Comparative sequence analysis of the SALT OVERLY SENSITIVE1 orthologous region in Thellungiella halophila and Arabidopsis thaliana

Gyoungju Nah, Christopher L. Pagliarulo, Peter G. Mohr, Meizhong Luo, Nick Sisneros, Yeisoo Yu, Kristi Collura, Jennifer Currie, Jose Luis Goicoechea, Rod A. Wing, Karen S. Schumaker

Research output: Contribution to journalArticle

11 Scopus citations

Abstract

To provide a framework for studies to understand the contribution of SALT OVERLY SENSITIVE1 (SOS1) to salt tolerance in Thellungiella halophila, we sequenced and annotated a 193-kb T. halophila BAC containing a putative SOS1 locus (ThSOS1) and compared the sequence to the orthologous 146-kb region of the genome of its salt-sensitive relative, Arabidopsis thaliana. Overall, the two sequences were colinear, but three major expansion/contraction regions in T. halophila were found to contain five Long Terminal Repeat retrotransposons, MuDR DNA transposons and intergenic sequences that contribute to the 47.8-kb size variation in this region of the genome. Twenty-seven genes were annotated in the T. halophila BAC including the putative ThSOS1 locus. ThSOS1 shares gene structure and sequence with A. thaliana SOS1 including 11 predicted transmembrane domains and a cyclic nucleotide-binding domain; however, different patterns of Simple Sequence Repeats were found within a 540-bp region upstream of SOS1 in the two species.

Original languageEnglish (US)
Pages (from-to)196-203
Number of pages8
JournalGenomics
Volume94
Issue number3
DOIs
StatePublished - Sep 1 2009

Keywords

  • Comparative sequence analysis
  • Microcolinearity
  • SALT OVERLY SENSITIVE1
  • Salt tolerance
  • Simple sequence repeats
  • Thellungiella halophila

ASJC Scopus subject areas

  • Genetics

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