Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology

Yang, Hui; Mao, Yunxiang; Kong, Fanna; Yang, Guanpin; Ma, Fei; Wang, Li

doi:10.1007/s11434-011-4546-4

Cited by 33 publications

(31 citation statements)

References 48 publications

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“…Dinucleotide repeats (DiNR) and hexanucleotide repeats (HexaNR) were approximately 1.3 and 4.4 %, respectively. Previous reports have also shown that TriNRs were most abundantly distributed in the coding sequence of Pyropia and other plants (Choi et al 2013;Yang et al 2011). Among TriNR, GGC was the most common motif, followed by CCG, CGG, GCG, GCC, and CGC.…”

Section: Identification Of Ssrsmentioning

confidence: 79%

“…With the advent of next-generation sequencing (NGS) methods such as Roche/454 and Illumina/Hi-seq, large-scale transcriptome sequences can be generated economically from a wider range of organisms (Cheung et al 2008;Huang et al 2012;Lister et al 2008;Qin et al 2008). NGS has also been used in marine algae to determine differentially expressed genes (DEG) between different culture conditions, including abiotic stressors (Choi et al 2013;Pearson et al 2010;Yang et al 2011), and for transcriptome characterization of Pyropia and Porphyra (Chan et al 2011(Chan et al , 2012aStiller et al 2012).…”

Section: Introductionmentioning

confidence: 99%

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De novo assembly of transcriptome from the gametophyte of the marine red algae Pyropia seriata and identification of abiotic stress response genes

Choi

Hwang

et al. 2014

J Appl Phycol

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Pyropia seriata, a marine red alga belonging to the order Bangiales (Rhodophyta), is one of the most valuable and widely cultivated Pyropia species. Water temperature and salinity are major factors affecting the growth and yield of Pyropia cultivation. Currently, there is limited data regarding the regulatory pathways and molecular mechanisms of the abiotic stress responses in red algae. In this study, we generated 1,403,321 expression sequence tags (ESTs) using 454 sequencing technology from the gametophyte thalli under control and high temperature conditions to identify the abiotic stress response genes. De novo assembly of the transcriptome reads generated 11,218 contigs, whereas 135,292 sequences remained as unassembled reads. Approximately 61.9 % of the contigs shared significant homology with known genes in our database, including the NCBI RefSeq database, plus Pyropia and Porphyra sequences. Sequence analyses demonstrated that the Pyropia transcriptome has a relatively high guaninecytosine (GC) content with predominant trinucleotide repeats (93.9 %). GGC was the most common motif in identified simple sequence repeats (SSRs). We selected 754 differentially expressed genes (DEGs) response to abiotic stress based on reads per kilobase per million reads (RPKM) values, many of which have no significant homology with known sequences in public database. These transcriptome sequences will facilitate future studies to understand the common processes and novel mechanisms involved in abiotic stress tolerance in red algae.

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Section: Identification Of Ssrsmentioning

confidence: 79%

Section: Introductionmentioning

confidence: 99%

De novo assembly of transcriptome from the gametophyte of the marine red algae Pyropia seriata and identification of abiotic stress response genes

Choi

Hwang

et al. 2014

J Appl Phycol

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“…The large number of reads and associated paired-end information that were produced resulted in a relatively high coverage depth (average = 33.56 ×). When these sequences were assembled, we obtained longer Unigenes (mean = 449 bp) than has been reported previously in studies using the same technology; for example, Camellia sinensi s (mean Unigene length = 355 bp) [29], Lycoris sprengeri (385 bp) [30], Porphyra yezoensis (419 bp) [31] and whitefly (clusters = 372 bp; singletons = 265 bp) [27]. The number of assembled Unigenes was 112-fold more than all the Chinese fir sequences that were currently deposited in GenBank (as of March 2012).…”

Section: Discussionmentioning

confidence: 99%

“…This simplifies the identification of transcription start sites, new splicing variants and rare transcripts, and allows allele expression to be monitored [20,21]. Furthermore it allows the direct transcriptome analysis of non-model organisms, and has been successfully applied to non-model organisms recently [22-31]. …”

Section: Introductionmentioning

confidence: 99%

De novo characterization of the Chinese fir (Cunninghamia lanceolata) transcriptome and analysis of candidate genes involved in cellulose and lignin biosynthesis

Huang

Tong

et al. 2012

BMC Genomics

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BackgroundChinese fir (Cunninghamia lanceolata) is an important timber species that accounts for 20–30% of the total commercial timber production in China. However, the available genomic information of Chinese fir is limited, and this severely encumbers functional genomic analysis and molecular breeding in Chinese fir. Recently, major advances in transcriptome sequencing have provided fast and cost-effective approaches to generate large expression datasets that have proven to be powerful tools to profile the transcriptomes of non-model organisms with undetermined genomes.ResultsIn this study, the transcriptomes of nine tissues from Chinese fir were analyzed using the Illumina HiSeq™ 2000 sequencing platform. Approximately 40 million paired-end reads were obtained, generating 3.62 gigabase pairs of sequencing data. These reads were assembled into 83,248 unique sequences (i.e. Unigenes) with an average length of 449 bp, amounting to 37.40 Mb. A total of 73,779 Unigenes were supported by more than 5 reads, 42,663 (57.83%) had homologs in the NCBI non-redundant and Swiss-Prot protein databases, corresponding to 27,224 unique protein entries. Of these Unigenes, 16,750 were assigned to Gene Ontology classes, and 14,877 were clustered into orthologous groups. A total of 21,689 (29.40%) were mapped to 119 pathways by BLAST comparison against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The majority of the genes encoding the enzymes in the biosynthetic pathways of cellulose and lignin were identified in the Unigene dataset by targeted searches of their annotations. And a number of candidate Chinese fir genes in the two metabolic pathways were discovered firstly. Eighteen genes related to cellulose and lignin biosynthesis were cloned for experimental validating of transcriptome data. Overall 49 Unigenes, covering different regions of these selected genes, were found by alignment. Their expression patterns in different tissues were analyzed by qRT-PCR to explore their putative functions.ConclusionsA substantial fraction of transcript sequences was obtained from the deep sequencing of Chinese fir. The assembled Unigene dataset was used to discover candidate genes of cellulose and lignin biosynthesis. This transcriptome dataset will provide a comprehensive sequence resource for molecular genetics research of C. lanceolata.

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“…changii [51], G . tenuistipitata [60], Porphyra yezoensis [61,67], P . haitanensis [59], Eucheuma denticulatum [74], Furcellaria lumbricalis [52], and Kappaphycus alvarezii [66], possibly indicating a general pattern of expression in red seaweeds.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic analysis of the red seaweed Laurencia dendroidea (Florideophyceae, Rhodophyta) and its microbiome

et al. 2012

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BackgroundSeaweeds of the Laurencia genus have a broad geographic distribution and are largely recognized as important sources of secondary metabolites, mainly halogenated compounds exhibiting diverse potential pharmacological activities and relevant ecological role as anti-epibiosis. Host-microbe interaction is a driving force for co-evolution in the marine environment, but molecular studies of seaweed-associated microbial communities are still rare. Despite the large amount of research describing the chemical compositions of Laurencia species, the genetic knowledge regarding this genus is currently restricted to taxonomic markers and general genome features. In this work we analyze the transcriptomic profile of L. dendroidea J. Agardh, unveil the genes involved on the biosynthesis of terpenoid compounds in this seaweed and explore the interactions between this host and its associated microbiome.ResultsA total of 6 transcriptomes were obtained from specimens of L. dendroidea sampled in three different coastal locations of the Rio de Janeiro state. Functional annotations revealed predominantly basic cellular metabolic pathways. Bacteria was the dominant active group in the microbiome of L. dendroidea, standing out nitrogen fixing Cyanobacteria and aerobic heterotrophic Proteobacteria. The analysis of the relative contribution of each domain highlighted bacterial features related to glycolysis, lipid and polysaccharide breakdown, and also recognition of seaweed surface and establishment of biofilm. Eukaryotic transcripts, on the other hand, were associated with photosynthesis, synthesis of carbohydrate reserves, and defense mechanisms, including the biosynthesis of terpenoids through the mevalonate-independent pathway.ConclusionsThis work describes the first transcriptomic profile of the red seaweed L. dendroidea, increasing the knowledge about ESTs from the Florideophyceae algal class. Our data suggest an important role for L. dendroidea in the primary production of the holobiont and the role of Bacteria as consumers of organic matter and possibly also as nitrogen source. Furthermore, this seaweed expressed sequences related to terpene biosynthesis, including the complete mevalonate-independent pathway, which offers new possibilities for biotechnological applications using secondary metabolites from L. dendroidea.

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Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology

Cited by 33 publications

References 48 publications

De novo assembly of transcriptome from the gametophyte of the marine red algae Pyropia seriata and identification of abiotic stress response genes

De novo assembly of transcriptome from the gametophyte of the marine red algae Pyropia seriata and identification of abiotic stress response genes

De novo characterization of the Chinese fir (Cunninghamia lanceolata) transcriptome and analysis of candidate genes involved in cellulose and lignin biosynthesis

Transcriptomic analysis of the red seaweed Laurencia dendroidea (Florideophyceae, Rhodophyta) and its microbiome

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