title: Transcriptome analysis identifies genes involved in adventitious branches formation of Gracilaria lichenoides in vitro.
abstract: Tissue culture could solve the problems associated with Gracilaria cultivation, including the consistent supply of high-quality seed stock, strain improvement, and efficient mass culture of high-yielding commercial strains. However, STC lags behind that of higher plants because of the paucity of genomic information. Transcriptome analysis and the identification of potential unigenes involved in the formation and regeneration of callus or direct induction of ABs are essential. Herein, the CK, EWAB and NPA G. lichenoides transcriptomes were analyzed using the Illumina sequencing platform in first time. A total of 17,922,453,300 nucleotide clean bases were generated and assembled into 21,294 unigenes, providing a total gene space of 400,912,038 nucleotides with an average length of 1,883 and N 50 of 5,055 nucleotides and a G + C content of 52.02%. BLAST analysis resulted in the assignment of 13,724 (97.5%), 3,740 (26.6%), 9,934 (70.6%), 10,611 (75.4%), 9,490 (67.4%), and 7,773 (55.2%) unigenes were annotated to the NR, NT, Swiss-Prot, KEGG, COG, and GO databases, respectively, and the total of annotated unigenes was 14,070. A total of 17,099 transcripts were predicted to possess open reading frames, including 3,238 predicted and 13,861 blasted based on protein databases. In addition, 3,287 SSRs were detected in G.lichenoides, providing further support for genetic variation and marker-assisted selection in the future. Our results suggest that auxin polar transport, auxin signal transduction, crosstalk with other endogenous plant hormones and antioxidant systems, play important roles for ABs formation in G. lichenoides explants in vitro. The present findings will facilitate further studies on gene discovery and on the molecular mechanisms underlying the tissue culture of seaweed.
authors.affiliation: Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Fujian, 361005, China.
authors.forename: Wenlei
authors.initials: W
authors.lastname: Wang
authors.affiliation: College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China.
authors.forename: Huanqin
authors.initials: H
authors.lastname: Li
authors.affiliation: Engineering Research Center of Marine Biological Resource Comprehensive Utilization, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China.
authors.forename: Xiangzhi
authors.initials: X
authors.lastname: Lin
authors.affiliation: Engineering Research Center of Marine Biological Resource Comprehensive Utilization, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China.
authors.forename: Shanjun
authors.initials: S
authors.lastname: Yang
authors.affiliation: Engineering Research Center of Marine Biological Resource Comprehensive Utilization, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China.
authors.forename: Zhaokai
authors.initials: Z
authors.lastname: Wang
authors.affiliation: College of Biochemistry and Engineering, Xiamen University, Xiamen 361005, China.
authors.forename: Baishan
authors.initials: B
authors.lastname: Fang
mesh_terms: D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D056726:Genetic Association Studies; D044724:Gracilaria / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D010641:Phenotype; D019655:Quantitative Trait, Heritable; D017422:Sequence Analysis, DNA; D046509:Tissue Culture Techniques; D059467:Transcriptome