Research Article: Transcriptome Sequencing of Gracilariopsis lemaneiformis to Analyze the Genes Related to Optically Active Phycoerythrin Synthesis

Date Published: January 30, 2017

Publisher: Public Library of Science

Author(s): Xiaoyun Huang, Xiaonan Zang, Fei Wu, Yuming Jin, Haitao Wang, Chang Liu, Yating Ding, Bangxiang He, Dongfang Xiao, Xinwei Song, Zhu Liu, Shilin Chen.


Gracilariopsis lemaneiformis (aka Gracilaria lemaneiformis) is a red macroalga rich in phycoerythrin, which can capture light efficiently and transfer it to photosystemⅡ. However, little is known about the synthesis of optically active phycoerythrinin in G. lemaneiformis at the molecular level. With the advent of high-throughput sequencing technology, analysis of genetic information for G. lemaneiformis by transcriptome sequencing is an effective means to get a deeper insight into the molecular mechanism of phycoerythrin synthesis. Illumina technology was employed to sequence the transcriptome of two strains of G. lemaneiformis- the wild type and a green-pigmented mutant. We obtained a total of 86915 assembled unigenes as a reference gene set, and 42884 unigenes were annotated in at least one public database. Taking the above transcriptome sequencing as a reference gene set, 4041 differentially expressed genes were screened to analyze and compare the gene expression profiles of the wild type and green mutant. By GO and KEGG pathway analysis, we concluded that three factors, including a reduction in the expression level of apo-phycoerythrin, an increase of chlorophyll light-harvesting complex synthesis, and reduction of phycoerythrobilin by competitive inhibition, caused the reduction of optically active phycoerythrin in the green-pigmented mutant.

Partial Text

The genus Gracilaria encompasses the greatest number of species in the family Gracilariaceae, with the majority of them being reported from warm-water and tropical regions. Gracilariopsisspp. are widely distributed around the world and are important economic macroalgae, as they are utilized for agar extraction and may play an important role in bioremediation [1, 2, 3, 4, 5]. G. lemaneiformis is the principal species for seaweed cultivation in China, used as a nutritious food source rich in beneficial proteins, minerals and trace elements [6]. Moreover, the majority of phycobiliproteins in G. lemaneiformis is phycoerythrin, as identified by fluorescence spectroscopy. Phycoerythrin is a bright red, fluorescent and water-soluble light harvesting pigment, commonly found in red algae. Phycoerythrin has a variety of characteristics, including solubility in water, antioxidant property, anti-tumor activity and so on, which promotes use of phycoerythrin in a wide range of applications in the food, cosmetic, clinical diagnostics, immunochemistry, biological engineering and other fields, as well as in research to develop other uses. The chromophore–protein complex in PBPs shows structural flexibility in response to environmental changes [7,8,9]. The green mutant of G. lemaneiformis has a completely different color, resembling green algae, along with changes of its spectral characteristics, which appear to result from the change in phycobiliprotein composition, especially the percentage of phycoerythrin. The green G. lemaneiformis pigmentation mutant could be useful for phycobiliprotein research, because the molecular mechanism of phycoerythrin biosynthesis in G.lemaneiformis is little known. Thus, in this study, next generation sequencing technology was used to help us analyze the differentially-expressed genes between the wild type and the pigment mutant at the level of transcription, with the objective of getting an improved understanding of the biosynthesis of phycoerythrin having optical activity.

RNA-Seq has proved useful for the detection of gene expression, the discovery of novel transcripts, and the identification of differentially expressed genes. Here, second generation sequencing technology was used to analyze the transcriptome of G. lemaneiformis, and DEG analysis was used to reveal the change of expression pattern in the green mutant.

G. lemaneiformis is a suitable alga for studying the metabolic pathway of phycoerythrin, as phycoerythrin accounts for the largest proportion of pigments in the phycobiliprotein. The green mutant provides a good comparison for finding differential expression of genes for phycoerythrin synthesis. Transcriptome sequencing technology provides an effective means for analyzing the genetic information of this species. We have assembled 86915 unigenes using the Trinity de novo method, including identifying 42884 annotated unigenes in data bases, and screening 4041 differentially expressed genes. This study helps to provide a better understanding of the molecular mechanisms of photosystem regulation. The transcriptome dataset will take an active role in identifying genes related to photosynthesis in red algae, and it will also serve as a public information platform for studying gene expression and function in G. lemaneiformis.