌物种基因组进行比较基因组学研究，分析薏苡黑粉菌的基因家族进化和系统发育关系。在pH 7的固体PDA和液体PDB培养基中实现了薏苡黑粉菌的纯化培养，固体培养菌落表现为白色、表面隆起、具褶皱，较湿润且不透明的形态特征。Illumina、Pacbio和Hi-C组装结果显示，薏苡黑粉菌具有20对染色体(2n=40)，基因组大小20.093 417 Mb，GC含量53.81%；共预测和注释到7 476个蛋白编码基因和164个非编码基因，占整个基因组长度的61.02%和0.285 3%；查找到3 674个散在重复序列和8 139个串联重复序列，分别占整个基因组长度的2.754 4%和1.605 4%。同源基因家族聚类显示，7个黑粉菌物种Ustilago coicis、U. bromivora、U. maydis、U. hordei、Sporisorium reilianum、S. scitamineum和S. graminicola的编码基因被聚类为6 999个基因家族，其中共有基因家族5 379个。薏苡黑粉菌包含5 339个单拷贝基因、105个多拷贝基因、89个特异基因、752个其他基因和188个未分类基因。基因家族进化和系统发育聚类表明，薏苡黑粉菌U. coicis在~60.9 MYA分化出来，与雀麦黑粉菌U. bromivova、大麦坚黑粉菌U. hordei聚为一支，表现为更近的亲缘关系；而玉米黑粉菌U. maydis在~66.6 MYA分化出来与3个孢堆黑粉菌物种S. scitamineum、S. graminicola和S. reilianum聚为一支。
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| 关 键 词： | 黑粉菌 基因组 系统发育 薏苡 |
| 收稿时间： | 2022-02-27 |
Sequencing of adlay smut fungus genome provides insights into pathogen taxonomy and adaptive evolution |
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| Authors: | LI Xiangdong ZHENG Chuanqi LU Xiujuan PAN Hong WEI Xinyuan SHI Ming FU Yuhua LU Ping GAO Ainong ZHOU Meiliang |
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| Affiliation: | 1 Southwest Guizhou Institute of Agricultural and Forestry Sciences, Xingyi 562400, Guizhou, China2 Adlay Engineering Technical Research Centre in Guizhou, Xingyi 562400, Guizhou, China3 Subtropical Crop Research Institute of Guizhou Province, Xingyi 562400, Guizhou, China4 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China |
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| Abstract: | Affected tissues of adlay (Coix L.) were selected as research materials and the adlay smut Ustilago coicis were separated, purified and observed in solid and liquid nutrient medium. The smut fungus genome were sequenced, assembled and annotated by Illumina, Pacbio and Hi-C technologies. The homology gene family evolution and phylogeny were studied by comparative genetics among adlay smut fungus and the other six smut fungus species. Ustilago coicis was successfully cultured and purified in solid PDA and liquid PDB media at pH 7. The colony on PDA is pulvinate and wrinkly, with white color, moist and opaque. Illumina, Pacbio and Hi-C sequencing and assembly showed that the whole genome of adlay smut fungus has 20 chromosome pairs (2n=40), with a size of 20.093 417 Mb and 53.81% GC content. There were a prediction and annotation of 7 476 protein-coding and 164 non-coding genes with a length ratio of 61.02% and 0.285 3% respectively. A sum of 3 674 dispersed duplications and 8 139 tandem duplications was hunted, occupying 2.754 4% and 1.605 4% of the whole genome length. Homology gene clustering exhibited that protein-coding genes of U. coicis, U. bromivora, U. maydis, U. hordei, Sporisorium reilianum, S. scitamineum, and S. graminicola were clustered into 6 999 gene families in which shared gene families totaled 5 379. There were 5 339 single-copy orthologs, 105 multiple-copy orthologs, 89 unique paralogs, 752 other othologs and 188 unclustered genes in U. coicis. The gene family evolution and phylogeny clustering also revealed that U. coicis was split in ~60.9 MYA, and clustered with U. bromivova and U. hordei, hinting their closer relatives; however, U. maydis, a species parasitized corn, was split in ~66.6 MYA, and clustered with S. scitamineum, S. graminicola and S. reilianum. |
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| Keywords: | smut genome phylogeny adlay |
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