Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica

Abstract

Tea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. In this study, we de novo assembled the chloroplast (cp) and mitochondrial (mt) genomes of C. sinensis var. assamica cv. Yunkang10 into a circular contig of 157,100 bp and two complete circular scaffolds (701719 bp and 177329 bp), respectively. We correspondingly annotated a total of 141 cp genes and 71 mt genes. 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. assamica presented in this study will become an important resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.

Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae

“…In recent years, a large number of plastid genomes have been revealed and compared for studying of taxonomy, evolution, breeding and conservation (Gruzdev et al, 2019a;Twyford & Ness, 2017;Zhong et al, 2019). The plastid genome of woody ornamental plant species such as Prunus (Cho, Yoon & Kim, 2018;Xue et al, 2019), Rosa (Jeon & Kim, 2019), Paeonia (Li, Guo & Zheng, 2018), Camellia (Li et al, 2019;Zhang et al, 2019), have also been established.…”

The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions

“…First, in contrast to the cpDNA genome, mtDNA is more often characterized by heteroplasmy phenomena (i.e., co-existence of additional mitochondrial genome types called mitotypes) [ 40 ] and by a variety of different arrangements and configurations (circular, linear or branched molecules) [ 41 , 42 , 43 ] that can strongly affect their correct and exhaustive assembly. Moreover, when compared to cpDNA genomes, mtDNA has proven to be bigger and to contain more repeat regions as well as significant amounts of nuclear and chloroplast genomic sequences [ 44 ]. All these peculiarities, along with technical issues linked to the amount and the type of available reads (short vs. long), may limit the accurate assembly of this organelle genome.…”

Comparative analysis of chloroplast genomes indicated different origin for Indian Tea (Camellia assamica) cv TV-1 as compared to Chinese tea

“…To perform the chloroplast based phylogenetic analysis, we have chosen previously published and well-annotated cp genome sequences of 15 Camellia species ( Camellia sinensis , C. grandibracteata, C. leptophylla, C. petelotii, C. pubicosta, C. reticulata, C. azalea, C. japonica, C. chekiangoleosa, C. cuspidata, C. danzaiensis, C. impressinervis, C. pitardii, C. yunnanensis and C. taliensis ) (Huang et al, 2014) and 2 recently published cp genome sequences including C. assamica (Rawal et al, 2019) and C. sinensis var. assamica (Zhang et al, 2019). All these 17 Camellia species belongs to the Theaceae family under Asterids group.…”