Genomics and Gene Discovery Research Unit, United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States of America.
PLoS One. 2011;6(8):e23980. doi: 10.1371/journal.pone.0023980. Epub 2011 Aug 24.
Switchgrass (Panicum virgatum L.) exists at multiple ploidies and two phenotypically distinct ecotypes. To facilitate interploidal comparisons and to understand the extent of sequence variation within existing breeding pools, two complete switchgrass chloroplast genomes were sequenced from individuals representative of the upland and lowland ecotypes. The results demonstrated a very high degree of conservation in gene content and order with other sequenced plastid genomes. The lowland ecotype reference sequence (Kanlow Lin1) was 139,677 base pairs while the upland sequence (Summer Lin2) was 139,619 base pairs. Alignments between the lowland reference sequence and short-read sequence data from existing sequence datasets identified as either upland or lowland confirmed known polymorphisms and indicated the presence of other differences. Insertions and deletions principally occurred near stretches of homopolymer simple sequence repeats in intergenic regions while most Single Nucleotide Polymorphisms (SNPs) occurred in intergenic regions and introns within the single copy portions of the genome. The polymorphism rate between upland and lowland switchgrass ecotypes was found to be similar to rates reported between chloroplast genomes of indica and japonica subspecies of rice which were believed to have diverged 0.2-0.4 million years ago.
柳枝稷（Panicum virgatum L.）存在于多种倍性和两种表型明显不同的生态型中。为了促进种间比较，并了解现有育种种群内的序列变异程度，我们从高地和低地生态型的代表个体中测序了两个完整的柳枝稷叶绿体基因组。结果表明，与其他已测序的质体基因组相比，基因内容和顺序具有非常高的保守性。低地生态型参考序列（Kanlow Lin1）长 139677 个碱基对，而高地序列（Summer Lin2）长 139619 个碱基对。低地参考序列与现有序列数据集的短读序列数据之间的比对，确定为高地或低地的序列，证实了已知的多态性，并表明存在其他差异。插入和缺失主要发生在基因间区的长串联重复序列附近，而大多数单核苷酸多态性（SNP）发生在基因组单拷贝区的基因间区和内含子中。高地和低地柳枝稷生态型之间的多态性率与水稻籼稻和粳稻亚种之间的质体基因组报告的多态性率相似，据信它们在 0.2-0.4 百万年前就已经分化。
