Assembly and comparative analysis of the first complete mitochondrial genome of Camellia sinensis var. assamica ‘Hainan Dayezhong’, endemic to Hainan Province, China

Camellia sinensis var. assamica ‘Hainan Dayezhong’ (C. sinensis var. assamica ‘Hainan Dayezhong’), an endemic, valuable tea plant from Hainan Province in China, has been utilized as a precious tea resource by local farmers. Nevertheless, no data on the mitochondrial genome of C. sinensis var. assamica ‘Hainan Dayezhong’ is available, which greatly limits our understanding of its phylogenetic classification and population identification. In this study, the Camellia sinensis var. assamica ‘Hainan Dayezhong’ complete mitochondrial genome was successfully assembled using the Nanopore and Illumina sequencing data for the first time. Key findings revealed a complex multi-branched structure comprising 12 contigs, with a total length of 793,531 bp and a GC content of 45.80%. A total of 70 genes were identified, including 38 protein-coding genes (PCGs), 28 tRNA genes, 3 rRNA genes, and one pseudogene (rps19). Out of the 31 PCGs shared by 18 Theaceae species, 28 of the PCGs were undergone purifying selection, and 3 genes (ccmC, rps1, and rps13) showed sign of positive selection. The codon usage analysis demonstrated that Leucine (Leu) and Serine (Ser) were the most preferred amino acids in C. sinensis var. assamica ‘Hainan Dayezhong’, and nearly all of the codons with RSCU > 1 showed the A/U bias at the third position. Tetramer repeats made up 40.71% of the simple sequence repeats (SSRs). 74 RNA editing sites were predicted in 17 PCGs, majority (91.89%) of them were C-to-U conversion pattern. 33 MTPTs were identified between the mitochondrial genome and chloroplast genome, with a combined length of 15,346 bp, accounting for 1.93% of the mitogenome. Moreover, the Maximum Likelihood phylogenetic trees were constructed of 38 shared PCGs in 30 plant species, the results showed that C. sinensis var. assamica ‘Hainan Dayezhong’ was phylogenetically independent of the species of sections Camellia, Chrysantha, and Oleifera. However, it didn’t support the independent subclade of C. sinensis var. assamica ‘Hainan Dayezhong’ due to the low support (BS = 55). Meanwhile, the chloroplast PCG-based phylogenetic analysis revealed that C. sinensis var. assamica ‘Hainan Dayezhong’ clustered together with C. sinensis var. assamica (MH019307.1) into a common subclade with high support (BS = 81). Our work presents the first complete mitogenome of Camellia sinensis var. assamica ‘Hainan Dayezhong’, which could not only provide a reference genome for the comprehensive analysis of Theaceae family, but also contribute to the valuable information for further genomic breeding and evolutionary research of Camellia.