Abstract
Background Camellia , comprising more than 200 species, is a valuable economic commodity due to its enormously popular commercial products: tea leaves, flowers, and high-quality edible oils. It is the largest and most important genus in the family Theaceae. However, phylogenetic resolution of the species has proven to be difficult. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. Phylogenomics is an attractive avenue that can be used to reconstruct the tree of life, especially at low taxonomic levels.Methodology/Principal FindingsSeven complete chloroplast (cp) genomes were sequenced from six species representing different subdivisions of the genus Camellia using Illumina sequencing technology. Four junctions between the single-copy segments and the inverted repeats were confirmed and genome assemblies were validated by PCR-based product sequencing using 123 pairs of primers covering preliminary cp genome assemblies. The length of the Camellia cp genome was found to be about 157kb, which contained 123 unique genes and 23 were duplicated in the IR regions. We determined that the complete Camellia cp genome was relatively well conserved, but contained enough genetic differences to provide useful phylogenetic information. Phylogenetic relationships were analyzed using seven complete cp genomes of six Camellia species. We also identified rapidly evolving regions of the cp genome that have the potential to be used for further species identification and phylogenetic resolution.Conclusions/SignificanceIn this study, we wanted to determine if analyzing completely sequenced cp genomes could help settle these controversies of interspecies relationships in Camellia . The results demonstrate that cp genome data are beneficial in resolving species definition because they indicate that organelle-based “barcodes”, can be established for a species and then used to unmask interspecies phylogenetic relationships. It reveals that phylogenomics based on cp genomes is an effective approach for achieving phylogenetic resolution between Camellia species.
Highlights
Camellia, a genus containing shrubs and trees, is the largest and most economically, socially, and ecologically valuable genus in the family Theaceae [1,2,3,4,5,6,7,8]
Seven individuals were sequenced to produce 6,539,876 to 7,233,285 paired-end reads (90 bp average read length) using the Illumina Hiseq 2000 system. After screening these pairedend reads by aligning them with reference cp genomes, 108,851 to 112,589 reads were mapped to the reference genomes, reaching, on average, over 100× coverage of the cp genome
We simultaneously corrected potential errors using PCR-based validation in order to eliminate assembly errors caused by heterogeneous indels from homopolymeric repeats, resulting in complete, high-quality cp genome sequences [38,68]
Summary
A genus containing shrubs and trees, is the largest and most economically, socially, and ecologically valuable genus in the family Theaceae [1,2,3,4,5,6,7,8]. Camellia, comprising more than 200 species, is a valuable economic commodity due to its enormously popular commercial products: tea leaves, flowers, and high-quality edible oils. It is the largest and most important genus in the family Theaceae. The results demonstrate that cp genome data are beneficial in resolving species definition because they indicate that organelle-based “barcodes”, can be established for a species and used to unmask interspecies phylogenetic relationships. It reveals that phylogenomics based on cp genomes is an effective approach for achieving phylogenetic resolution between Camellia species
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