Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family in rice ( Oryza sativa)

• Published in: Genomics (San Diego, Calif.) Calif.), 2006-09, Vol.88 (3), p.360-371
• Main Authors: Jain, Mukesh, Tyagi, Akhilesh K., Khurana, Jitendra P.
• Format: Article
• Language: English
• Subjects: Arabidopsis; Auxin; auxin-responsive elements; auxins; Base Sequence; Biological and medical sciences; complementary DNA; Evolution; Evolution, Molecular; Expressed Sequence Tags; Expression; Fundamental and applied biological sciences. Psychology; Gene Duplication; gene expression; gene expression regulation; Gene Expression Regulation, Plant - physiology; genes; Genes. Genome; Genetics of eukaryotes. Biological and molecular evolution; Genome, Plant - genetics; Indoleacetic Acids; messenger RNA; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; multigene family; nucleotide sequences; Oryza - genetics; Oryza sativa; Oryza sativa japonica; Phylogeny; plant proteins; Plant Proteins - genetics; pseudogenes; Real-time PCR; regulatory sequences; rice; Rice ( Oryza sativa); SAUR; small auxin-up RNAs
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2006.04.008

Small auxin-up RNAs ( SAURs) are the early auxin-responsive genes represented by a large multigene family in plants. Here, we report the identification of 58 OsSAUR gene family members from rice ( Oryza sativa japonica cv Nipponbare), the model monocot plant, by a reiterative database search and manual reannotation; 2 of these are pseudogenes. The coding sequences of OsSAURs do not possess any intron. Most of the predicted OsSAUR protein sequences harbor a putative nuclear localization signal at their N-terminus. Localized gene duplications appear to be the primary genetic event responsible for SAUR gene family expansion in rice. Interestingly, the duplication of OsSAURs was found to be associated with the chromosomal block duplication as well. The phylogenetic analysis revealed that the SAUR gene family expanded in rice and Arabidopsis due to species-specific expansion of the family in monocots and dicots. The auxin-responsive elements and downstream element are conserved in the upstream and downstream sequences, respectively, of OsSAURs. In addition to the 21 OsSAURs with full-length cDNA sequences and 20 with expressed sequence tags, gene expression analyses of at least 7 OsSAURs by RT-qPCR indicated that the majority of identified OsSAURs most likely are expressed in rice. The transcript abundance of the OsSAURs examined increased within a few minutes of exogenous auxin application with varying kinetics. The present study provides basic genomic information for the rice SAUR gene family and will pave the way for deciphering the precise role of SAURs in plant growth and development.