TY - JOUR
T1 - Comparative sequence analysis of the SALT OVERLY SENSITIVE1 orthologous region in Thellungiella halophila and Arabidopsis thaliana
AU - Nah, Gyoungju
AU - Pagliarulo, Christopher L.
AU - Mohr, Peter G.
AU - Luo, Meizhong
AU - Sisneros, Nick
AU - Yu, Yeisoo
AU - Collura, Kristi
AU - Currie, Jennifer
AU - Goicoechea, Jose Luis
AU - Wing, Rod A.
AU - Schumaker, Karen S.
N1 - Funding Information:
This research was supported by grants from the Bud Antle Endowed Chair to R.A.W. and the United States Department of Agriculture CSREES/Southwest Consortium on Plant Genetics and Water Resources (06N08/07R08) and the Department of Energy (DE-FG02-04ER15616) to K.S.S.
PY - 2009/9
Y1 - 2009/9
N2 - 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.
AB - 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.
KW - Comparative sequence analysis
KW - Microcolinearity
KW - SALT OVERLY SENSITIVE1
KW - Salt tolerance
KW - Simple sequence repeats
KW - Thellungiella halophila
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U2 - 10.1016/j.ygeno.2009.05.007
DO - 10.1016/j.ygeno.2009.05.007
M3 - Article
C2 - 19481598
AN - SCOPUS:68549092442
SN - 0888-7543
VL - 94
SP - 196
EP - 203
JO - Genomics
JF - Genomics
IS - 3
ER -