PRJNA181961
Characterization of the global transcriptome for Pyropia haitanensis (Bangiales, Rhodophyta) and development of cSSR markers
Pyropia haitanensis is an economically important mariculture crop in China and also has a high research value for several life phenomena. However, the lack of genetic information on this organism hinders understanding the molecular mechanisms of specific traits. Thus, high-throughput sequencing is needed to generate a mass of transcriptome sequences for gene discovery and molecular marker development. In this study, high-throughput sequencing technology was used to analyze the global transcriptome of P. haitanensis. Approximately 103 million 90 bp paired-end reads were generated from an Illumina Genome Analyzer. De novo assembly with paired-end information yielded 24,575 unigenes with an average length of 645 bp. Based on sequence similarity searches with known proteins, a total of 16,377 (66.64%) genes were identified. Of these annotated unigenes, 5,471 and 9,168 unigenes were assigned to gene ontology and clusters of orthologous groups, respectively. Searching against the KEGG database indicated that 12,167 (49.51%) unigenes mapped to 124 KEGG pathways. Among the carbon fixation pathways, almost all the essential genes related to the C3- and C4-pathways for P. haitanensis were discovered. Significantly different expression levels of three key genes (Rubisco, PEPC and PEPCK) in different lifecycle stages of P. haitanensis indicated that the carbon fixation pathway in the conchocelis and thallus are different, and the C4-like pathway might play important roles in the conchocelis stage. In addition, 2,727 cSSRs loci were identified in our unigenes. Among them, trinucletide SSRs were the dominant repeat motif (87.17%, 2,377) and GCC/CCG motifs were the most common repeats (60.07%, 1,638). High quality primers to 824 loci were designed and 100 primer pairs were randomly evaluated in six strains of P. haitanensis. Altogether, 87 primer pairs successfully yielded amplicons.This study generated a huge number of P. haitanensis transcript sequences, which can be used for novel gene discovery and gene expression profiling analyses under different physiological conditions. A number of the cSSR markers identified can be used for molecular markers and will facilitate marker assisted selection in P. haitanensis breeding. These sequences and markers will provide valuable resources for further P. haitanensis studies.