DataSheet_1_Complete mitochondrial genome assembly and comparison of Camellia sinensis var. Assamica cv. Duntsa.docx

Camellia sinensis var. Assamica cv. Duntsa (C.duntsa), a valuable Theaceae from Hunan Province, has been looked at as a precious tea resource by local farmers because of its economic and ecological value. Genomics study on C.duntsa is essential for the domestication and enhancement of tea tree varieties. In the present study, we used a hybrid approach based on Illumina and PacBio data to sequence and assemble the mitochondrial genome of C.duntsa. The mitochondrial genome of C.duntsa was estimated to be 1,081,996 base pairs (bp) and eighty-one genes consisting of one pseudogene, three ribosomal RNA (rRNA) genes, thirty transfer RNA (tRNA) genes, and forty-seven protein-coding genes (PCGs). Tetramer repetitions made up 43.90% of simple sequence repeats (SSRs). The codon usage bias of the Theaceae mitochondrial gene atp9 was altered by mutation, but the codon usage of other genes was shaped by natural selection. Besides, there are eighteen gene-containing homologous regions between the chloroplast and mitochondrial genomes of C. duntsa.Some genomes including atp8, cox1, cox3, nad7, nad9, rpl16, rpl2, rps19, rps4, and sdh4 are absent in the mitochondrial genome of several Theaceae plant. However, C. duntsa maintains these genes integrity and functionality. Another gene, rps16, is either lacking from the mitochondrial genome of C. duntsa or is present as a pseudogene. C. duntsa and C. sinensis (OM809792) are very similar, as shown by a collinear match across four species of Theaceae; the most conservative genes are nad5, atp9, cox2, rps3, trnA-TGC, trnI-GAT, rrn18, trnV-GAC, and ccmFN. Similarly, the genome’s phylogenetic trees revealed that C. duntsa was the sister species to C. sinensis. The results confirmed that the C. duntsa and C. sinensis (OM809792) mitochondrial genome underwent gene rearrangement.In general, our results shows that genomic information from organelles can help us understand plant phylogeny and can also be used to make molecular markers and study how genetic traits change over time. Our research will contribute to the population genetics and evolution of tea plant.

茶树科植物 Camellia sinensis var. Assamica cv. Duntsa (C.duntsa)，作为湖南省的宝贵资源，因其经济和生态价值而被当地农民视为珍稀茶叶资源。对于茶树品种的驯化和改良，对C.duntsa的基因组学研究至关重要。在本研究中，我们采用Illumina和PacBio数据的混合方法，对C.duntsa的线粒体基因组进行了测序和组装。C.duntsa的线粒体基因组估计含有1,081,996个碱基对（bp）和八十一基因，包括一个假基因、三个核糖体RNA（rRNA）基因、三十个转移RNA（tRNA）基因以及四十七个编码蛋白质基因（PCGs）。四联体重复序列占简单序列重复（SSR）的43.90%。茶树科线粒体基因atp9的密码子使用偏好因突变而改变，而其他基因的密码子使用则受自然选择塑造。此外，C. duntsa的叶绿体和线粒体基因组之间存在十八个含基因的同源区域。一些基因组，包括atp8、cox1、cox3、nad7、nad9、rpl16、rpl2、rps19、rps4和sdh4，在多种茶树科植物的线粒体基因组中缺失。然而，C. duntsa保持了这些基因的完整性和功能。另一个基因rps16，在C. duntsa的线粒体基因组中要么缺失，要么以假基因的形式存在。C. duntsa与C. sinensis (OM809792) 非常相似，这通过茶树科四种物种的共线性匹配得以证实；保守性最高的基因包括nad5、atp9、cox2、rps3、trnA-TGC、trnI-GAT、rrn18、trnV-GAC和ccmFN。同样，基因组的系统发育树揭示了C. duntsa是C. sinensis的姐妹种。研究结果证实，C. duntsa和C. sinensis (OM809792) 的线粒体基因组经历了基因重排。总的来说，我们的结果表明，细胞器中的基因组信息有助于我们理解植物系统发育，并可用于构建分子标记，研究遗传性状随时间的变化。我们的研究将有助于茶树植物的种群遗传学和进化研究。