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甘新军,宾粤,陈焕锦,朱韦光,熊露桥,余恩萍,王峥峰,徐凤霞,曹洪麟.厚叶木莲(Manglietia pachyphylla)基因组草图[J].广西科学,2023,30(6):1079-1090. [点击复制]
- GAN Xinjun,BIN Yue,CHEN Huanjin,ZHU Weiguang,XIONG Luqiao,YU Enping,WANG Zhengfeng,XU Fengxia,CAO Honglin.Draft Genome of Manglietia pachyphylla[J].Guangxi Sciences,2023,30(6):1079-1090. [点击复制]
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| 厚叶木莲(Manglietia pachyphylla)基因组草图 |
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甘新军1, 宾粤2,3, 陈焕锦1, 朱韦光2,3, 熊露桥1, 余恩萍2,3,4, 王峥峰2,3, 徐凤霞3,5, 曹洪麟2,3
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| (1.广东从化陈禾洞省级自然保护区管理处, 广东广州 510950;2.中国科学院华南植物园, 广东省应用植物学重点实验室, 中国科学院退化生态系统植被恢复与管理重点实验室, 广东广州 510650;3.华南国家植物园, 广东广州 510650;4.中国科学院大学, 北京 100049;5.中国科学院华南植物园, 中国科学院植物资源保护与可持续利用重点实验室, 广东广州 510650) |
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| 摘要: |
| 厚叶木莲（Manglietia pachyphylla）为木兰科（Magnoliaceae）木莲属（Manglietia）的木本植物，零星分布于我国广东省和广西壮族自治区，为国家二级重点保护野生植物。了解濒危物种基因组信息及其遗传多样性有助于合理地保护和利用濒危物种，实现濒危物种的解濒和复壮。为此，本研究通过高通量测序方法对厚叶木莲基因组进行测序，并利用测序数据开展厚叶木莲基因组草图的组装；之后，基于组装的基因组预测其中的重复序列和基因，进行系统发育和基因家族分析。结果表明，组装的厚叶木莲基因组大小为2 092 298 891 bp，包含676个组装序列，N50（将组装的序列按照长度由大到小进行累加，当累加到某个序列时，累加的值为基因组50%的长度时，此序列的长度即为N50）为7 961 115 bp；利用BUSCO （Benchmarking Universal Single-Copy Orthologs），针对“eudicots”和“embryophyta”这两个BUSCO单拷贝基因库，对基因组组装的完整性进行评估，组装的厚叶木莲基因组完整性分别为96.6%和98.8%。厚叶木莲基因组有76.5%的序列为重复序列，共有37 900个基因，这些基因编码了41 675个蛋白质序列。系统发育分析发现厚叶木莲与望春玉兰（Magnolia biondii）聚在一起，两者分化时间大致为10 500 000年前。厚叶木莲中与木质部/韧皮部、肌动蛋白丝、热、光合作用以及多种次生代谢相关的基因家族显著扩张，其中次生代谢相关基因在厚叶木莲基因组上呈串联和近端重复，这些基因的扩张和重复形成方式可能与厚叶木莲适应高海拔环境有关。本研究是国内外木兰科木莲属首个基因组报道，为更好地保护和开发厚叶木莲及木兰科其他物种的种质资源提供了遗传信息和参考。 |
| 关键词: 厚叶木莲 木兰科 木莲属 濒危植物 基因组组装 基因预测 基因家族 基因重复 |
| DOI：10.13656/j.cnki.gxkx.20240125.006 |
| 投稿时间：2023-06-10修订日期：2023-07-22 |
| 基金项目:广东省重点领域研发计划项目（2022B1111230001）及其子课题（2022B1111230001-2-5），广东从化陈禾洞省级自然保护区“厚叶木莲种群调查、评价及扩繁”项目和广东省林业局生态林业建设专项资金项目“高水平专类园珍稀特有植物保护与建设”资助。 |
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| Draft Genome of Manglietia pachyphylla |
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GAN Xinjun1, BIN Yue2,3, CHEN Huanjin1, ZHU Weiguang2,3, XIONG Luqiao1, YU Enping2,3,4, WANG Zhengfeng2,3, XU Fengxia3,5, CAO Honglin2,3
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| (1.Administrative Office of Guangdong Conghua Chenhedong Provincial Nature Reserve, Guangzhou, Guangdong, 510950, China;2.Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China;3.South China National Botanical Garden, Guangzhou, Guangdong, 510650, China;4.University of Chinese Academy of Sciences, Beijing, 100049, China;5.Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China) |
| Abstract: |
| Manglietia pachyphylla is in the family of Magnoliaceae, one of the earliest divergent lineages of angiosperms. Magnoliaceae are valued for their large and fragrant colorful flowers, and medicine and timber sources.Manglietia pachyphylla is endemic to China, and only distributes in Guangdong Province and Guangxi Zhuang Autonomous Region.It is now national class Ⅱ key protected wild species. In this study, we sequenced the genome of Manglietia pachyphylla by high-throughput sequencing, and the sequencing data were used to assemble a sketch of the genome, based on which, we predict its repeat sequences and genes, and perform phylogentic and gene familes analyses. The assembly size of Manglietia pachyphylla was 2 092 298 891 bp, comprised 676 contigs with N50 (the contig length, included in the sum length of contigs from the longest to the shortest, covers ~50% of the total genome length) of 7 961 115 bp.Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment revealed 98.8% and 96.6% completeness of the assembly using "embryophyta" and "eudicots" BUSCO database, respectively. Up to 76.5% of the genome is repetitive, with 37 900 genes encoding 41 675 proteins. Phylogenetic analyses of relative 10 species indicated that Manglietia pachyphylla was clustered in the same clade with Magnolia biondii, and divergence time between them were estimated to be 10.5 million years ago.We investigated genes related to phloem/xylem, actin filament, heat, photosynthesis and various plant secondary metabolites were significantly expanded, in which the secondary metabolites were mainly derived from tandem and proximal duplications.The gene expansions and duplications should play important roles in the adaption of Manglietia pachyphylla to the high altitude. This study is the first genomic report of the genus Manglietia at home and abroad, which provides genetic information and reference for better conservation and development of the germplasm resources of Manglietia pachyphylla and other species in the family of Magnoliaceae. |
| Key words: Manglietia pachyphylla Magnoliaceae Manglietia endangered plant genome assembly gene prediction gene family gene duplication |
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