Evolutionary Insights into Carex Chloroplast Genome Structure

A typical chloroplast genome in angiosperms has a stable size (ca. 160 kbp) and structure consisting of a pair of inverted repeat (IR) regions separated by a large single-copy (LSC) region and a small single-copy (SSC) region. However, recent studies showed that the chloroplast genome of Carex (Cyperaceae) species has high structural variations and contains short repeat sequences compare to other angiosperm taxa. When a genome contains short repeat sequences with many structural variations, data from the most common NGS platform, the Illumina sequencing, is not sufficient to get complete genome. On the other hand, Oxford Nanopore Technologies (ONT) platform can generate tens of kbp of long-read, which is expected to facilitate the determination of chloroplast complete genomes with complex structures.

被子植物（angiosperms）中典型的叶绿体基因组具有稳定的大小（约160 kbp）与结构，其结构由一对被大单拷贝（LSC，large single-copy）区和小单拷贝（SSC，small single-copy）区隔开的反向重复（IR，inverted repeat）区域组成。然而，近期研究表明，薹草属（Carex）物种（隶属于莎草科Cyperaceae）的叶绿体基因组相较于其他被子植物类群，不仅存在更高程度的结构变异，还包含更多短重复序列。当基因组含有大量携带结构变异的短重复序列时，当前最主流的下一代测序（NGS，Next-Generation Sequencing）平台——Illumina测序所产生的数据，不足以完成完整叶绿体基因组的获取。另一方面，牛津纳米孔技术（ONT，Oxford Nanopore Technologies）平台可生成数十千碱基对的长读长序列，有望助力解析结构复杂的完整叶绿体基因组。