Background

Miscanthus has been considered as potentially high-yielding biomass crop with the low-nutrient requirements, high capability of Carbon mitigation and water-use efficiency. Miscanthus species have restricted to investigate functional genomics of their large genome size, which leads to challenges to genomics-aided crop improvement. Sequencing of the plastid genomes of Miscanthus is one of complementary tool making it available for genetic researches.

Results

The complete chloroplast (cp) genomes of five Miscanthus species were sequenced using Illumina sequencing. Comparisons between the five chloroplast genome sequences revealed their conservation in gene content and order, including the IR/SC boundaries. However, some hotspots in coding regions and intergenic regions also occurred. Specifically a 13 bp deletion in the intergenic region of rps16-trnQ and a 17 bp deletion in rps4-trnT are shared by Miscanthus lutarioriparius L., Miscanthus sacchariflorus N. and Miscanthus × giganteus. In addition, a 39 bp deletion in trnL-trnF is shared by Miscanthus sinensis A. and Miscanthus floridulus W.. Comparisons of complete chloroplast genome of Miscanthus lutarioriparius to five published grass chloroplast genomes also reveal several hotspot regions with high polymorphism. Phylogenetic analysis based on complete chloroplast genomes and coding sequences of 77 protein genes suggest a sister relationship between the Eumiscanthus clade and the Triarrhena clade.

Conclusions

This report is the first comprehensive comparative analyses on Miscanthus species cp genome combining other published grass chloroplast genomes. The availability of these results will supplement valuable genetic information and framework for further phylogeography, population genetics and plastid genetic engineering researches in Miscanthus.sp.

中文翻译：

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五种芒草的完整叶绿体基因组序列，并与其他草质体组进行比较分析

背景

芒草被认为是潜在的高产生物质作物，具有低养分需求，高减碳能力和水分利用效率。芒草种限制了研究其大基因组大小的功能基因组学的研究，这给基因组学辅助的作物改良带来了挑战。芒草质体基因组的测序是使其可用于遗传研究的补充工具之一。

结果

使用Illumina测序对五个芒草属物种的完整叶绿体（cp）基因组进行了测序。五个叶绿体基因组序列之间的比较表明，它们在基因含量和顺序（包括IR / SC边界）方面保持保守。但是，在编码区和基因间区也出现了一些热点。具体而言，rps16 - trn Q基因间区域的13 bp缺失和rps4-trnT基因的17 bp的缺失由Miscanthus lutarioriparius L.，Miscanthus sacchariflorus N.和Miscanthus × giganteus共有。另外，trnL - trnF中有39 bp的缺失由Miscanthus sinensis A.和Miscanthus floridulus W.共享。将Miscanthus lutarioriparius的完整叶绿体基因组与五个已发布的草叶绿体基因组进行比较，还发现了几个具有高多态性的热点地区。系统发育分析基于完整的叶绿体基因组和77个蛋白质基因的编码序列，表明Eumiscanthus进化枝和Triarrhena进化枝之间存在姐妹关系。

结论

该报告是结合其他已发表的草叶绿体基因组对芒草属植物cp基因组进行的首次综合比较分析。这些结果的可获得性将为Miscanthus.sp中进一步的系统地理学，群体遗传学和质体遗传工程研究提供有价值的遗传信息和框架。