title: Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, Thellungiella halophila.
abstract: BACKGROUND
  Thellungiella halophila (also known as T. salsuginea) is a model halophyte with a small size, short life cycle, and small genome. Thellungiella genes exhibit a high degree of sequence identity with Arabidopsis genes (90% at the cDNA level). We previously generated a full-length enriched cDNA library of T. halophila from various tissues and from whole plants treated with salinity, chilling, freezing stress, or ABA. We determined the DNA sequences of 20 000 cDNAs at both the 5'- and 3' ends, and identified 9569 distinct genes.
  
  
  RESULTS
  Here, we completely sequenced 1047 Thellungiella full-length cDNAs representing abiotic-stress-related genes, transcription factor genes, and protein phosphatase 2C genes. The predicted coding sequences, 5'-UTRs, and 3'-UTRs were compared with those of orthologous genes from Arabidopsis for length, sequence similarity, and structure. The 5'-UTR sequences of Thellungiella and Arabidopsis orthologs shared a significant level of similarity, although the motifs were rearranged. While examining the stress-related Thellungiella coding sequences, we found a short splicing variant of T. halophila salt overly sensitive 1 (ThSOS1), designated ThSOS1S. ThSOS1S contains the transmembrane domain of ThSOS1 but lacks the C-terminal hydrophilic region. The expression level of ThSOS1S under normal growth conditions was higher than that of ThSOS1. We also compared the expression levels of Na+-transport-system genes between Thellungiella and Arabidopsis by using full-length cDNAs from each species as probes. Several genes that play essential roles in Na+ excretion, compartmentation, and diffusion (SOS1, SOS2, NHX1, and HKT1) were expressed at higher levels in Thellungiella than in Arabidopsis.
  
  
  CONCLUSIONS
  The full-length cDNA sequences obtained in this study will be essential for the ongoing annotation of the Thellungiella genome, especially for further improvement of gene prediction. Moreover, they will enable us to find splicing variants such as ThSOS1S (AB562331).
authors.affiliation: Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan. t3teruak@nodai.ac.jp
authors.forename: Teruaki
authors.initials: T
authors.lastname: Taji
authors.forename: Kenji
authors.initials: K
authors.lastname: Komatsu
authors.forename: Taku
authors.initials: T
authors.lastname: Katori
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Kawasaki
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Sakata
authors.forename: Shigeo
authors.initials: S
authors.lastname: Tanaka
authors.forename: Masatomo
authors.initials: M
authors.lastname: Kobayashi
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D020121:5' Untranslated Regions / Q000235:genetics; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D015152:Blotting, Northern; D019607:Brassicaceae / Q000235:genetics*; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D055051:Salt-Tolerant Plants / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D018076:DNA, Complementary; D010940:Plant Proteins