Organellar genome assembly methods and comparative analysis of horticultural plants.
Organellar genome assembly methods and comparative analysis of horticultural plants.
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园艺植物细胞器基因组组装方法及比较分析。
DOI：
10.1038/s41438-017-0002-1
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发表时间：
2018
影响因子：
8.7
通讯作者：
Ye N
中科院分区：
文献类型：
--
作者：
Wang X;Cheng F;Rohlsen D;Bi C;Wang C;Xu Y;Wei S;Ye Q;Yin T;Ye N
尽管细胞器基因组（包括叶绿体和线粒体基因组）在大小和基因数量上都小于核基因组，但细胞器基因组对于植物进化和分子生态学机制的研究非常重要。很少有研究关注园艺植物的细胞器基因组。美国国家生物技术信息中心 (NCBI) 提供了大约 1193 个陆地植物叶绿体基因组和 199 个线粒体基因组，其中只有 39 个来自园艺植物。在本文中，我们报告了一种利用下一代测序（NGS）数据组装高质量园艺细胞器基因组的创新且有效的方法。测序读数首先由 Newbler、Amos 和 Minimus 软件使用默认参数进行组装。然后通过 BLASTN 搜索和 PCR 填补剩余的空白。使用 BWA（Burrows-Wheeler 比对工具）软件根据 Illumina 测序数据校正完整的 DNA 序列。这种方法的优点是在样品制备过程中无需从总 DNA 中分离细胞器 DNA。使用该程序，鉴定了观赏植物 Salix Suchowensis 和果树 Ziziphus jujuba 的完整线粒体和叶绿体基因组。这项研究表明，园艺植物与其他种子植物具有相似的线粒体和叶绿体序列组织。大多数园艺植物都表现出对线粒体基因组中富含 A+T 的特征略有偏向。此外，基于15个蛋白质编码基因对39种园艺植物进行的系统发育分析表明，一些线粒体基因是从叶绿体DNA水平转移的。我们的研究将为其他园艺植物细胞器基因组组装提供重要参考。此外，对园艺植物细胞器基因组的系统发育分析可以准确地阐明这些植物之间意想不到的关系。一种新方法可以更轻松地组装园艺植物线粒体和叶绿体基因组的 DNA 序列。大多数组装叶绿体（进行光合作用）和线粒体（提供细胞能量）基因组的策略都需要从总 DNA 中分离细胞器 DNA。然而，中国南京林业大学的 Tongming Yin 和 Ning Ye 领导的团队使用生物信息学软件，找到了一种方法，可以从完整的下一代测序数据中提取这些细胞器的所有 DNA 序列读数，而无需专门的样品制备。作为原理验证，研究人员使用该协议解码了观赏植物 Salix Suchowensis 和果树 Ziziphus jujube 的线粒体和叶绿体基因组。以这种方式组装的线粒体和叶绿体基因组的比较分析可以揭示对植物进化关系的新见解。
Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear genomes in size and gene number, organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms. Few studies have focused on the organellar genomes of horticultural plants. Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information (NCBI), of which only 39 are from horticultural plants. In this paper, we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing (NGS) data. Sequencing reads were first assembled by Newbler, Amos, and Minimus software with default parameters. The remaining gaps were then filled through BLASTN search and PCR. The complete DNA sequence was corrected based on Illumina sequencing data using BWA (Burrows–Wheeler Alignment tool) software. The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation. Using this procedure, the complete mitochondrial and chloroplast genomes of an ornamental plant, Salix suchowensis, and a fruit tree, Ziziphus jujuba, were identified. This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants. Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome. In addition, a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA. Our study will provide an important reference for organellar genome assembly in other horticultural plants. Furthermore, phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants. A new method makes it easier to assemble the DNA sequences of mitochondrial and chloroplast genomes for horticultural plants. Most strategies for assembling the genomes of chloroplasts (which conduct photosynthesis) and mitochondria (which supply cellular energy) require the isolation of organellar DNA from total DNA. However, using bioinformatics software, a team led by Tongming Yin and Ning Ye from Nanjing Forestry University, China, identified a way to pull out all the DNA sequence reads for these organelles from complete next-generation sequencing data, without the need for specialized sample preparation. As a proof-of-principle, the researchers used the protocol to decode the mitochondrial and chloroplast genomes of the ornamental plant Salix suchowensis and the fruit tree Ziziphus jujube. Comparative analyses of mitochondrial and chloroplast genomes assembled in this way could reveal new insights into plant evolutionary relationships.
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影响因子：
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作者：
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通讯作者：
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