title: De novo transcriptome analysis of an aerial microalga Trentepohlia jolithus: pathway description and gene discovery for carbon fixation and carotenoid biosynthesis.
abstract: BACKGROUND
  Algae in the order Trentepohliales have a broad geographic distribution and are generally characterized by the presence of abundant β-carotene. The many monographs published to date have mainly focused on their morphology, taxonomy, phylogeny, distribution and reproduction; molecular studies of this order are still rare. High-throughput RNA sequencing (RNA-Seq) technology provides a powerful and efficient method for transcript analysis and gene discovery in Trentepohlia jolithus.
  
  
  RESULTS
  Illumina HiSeq 2000 sequencing generated 55,007,830 Illumina PE raw reads, which were assembled into 41,328 assembled unigenes. Based on NR annotation, 53.28% of the unigenes (22,018) could be assigned to gene ontology classes with 54 subcategories and 161,451 functional terms. A total of 26,217 (63.44%) assembled unigenes were mapped to 128 KEGG pathways. Furthermore, a set of 5,798 SSRs in 5,206 unigenes and 131,478 putative SNPs were identified. Moreover, the fact that all of the C4 photosynthesis genes exist in T. jolithus suggests a complex carbon acquisition and fixation system. Similarities and differences between T. jolithus and other algae in carotenoid biosynthesis are also described in depth.
  
  
  CONCLUSIONS
  This is the first broad transcriptome survey for T. jolithus, increasing the amount of molecular data available for the class Ulvophyceae. As well as providing resources for functional genomics studies, the functional genes and putative pathways identified here will contribute to a better understanding of carbon fixation and fatty acid and carotenoid biosynthesis in T. jolithus.
authors.affiliation: Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Qianqian
authors.initials: Q
authors.lastname: Li
authors.affiliation: Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
authors.forename: Jianguo
authors.initials: J
authors.lastname: Liu
authors.affiliation: Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
authors.forename: Litao
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Liu
mesh_terms: D057486:Carbon Cycle / Q000235:genetics; D002338:Carotenoids / Q000096:biosynthesis; D000460:Chlorophyta / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005227:Fatty Acids / Q000096:biosynthesis; D020869:Gene Expression Profiling; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D059467:Transcriptome
chemical_list: D005227:Fatty Acids; D012337:RNA, Ribosomal, 18S; D002338:Carotenoids