Pyropia yezoensis is a popular edible macro-alga that is present mostly in intertidal zones. This species is one of the most economically important seaweed and has been cultivated extensively in the cold water of East Asia. Various reports on isolation and characterization of improved strains of Pyr...
Pyropia yezoensis is a popular edible macro-alga that is present mostly in intertidal zones. This species is one of the most economically important seaweed and has been cultivated extensively in the cold water of East Asia. Various reports on isolation and characterization of improved strains of Pyropia have been published. However, there are very few studies focusing on the molecular basis underlying these mutants. Genetic analysis of Pyropia is hindered largely due to the quantity and quality of existing molecular data. In this context, we carried out a comparative analysis of whole transcriptomes of a wildtype (PyWT) and a high-growth strain of P. yezoensis (Py500G) using Next generation RNA Sequencing (RNA-Seq). By sequencing with Illumina HiSeq 2000 system, 184,381,412 paired-end reads with the length of 151 nt were obtained. De novo assembly generated 16,892 and 17,501 transcripts for Py500G and PyWT, respectively. To facilitate downstream analysis, the two transcriptomes were annotated by searching homologous sequences in NCBI NR, Swissprot, Pfam, and KEGG databases. To unravel the differences in Py500G and PyWT, we first identified the shared sequences of Py500G and PyWT. Next, we analyzed expression patterns and identified differentially expressed transcripts. GO terms retrieved via InterProScan were used to perform GO enrichment analysis of DEG list. We also discovered putative Single Nucleotide Polymorphisms (SNPs) in the shared sequences of Py500G and PyWT and determined the common and novel SNPs. All the analyzed data were finally integrated to form a candidate gene list that might be responsible for Py500G phenotype characteristic. In total, there were 70 candidate genes proposed to be important in explaining the difference between Py500G and PyWT. We discussed the biological importance of some of the candidate genes such as elongation factor 1A gene, proton-pumping pyrophosphate, and the difference in the ribosomal protein compositions between Py500G and PyWT. In addition, based on the transcriptome data, we proposed a putative carotenoid biosynthesis pathway in P. yezoensis. This study not only brings out the candidate genes responsible for the difference in the high-growth strain Py500G and PyWT but also provide a high quality genomic data for future genetics research in P. yezoensis.
Pyropia yezoensis is a popular edible macro-alga that is present mostly in intertidal zones. This species is one of the most economically important seaweed and has been cultivated extensively in the cold water of East Asia. Various reports on isolation and characterization of improved strains of Pyropia have been published. However, there are very few studies focusing on the molecular basis underlying these mutants. Genetic analysis of Pyropia is hindered largely due to the quantity and quality of existing molecular data. In this context, we carried out a comparative analysis of whole transcriptomes of a wildtype (PyWT) and a high-growth strain of P. yezoensis (Py500G) using Next generation RNA Sequencing (RNA-Seq). By sequencing with Illumina HiSeq 2000 system, 184,381,412 paired-end reads with the length of 151 nt were obtained. De novo assembly generated 16,892 and 17,501 transcripts for Py500G and PyWT, respectively. To facilitate downstream analysis, the two transcriptomes were annotated by searching homologous sequences in NCBI NR, Swissprot, Pfam, and KEGG databases. To unravel the differences in Py500G and PyWT, we first identified the shared sequences of Py500G and PyWT. Next, we analyzed expression patterns and identified differentially expressed transcripts. GO terms retrieved via InterProScan were used to perform GO enrichment analysis of DEG list. We also discovered putative Single Nucleotide Polymorphisms (SNPs) in the shared sequences of Py500G and PyWT and determined the common and novel SNPs. All the analyzed data were finally integrated to form a candidate gene list that might be responsible for Py500G phenotype characteristic. In total, there were 70 candidate genes proposed to be important in explaining the difference between Py500G and PyWT. We discussed the biological importance of some of the candidate genes such as elongation factor 1A gene, proton-pumping pyrophosphate, and the difference in the ribosomal protein compositions between Py500G and PyWT. In addition, based on the transcriptome data, we proposed a putative carotenoid biosynthesis pathway in P. yezoensis. This study not only brings out the candidate genes responsible for the difference in the high-growth strain Py500G and PyWT but also provide a high quality genomic data for future genetics research in P. yezoensis.
주제어
#rna-seq next generation sequencing Pyropia yezoensis red algae
학위논문 정보
저자
Tran Kim Ngan
학위수여기관
전남대학교
학위구분
국내석사
학과
바이오에너지및바이오소재협동과정
지도교수
Choi Jong-il
발행연도
2017
총페이지
67
키워드
rna-seq next generation sequencing Pyropia yezoensis red algae
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