Characterization of the global transcriptome for Pyropia haitanensis(Bangiales, Rhodophyta) and development of cSSR markers

Abstract

BackgroundPyropia haitanensis is an economically important mariculture crop in China and is also valuable in life science research. However, the lack of genetic information of this organism hinders the understanding of the molecular mechanisms of specific traits. Thus, high-throughput sequencing is needed to generate a number of transcriptome sequences to be used for gene discovery and molecular marker development.ResultsIn this study, high-throughput sequencing was used to analyze the global transcriptome of P. haitanensis. Approximately 103 million 90 bp paired-end reads were generated using an Illumina HiSeq 2000. 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 were different, and the C4-like pathway might play important roles in the conchocelis stage. In addition, 2,727 cSSRs loci were identified in the unigenes. Among them, trinucleotide 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. Eighty-seven primer pairs successfully yielded amplicons.ConclusionThis study generated a large number of putative 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.

A multifunctional lipoxygenase from Pyropia haitanensis— The cloned and functioned complex eukaryotic algae oxylipin pathway enzyme

“…In their study on the genome of C. crispus, Collén et al surprisingly found that there were only two genes encoding LOX but no candidates for AOS, HPL, and DES. The present study also searched the P. haitanensis transcriptomic information published by Xie et al [16] and the genomic data of P. yezoensis but did not find candidate genes for these enzymes. To date, no evidence has indicated that CYP74 family existed at the evolutionary stage when Rhodophyta emerged.…”

“…In addition, there is the question of whether these pathways evolved independently in the different kingdoms. In this study, a LOX gene from P. haitanensis (Bangiales, Rhodophytes), a typical warm, temperate zone species [16], was identified and its versatile functions and enzyme products described. The results raised interesting questions concerning this enzyme's evolutionary heritage and its relationship to the known diversity of oxylipin structures and functions.…”

Developmental and physiological properties of Pyropia dentata (Bangiales, Rhodophyta) conchocelis in culture

“…Draft genome of Pyropia yezoensis has been released (Niu et al 2011;Nakamura et al 2013), and transcriptome of Pyropia and Porphyra has been compared for life stages and under stress (Chan et al 2012;Choi et al 2013;Xie et al 2013;Im et al 2015).…”

Reference genes for transcript quantification in Gracilaria tenuistipitata under drought stress

“…However, little is known about transcription level changes in response to dehydration. Efforts to sequence the genomes and transcriptomes of species such as Chondrus crispus, Gracilariopsis lemaneiformis, Pyropia yezoensis, Pyropia haitanensis, and Gracilaria changii are beginning to change this situation (Collén et al 2006b;2006a;Teo et al 2009;Choi et al 2012;Xie et al 2013;Zhou et al 2013;Kowalczyk et al 2014;Im et al 2015).…”