Comparative Analyses and Phylogenetic Relationships between Cryptomeria fortunei and Related Species Based on Complete Chloroplast Genomes

Cryptomeria fortunei (Chinese cedar) is a highly adaptable woody species and one of the main forest plantation trees in subtropical high-altitude areas in China. However, there are few studies on its chloroplast (cp) genome. In this study, the complete cp genome of C. fortunei was sequenced and evaluated via comparative analyses with those of related species (formerly the Taxodiaceae) in Cupressaceae. The C. fortunei cp genome was 131,580 bp in length, and the GC content of the whole genome was 35.38%. It lost one relevant large inverted repeat and contained 114 unique genes, including 82 protein-coding genes, 28 tRNAs and 4 rRNAs. The relative synonymous codon usage (RSCU) of codons ending with A/U was more than twice that of codons ending with G/C. Thirty long repeat structures (LRSs) and 213 simple sequence repeat (SSR) loci were detected in the C. fortunei cp genome. Comparative analyses of 10 cp genomes revealed that substantial rearrangements occurred in the gene organization. Additionally, 6 cp hotspot regions (trnS-GGA, ycf1 , trnP-GGG, trnC-GCA, psbZ and accD) were identified, and 4 genes (petL, psbM, rpl22 and psaM) had likely underwent positive selection. Phylogenetic analysis showed that Cupressaceae, Taxaceae and Cephalotaxaceae clustered to form a Glade and that C. fortunei was most closely related to C. japonica (Japanese cedar), C. japonica cv. Wogon Hort and Taxodium distichum (baldcypress). These results provide references for future studies of population genetics, phylogenetic status and molecular markers among Cupressaceae species and for the cultivation of improved varieties.