Structural analysis of 83-kb genomic DNA from Thellungiella halophila: sequence features and microcolinearity between salt cress and Arabidopsis thaliana.

Abstract

Salt cress (Thellungiella halophila) has become a desirable plant model for molecular analysis of the mechanisms of salt tolerance. Analysis of its physiological action and expressed EST has resulted in better understanding. However, less is known about its genomic features. Here we determined a continuous sequence approximately 83 kb from a salt cress BAC clone, providing the first insight into the genomic feature for this species. The gene density is approximately one gene per 3.6 kb in this sequence. Many types of repetitive sequences are present in this salt cress sequence, including LTR retroelements, DNA transposons and a number of simple sequence repeats. Comparison of sequence similarity indicated that salt cress shares a close relationship with Arabidopsis. Extensive conservation and high-level microcolinearity were uncovered for both genomes. Our study also indicated that genomic DNA alternations (involving chromosome inversion, sequence loss and gene translocation) contributed to the genomic discrepancies between salt cress and Arabidopsis.

• Authors: Zhiyong Deng, Yin Li, Ran Xia, Weiquan Wang, Xiahe Huang, Ling Zhang, Shengli Zhang, Cuiping Yang, Yiyue Zhang, Mingsheng Chen, Qi Xie
• Journal: Genomics (Genomics) Vol. 94 Issue 5 Pg. 324-32 (Nov 2009) ISSN: 1089-8646 [Electronic] United States
• PMID: 19646522 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• DNA Transposable Elements
• DNA, Plant
• Sodium Chloride

Topics

• Arabidopsis (drug effects, genetics, metabolism)
• Brassicaceae (classification, drug effects, genetics, metabolism)
• Chromosomes, Artificial, Bacterial (genetics)
• Computational Biology (methods)
• DNA Transposable Elements
• DNA, Plant (genetics)
• Gene Expression Profiling
• Gene Expression Regulation, Plant
• Genome, Plant (drug effects)
• Molecular Sequence Data
• Salt Tolerance (genetics)
• Salt-Tolerant Plants (drug effects, genetics)
• Sequence Analysis, DNA
• Sequence Inversion
• Sodium Chloride (pharmacology)
• Terminal Repeat Sequences (genetics)