Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, Thellungiella halophila View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-11-24

AUTHORS

Teruaki Taji, Kenji Komatsu, Taku Katori, Yoshikazu Kawasaki, Yoichi Sakata, Shigeo Tanaka, Masatomo Kobayashi, Atsushi Toyoda, Motoaki Seki, Kazuo Shinozaki

ABSTRACT

BackgroundThellungiella 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.ResultsHere, 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. halophilasalt 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.ConclusionsThe 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). More... »

PAGES

261

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URI

http://scigraph.springernature.com/pub.10.1186/1471-2229-10-261

DOI

http://dx.doi.org/10.1186/1471-2229-10-261

DIMENSIONS

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PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/21106055


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32 schema:description BackgroundThellungiella 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.ResultsHere, 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. halophilasalt 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.ConclusionsThe 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).
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39 Arabidopsis
40 Arabidopsis genes
41 C-terminal hydrophilic region
42 DNA sequences
43 ResultsHere
44 T. halophila
45 Thellungiella
46 Thellungiella halophila
47 analysis
48 annotation
49 cDNA
50 cDNA library
51 cDNA sequence
52 comparative genomic analysis
53 compartmentation
54 conditions
55 cycle
56 degree
57 diffusion
58 distinct genes
59 domain
60 end
61 essential role
62 excretion
63 expression levels
64 factor genes
65 full-length cDNA
66 full-length cDNA sequence
67 further improvement
68 gene prediction
69 genes
70 genome
71 genomic analysis
72 growth conditions
73 halophila
74 halophytes
75 high degree
76 high levels
77 hydrophilic region
78 identity
79 improvement
80 length
81 levels
82 library
83 life cycle
84 model halophyte
85 motif
86 normal growth conditions
87 ongoing annotation
88 orthologous genes
89 plants
90 prediction
91 probe
92 protein phosphatase 2C gene
93 region
94 role
95 salinity
96 sequence
97 sequence identity
98 sequence similarity
99 short life cycle
100 short splicing variant
101 significant levels
102 similarity
103 size
104 small genomes
105 small size
106 species
107 splicing variants
108 stress
109 structure
110 study
111 tissue
112 transcription factor genes
113 transmembrane domain
114 transport system genes
115 variants
116 whole plant
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