AUTHOR=Li Jin , Tang Han , Luo Hua , Tang Jun , Zhong Ni , Xiao Lizheng 

TITLE=Complete mitochondrial genome assembly and comparison of Camellia sinensis var. Assamica cv. Duntsa

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1117002

DOI=10.3389/fpls.2023.1117002

ISSN=1664-462X

ABSTRACT=<p><italic>Camellia sinensis</italic> var. <italic>Assamica</italic> cv. <italic>Duntsa</italic> (<italic>C.duntsa</italic>), a valuable <italic>Theaceae</italic> 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 <italic>C.duntsa</italic> 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 <italic>C.duntsa</italic>. The mitochondrial genome of <italic>C.duntsa</italic> 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 <italic>Theaceae</italic> mitochondrial gene <italic>atp9</italic> 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 <italic>C. duntsa</italic>.Some genomes including <italic>atp8</italic>, <italic>cox1</italic>, <italic>cox3</italic>, <italic>nad7</italic>, <italic>nad9</italic>, <italic>rpl16</italic>, <italic>rpl2</italic>, <italic>rps19</italic>, <italic>rps4</italic>, and <italic>sdh4</italic> are absent in the mitochondrial genome of several <italic>Theaceae</italic> plant. However, <italic>C. duntsa</italic> maintains these genes integrity and functionality. Another gene, <italic>rps16</italic>, is either lacking from the mitochondrial genome of <italic>C. duntsa</italic> or is present as a pseudogene. <italic>C. duntsa</italic> and <italic>C. sinensis</italic> (OM809792) are very similar, as shown by a collinear match across four species of <italic>Theaceae</italic>; the most conservative genes are <italic>nad5</italic>, <italic>atp9</italic>, <italic>cox2</italic>, <italic>rps3</italic>, <italic>trnA-TGC</italic>, <italic>trnI-GAT</italic>, <italic>rrn18</italic>, <italic>trnV-GAC</italic>, and <italic>ccmFN</italic>. Similarly, the genome’s phylogenetic trees revealed that <italic>C. duntsa</italic> was the sister species to <italic>C. sinensis</italic>. The results confirmed that the <italic>C. duntsa</italic> and <italic>C. sinensis</italic> (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.</p>