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首页> 外文期刊>Gene: An International Journal Focusing on Gene Cloning and Gene Structure and Function >The complete chloroplast genome sequence of yellow mustard (Sinapis alba L.) and its phylogenetic relationship to other Brassicaceae species
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The complete chloroplast genome sequence of yellow mustard (Sinapis alba L.) and its phylogenetic relationship to other Brassicaceae species

机译：黄芥菜（Sinapis Alba L.）的完整叶绿体基因组序列及其与其他芸苔属物种的系统发育关系

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摘要

As a member of the large Brassicaceae family, yellow mustard (Sinapis alba L.) has been used as an important gene pool for the genetic improvement of cash crops in Brassicaceae. Understanding the phylogenetic relationship between Sinapis alba (S. alba) and other Brassicaceae crops can provide guidance on the introgression of its favorable alleles into related species. The chloroplast (cp) genome is an ideal model for assessing genome evolution and the phylogenetic relationships of complex angiosperm families. Herein, we de novo assembled the complete cp genome of S. alba by integrating the PacBio and Illumina sequencing platforms. A 153,760 bp quadripartite cycle without any gap was obtained, including a pair of inverted repeats (IRa and IRb) of 26,221 bp, separated by a large single copy (LSC) region of 83,506 bp and a small single copy (SSC) region of 17,821 bp. A total of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes were identified in this cp genome, as were 89 simple sequence repeat (SSR) loci of 18 types. The codon usage analysis revealed a preferential use of the Leu codon with the A/U ending. The phylogenetic analysis using 82 Brassicaceae species demonstrated that S. alba had a close relationship with important Brassica and Raphanus species; moreover, it likely originated from a separate evolutionary pathway compared with the congeneric Sinapis arvensis. The synonymous (Ks) and non-synonymous (Ks) substitution rate analysis showed that genes encoding "Subunits of cytochrome b/f complex" were under the lowest purifying selection pressure, whereas those associated with "Maturase", "Subunit of acetyl-CoA", and "Subunits of NADH-dehydrogenase" underwent relatively higher purifying selection pressures. Our results provide valuable information for fully utilizing the S. alba cp genome as a potential genetic resource for the genetic improvement of Brassica and Raphanus species.
机译：作为大型Brassicaceae家族的成员，黄芥末（Sinapis Alba L.）已被用作碳粉质遗传改善的重要基因库。了解Sinapis Alba（alba）和其他Brassicaceae作物之间的系统发育关系可以为其有利等位基因迟钝的引导提供指导。叶绿体（CP）基因组是评估基因组进化的理想模型和复杂的高血管植物家族的系统发育关系。在此，我们通过整合PACBIO和Illumina测序平台组装了S. Alba的完整CP基因组。获得153,760bp Quadriparte循环，没有任何间隙，包括26,221bp的一对倒反转的重复（IRA和IRB），由83,506bp的大单拷贝（LSC）区域和17,821的小单拷贝（SSC）区域分开。 BP。在该CP基因组中鉴定了总共78个蛋白质编码基因，30个TRNA基因和四个RRNA基因，如18种的89个简单的序列重复（SSR）基因座。密码子使用分析显示使用A / U结束的Leu Codon优先使用。使用82 Brassicaceae物种的系统发育分析证明了S. Alba与重要的芸苔和Raphanus物种密切相关;此外，与Congeneric SINAPIS arvensis相比，它可能来自单独的进化途径。同义（KS）和非同义（KS）替代率分析表明，编码“细胞色素B / F复合物的亚基”的基因在最低净化的选择压力下，而与“Maturase”相关的那些，“乙酰-CoA的亚基“和”NADH-脱氢酶的亚基“接受了相对较高的纯化选择压力。我们的结果提供了有价值的信息，可以充分利用S. Alba CP基因组作为芸苔属和Raphanus物种遗传改善的潜在遗传资源。

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