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

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. 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.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).

Growth Platform-Dependent and -Independent Phenotypic and Metabolic Responses of Arabidopsis and Its Halophytic Relative, Eutrema salsugineum, to Salt Stress

“…The high similarity of E. salsugineum to Arabidopsis in morphology, complementary DNA sequence, and metabolic pathways, yet its dramatic difference in stress tolerance, has allowed fruitful comparative analyses of the stress responses of the two species. Furthermore, a growing body of technical resources has been developed, including ecotype collections (Lee et al, 2012), ESTs (Wong et al, 2005;Zhang et al, 2008), full-length complementary DNA libraries (Du et al, 2008;Taji et al, 2008Taji et al, , 2010, microarrays (Wong et al, 2006), and a genome sequence of both E. salsugineum and E. parvulum (Dassanayake et al, 2011;Wu et al, 2012;Yang et al, 2013).…”

Comparative Proteomics of Thellungiella halophila Leaves from Plants Subjected to Salinity Reveals the Importance of Chloroplastic Starch and Soluble Sugars in Halophyte Salt Tolerance

“…Similar to Arabidopsis, Thellungiella has many advantages, such as a small genome with a high sequence homology (average 92%) to the Arabidopsis genome, a short life cycle, a large seed yield, and easy transformation by floral dipping (2,11,12). Its ability to adapt to high levels of salinity stress may be attributed to global changes in gene regulation at both transcriptional and proteomic levels, rather than to the acquisition of novel gene functions (13,14).…”

“…Recently, a draft sequence of the Thellungiella genome was assembled de novo (10). Simultaneously, large amounts of full-length enriched cDNA were sequenced, and the functions of many distinct genes were determined (12,15). These annotated sequences are essential for the ongoing analysis of the Thellungiella proteome.…”

Homologous cloning, characterization and expression of a new halophyte phytochelatin synthase gene in Suaeda salsa

“…halophila PCS , was found using a large-scale analysis of enriched cDNAs from T . halophila , a related halophyte model to Arabidopsis (Taji et al, 2010). Presently, no detailed study has described the function of the T .…”

“…This reaction is catalyzed by the phytochelatin synthase gene ( PCS ) that has been widely found in many kinds of organisms (Cobbett, 1999;Brulle et al, 2008). To our knowledge, the PCS gene was isolated from the halophyte Thellungiella halophila , a model plant for salt tolerance research (Taji et al, 2010). However, there are no reports from other salt-tolerant plants.…”