The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae.
The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae.
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DOI：
10.1371/journal.pone.0196069
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Poczai P
中科院分区：
文献类型：
--
作者：
Amiryousefi A;Hyvönen J;Poczai P
苦甜（Solanum dulcamara）是茄科的一种原产于旧大陆的植物。这种欧洲二倍体物种可以从沼泽地到高山地区找到，它是一种常见的杂草，作为替代宿主和抗植物病原体（如晚疫病（Phytophthora infestans））的抗性基因来源。我们测定了甘薯叶绿体基因组的全序列，该基因组全长155，580 bp，具有典型的四分体结构，由一个大的（85，901 bp）和一个小的（18，449 bp）单拷贝区组成，其间散布着两个相同的反向重复序列（25，615 bp）。它由112个独特的基因组成，其中81个编码蛋白质，27个tRNA和4个rRNA基因。所有的甘薯质体基因，包括非功能基因，甚至基因间间隔区都转录在初级质体转录物中，覆盖基因组的95.22%。这些随后在转录后阶段被大量编辑以激活基因功能。通过比较所有可用的茄科序列，我们发现，基因的内容和同线性是高度保守的整个家庭甜质体基因组。在基因组比较过程中，我们已经确定了几个注释错误，我们已经在手动管理过程中纠正了这些错误，然后我们确定了茄科中主要的质体基因组结构变化。在系统发育的背景下解释，他们似乎提供了更大的分支的额外支持。本研究所获得的甘薯质体基因组序列可作为茄科植物质体基因组注释的基准，为进一步研究提供参考。这种可靠的注释对于基因多样性计算、同线性图谱构建以及分配分区以用于重新测序的茄科质体的系统发育分析非常重要。
Bittersweet (Solanum dulcamara) is a native Old World member of the nightshade family. This European diploid species can be found from marshlands to high mountainous regions and it is a common weed that serves as an alternative host and source of resistance genes against plant pathogens such as late blight (Phytophthora infestans). We sequenced the complete chloroplast genome of bittersweet, which is 155,580 bp in length and it is characterized by a typical quadripartite structure composed of a large (85,901 bp) and small (18,449 bp) single-copy region interspersed by two identical inverted repeats (25,615 bp). It consists of 112 unique genes from which 81 are protein-coding, 27 tRNA and four rRNA genes. All bittersweet plastid genes including non-functional ones and even intergenic spacer regions are transcribed in primary plastid transcripts covering 95.22% of the genome. These are later substantially edited in a post-transcriptional phase to activate gene functions. By comparing the bittersweet plastid genome with all available Solanaceae sequences we found that gene content and synteny are highly conserved across the family. During genome comparison we have identified several annotation errors, which we have corrected in a manual curation process then we have identified the major plastid genome structural changes in Solanaceae. Interpreted in a phylogenetic context they seem to provide additional support for larger clades. The plastid genome sequence of bittersweet could help to benchmark Solanaceae plastid genome annotations and could be used as a reference for further studies. Such reliable annotations are important for gene diversity calculations, synteny map constructions and assigning partitions for phylogenetic analysis with de novo sequenced plastomes of Solanaceae.
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影响因子：
18
作者：
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通讯作者：
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影响因子：
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作者：
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影响因子：
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Wolf PG
DOI：
10.1093/bioinformatics/bts199
发表时间：
2012-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
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Drummond A
影响因子：
1.9
作者：
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