Chloroplast genome information is critical to understanding forms of photosynthesis in the plant kingdom. During the evolutionary process, plants have developed different photosynthetic strategies that are accompanied by complementary biochemical and anatomical features. Members of family Chenopodiaceae have species with C3 photosynthesis, and variations of C4 photosynthesis in which photorespiration is reduced by concentrating CO2 around Rubisco through dual coordinated functioning of dimorphic chloroplasts. Among dicots, the family has the largest number of C4 species, and greatest structural and biochemical diversity in forms of C4 including the canonical dual-cell Kranz anatomy, and the recently identified single cell C4 with the presence of dimorphic chloroplasts separated by a vacuole. This is the first comparative analysis of chloroplast genomes in species representative of photosynthetic types in the family. Methodology with high throughput sequencing complemented with Sanger sequencing of selected loci provided high quality and complete chloroplast genomes of seven species in the family and one species in the closely related Amaranthaceae family, representing C3, Kranz type C4 and single cell C4 (SSC4) photosynthesis six of the eight chloroplast genomes are new, while two are improved versions of previously published genomes. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality and repeat region sequences. Comparison of the chloroplast genomes with previously sequenced plastid genomes revealed similar genome organization, gene order and content with a few revisions. High-quality complete chloroplast genome sequences resulted in correcting the orientation the LSC region of the published Bienertia sinuspersici chloroplast genome, identification of stop codons in the rpl23 gene in B. sinuspersici and B. cycloptera, and identifying an instance of IR expansion in the Haloxylon ammodendron inverted repeat sequence. The rare observation of a mitochondria-to-chloroplast inter-organellar gene transfer event was identified in family Chenopodiaceae. This study reports complete chloroplast genomes from seven Chenopodiaceae and one Amaranthaceae species. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality, and repeat region sequences. Therefore, the use of high throughput and Sanger sequencing, in a hybrid method, reaffirms to be rapid, efficient, and reliable for chloroplast genome sequencing.

中文翻译：

---

藜科 C3、Kranz 型 C4 和单细胞 C4 光合成员叶绿体基因组的分析方法。


叶绿体基因组信息对于了解植物界光合作用的形式至关重要。在进化过程中，植物发展了不同的光合作用策略，并伴随着互补的生化和解剖特征。藜科成员的物种具有 C3 光合作用和 C4 光合作用的变异，其中通过二态叶绿体的双重协调功能将 CO2 集中在 Rubisco 周围，从而减少光呼吸。在双子叶植物中，该科拥有数量最多的 C4 物种，以及 C4 形式的最大结构和生化多样性，包括典型的双细胞 Kranz 解剖结构，以及最近鉴定的存在由液泡分隔的二态叶绿体的单细胞 C4。这是对该科中代表光合类型的物种的叶绿体基因组的首次比较分析。高通量测序方法与选定基因座的桑格测序相辅相成，提供了该科中七个物种和密切相关的苋科科中一个物种的高质量和完整叶绿体基因组，代表 C3、Kranz 型 C4 和单细胞 C4 (SSC4) 光合作用六八个叶绿体基因组中有两个是新的，另外两个是先前发表的基因组的改进版本。使用高通量测序获得的覆盖深度辅以某些基因座的靶向重测序，可以实现边界连接、方向性和重复区域序列的高分辨率。将叶绿体基因组与先前测序的质体基因组进行比较，发现相似的基因组组织、基因顺序和内容，但有一些修改。 高质量的完整叶绿体基因组序列纠正了已发表的 Bienertia sinospersici 叶绿体基因组的 LSC 区域方向，鉴定了 B. sinuspersici 和 B. cycloptera 中 rpl23 基因的终止密码子，并鉴定了梭梭中 IR 扩展的实例梭梭反向重复序列。在藜科中发现了罕见的线粒体到叶绿体的细胞器间基因转移事件。这项研究报告了七种藜科植物和一种苋科植物的完整叶绿体基因组。使用高通量测序获得的覆盖深度辅以某些基因座的靶向重测序，可以实现边界连接、方向性和重复区域序列的高分辨率。因此，在混合方法中使用高通量和桑格测序再次证实了叶绿体基因组测序的快速、高效和可靠。