Codon Usage Profiles And Fruit Quality Related Functional Gene Expression Characteristics Of Chinese Bayberry(Myrica Rubra) Revealed By RNA-Seq

Chinese bayberry (Myrica rubra Sieb. et. Zucc.) is a special fruit crop native to China, however, the research on basic biology is weak, especially in the area of molecular biology. In the present work, an RNA-Seq project was initiated, and amount of sequence information and expression data were obtained. Furthermore, codon usage profiles and fruit quality related functional gene expression characteristics were revealed by bioinformatics and experimental biology. The main results are as follows:1. RNA-Seq and de-novo assembly on the Chinese bayberry. Four libraries (MR1-4) were built for RNA-Seq. The MR1library was constructed by mixing equal quantities of RNA from different tissues. The MR2-4libraries consisted of separate RNA samples from fruit of three different ripening stages (breaker stage, red ripe stage and full ripe stage). RNA-Seq generated1.92G raw data, which was then mixed and de novo assembled into41,239Unigenes with a mean length of531bp. Approximately80%of the Unigenes were annotated against public protein databases, and coding sequences of31,665Unigenes were determined.2. Codon usage profiles were analyzed based on the RNA-Seq data.1,066full-length coding sequences were used for codon usage analysis. Four high frequency codons and397high frequency codon pairs were observed. Meanwhile,26preferred and141avoided neighboring codon pairs were also identified. Codon patterns were also analyzed at the plant kingdom, organism and gene levels, respectively. Changes during plant evolution were evident using RSCU (relative synonymous codon usage), which was even more significant than GC3S (GC content of3rd synonymous codons). Nine GO categories were differentially and independently influenced by CAI (codon adaptation index) or GC3S. Within a gene, the average CAI increased from0.720to0.785in the first50codons, and then more slowly thereafter, while the first codon just following the start codon AUG has the lowest CAI, which may play role in regulating the protein translate rate. 3. The expression characteristics of genes related Chinese bayberry fruit quality were analyzed. Transcriptional network during fruit development and ripening was built by bioinformatics analysis. All genes involved in anthocyanin biosynthesis exhibited up-regulated profiles during the fruit ripening, consistent with color change. The sucrose phosphate synthase (SPS) and glutamate decarboxylase (GAD) were identified as the key genes related to the accumulation of sucrose and degradation of organic acid during fruit ripening. The gene expression profiles above were also confirmed by real-time q-PCR. Furthermore, four libraries with two high-acidy cultivars and two low-acidy cultivars were built for RNA-Seq. After analysis, B subunit of Vacuolar H+-ATPase (V-ATPase) showed very strong positive correction with organic acid content, which might be the key point to regulate the different organic acid content among different cultivars.