title: De novo sequencing and analysis of the Ulva linza transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems.
abstract: BACKGROUND
  The green algal genus Ulva Linnaeus (Ulvaceae, Ulvales, Chlorophyta) is well known for its wide distribution in marine, freshwater, and brackish environments throughout the world. The Ulva species are also highly tolerant of variations in salinity, temperature, and irradiance and are the main cause of green tides, which can have deleterious ecological effects. However, limited genomic information is currently available in this non-model and ecologically important species. Ulva linza is a species that inhabits bedrock in the mid to low intertidal zone, and it is a major contributor to biofouling. Here, we presented the global characterization of the U. linza transcriptome using the Roche GS FLX Titanium platform, with the aim of uncovering the genomic mechanisms underlying rapid and successful colonization of the coastal ecosystems.
  
  
  RESULTS
  De novo assembly of 382,884 reads generated 13,426 contigs with an average length of 1,000 bases. Contiguous sequences were further assembled into 10,784 isotigs with an average length of 1,515 bases. A total of 304,101 reads were nominally identified by BLAST; 4,368 isotigs were functionally annotated with 13,550 GO terms, and 2,404 isotigs having enzyme commission (EC) numbers were assigned to 262 KEGG pathways. When compared with four other full sequenced green algae, 3,457 unique isotigs were found in U. linza and 18 conserved in land plants. In addition, a specific photoprotective mechanism based on both LhcSR and PsbS proteins and a C4-like carbon-concentrating mechanism were found, which may help U. linza survive stress conditions. At least 19 transporters for essential inorganic nutrients (i.e., nitrogen, phosphorus, and sulphur) were responsible for its ability to take up inorganic nutrients, and at least 25 eukaryotic cytochrome P450s, which is a higher number than that found in other algae, may be related to their strong allelopathy. Multi-origination of the stress related proteins, such as glutamate dehydrogenase, superoxide dismutases, ascorbate peroxidase, catalase and heat-shock proteins, may also contribute to colonization of U. linza under stress conditions.
  
  
  CONCLUSIONS
  The transcriptome of U. linza uncovers some potential genomic mechanisms that might explain its ability to rapidly and successfully colonize coastal ecosystems, including the land-specific genes; special photoprotective mechanism based on both LhcSR and PsbS; development of C4-like carbon-concentrating mechanisms; muti-origin transporters for essential inorganic nutrients; multiple and complex P450s; and glutamate dehydrogenase, superoxide dismutases, ascorbate peroxidase, catalase, and heat-shock proteins that are related to stress resistance.
authors.affiliation: Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Zhang
authors.forename: Naihao
authors.initials: N
authors.lastname: Ye
authors.forename: Chengwei
authors.initials: C
authors.lastname: Liang
authors.forename: Shanli
authors.initials: S
authors.lastname: Mou
authors.forename: Xiao
authors.initials: X
authors.lastname: Fan
authors.forename: Jianfang
authors.initials: J
authors.lastname: Xu
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.forename: Zhimeng
authors.initials: Z
authors.lastname: Zhuang
mesh_terms: D060387:Ascorbate Peroxidases / Q000235:genetics / Q000378:metabolism; D061006:Bays; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D002374:Catalase / Q000235:genetics / Q000378:metabolism; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics / Q000378:metabolism; D017753:Ecosystem; D063366:Estuaries; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018745:Genome, Plant; D005969:Glutamate Dehydrogenase / Q000235:genetics / Q000378:metabolism; D006360:Heat-Shock Proteins / Q000235:genetics / Q000378:metabolism; D045342:Light-Harvesting Protein Complexes / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D054712:Salinity; D017422:Sequence Analysis, DNA; D013312:Stress, Physiological; D013482:Superoxide Dismutase / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D014466:Ultraviolet Rays; D044445:Ulva / Q000235:genetics* / Q000378:metabolism / Q000528:radiation effects
chemical_list: D002352:Carrier Proteins; D006360:Heat-Shock Proteins; D045342:Light-Harvesting Protein Complexes; D010940:Plant Proteins; D003577:Cytochrome P-450 Enzyme System; D060387:Ascorbate Peroxidases; D002374:Catalase; D013482:Superoxide Dismutase; D005969:Glutamate Dehydrogenase