因为频繁的杂交和多倍体化，茶组植物被认为是开花植物中最难进行分类和进化研究的类群之一，因此基于形态学对茶组植物的系统分类一直存在问题。而叶绿体（cp）基因组因为其相对保守的基因组结构、母系遗传、相对低的重组率等特点能够为系统分类、进化重建提供许多有价值的信息进而有助于解决物种间复杂的进化关系问题。从遗传学角度来说，叶绿体基因组比线粒体（mt）基因组更为保守，后者在自然界中具有较多的异质性，通常认为线粒体DNA（mtDNA）具有倾向于通过细胞内和水平转移来整合不同来源的DNA，因此导致不同物种中线粒体基因组大小差异很大。

在本研究中，作者从前期进行的‘云抗10号’基因组测序数据中过滤出cpDNA和mtDNA，首次拼装出了阿萨姆种茶树的叶绿体基因组和线粒体基因组。其中将叶绿体基因组拼装成了一个157100 bp大小的环形重叠群，包含一个86649 bp的大单拷贝区域（LSC）和一个18285 bp的小单拷贝区域（SSC），二者中间被一对反向重复区域隔开；共注释到141个cp基因，其中87个为蛋白编码基因、46个为tRNA基因、8个为rRNA基因。

而将线粒体基因组拼装成两个环形scaffolds（702253 bp 和 178082 bp)，共注释到71个mt基因，包括44个蛋白编码基因、24个tRNA基因和3个rRNA基因。对比分析发现mt基因组比cp基因组具有更高的重复性，且mt的蛋白编码基因比cp的蛋白表达基因具有更多的RNA编辑位点。

Abstract

Tea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. Despite its enormous industrial, cultural and medicinal values, the chloroplast (cp) and mitochondrial (mt) genomes are not available for Camellia sinensis var. assamica. In this study, we de novo assembled the cp genome sequence of C. sinensis var. assamica into a circular contig of 157,100 bp in length with an overall GC content of 37.29%, comprising a large single-copy region (LSC, 86,649 bp) and a small single-copy region (SSC, 18,285 bp) separated by a pair of inverted repeats (IRs, 26,083 bp). We annotated a total of 141 cp genes, of which 87 are protein-coding genes, 46 are tRNA genes, and eight are rRNA genes. We also de novoassembled the mt genome of C. sinensis var. assamica into two complete circular scaffolds (702,253 bp and 178,082 bp) with overall GC contents of 45.63% and 45.81%, respectively. We annotated a total of 71 mt genes, including 44 protein-coding genes, 24 tRNAs, and 3 rRNAs. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878 bp and 149 bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are ~4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamicapresented in this study will become an invaluable resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.