Abstract
BackgroundRapidly driven by the need for developing sustainable sources of nutritionally important fatty acids and the rising concerns about environmental impacts after using fossil oil, oil-plants have received increasing awareness nowadays. As an important oil-rich plant in China, Camellia oleifera has played a vital role in providing nutritional applications, biofuel productions and chemical feedstocks. However, the lack of C. oleifera genome sequences and little genetic information have largely hampered the urgent needs for efficient utilization of the abundant germplasms towards modern breeding efforts of this woody oil-plant.ResultsHere, using the 454 GS-FLX sequencing platform, we generated approximately 600,000 RNA-Seq reads from four tissues of C. oleifera. These reads were trimmed and assembled into 104,842 non-redundant putative transcripts with a total length of ∼38.9 Mb, representing more than 218-fold of all the C. oleifera sequences currently deposited in the GenBank (as of March 2014). Based on the BLAST similarity searches, nearly 42.6% transcripts could be annotated with known genes, conserved domains, or Gene Ontology (GO) terms. Comparisons with the cultivated tea tree, C. sinensis, identified 3,022 pairs of orthologs, of which 211 exhibited the evidence under positive selection. Pathway analysis detected the majority of genes potentially related to lipid metabolism. Evolutionary analysis of omega-6 fatty acid desaturase (FAD2) genes among 20 oil-plants unexpectedly suggests that a parallel evolution may occur between C. oleifera and Olea oleifera. Additionally, more than 2,300 simple sequence repeats (SSRs) and 20,200 single-nucleotide polymorphisms (SNPs) were detected in the C. oleifera transcriptome.ConclusionsThe generated transcriptome represents a considerable increase in the number of sequences deposited in the public databases, providing an unprecedented opportunity to discover all related-genes associated with lipid metabolic pathway in C. oleifera. It will greatly enhance the generation of new varieties of C. oleifera with increased yields and high quality.
Highlights
The tea-oil camellia (Camellia oleifera), a member of the family Theaceae, is well recognized as one of the world’s four major woody oil tree together with oil palm, olive and coconut
Due to the fact that many genes in the transcriptome are expressed at levels low enough to hinder adequate sampling for 454 sequencing [18], reads that had no apparent overlapping with other reads in the database may contain useful gene information, which could not be obtained from isotigs
To examine the dynamic evolution of othologous genes between C. sinensis and C. oleifera, we identified 3,022 pairs of orthogous genes, of which 211 were under positive selection with Ks/Ks ratio .1, suggesting that they may probably play a vital role in the evolutionary process of Camellia species
Summary
The tea-oil camellia (Camellia oleifera), a member of the family Theaceae, is well recognized as one of the world’s four major woody oil tree together with oil palm, olive and coconut. It is an important and promoted woody oil plant in China, and has been widely utilized in many areas, such as food supplies, inks, lubricants, and cosmetics [1,2]. The lack of C. oleifera genome sequences and little genetic information have largely hampered the urgent needs for efficient utilization of the abundant germplasms towards modern breeding efforts of this woody oil-plant
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