title: Genomic organization, phylogenetic comparison, and expression profiles of the SPL family genes and their regulation in soybean.
abstract: SQUAMOSA Promoter-Binding Protein-Like (SPL) genes form a major family of plant-specific transcription factors and play an important role in plant growth and development. In this study, we report the identification of 41 SPL genes (GmSPLs) in the soybean genome. Phylogenetic analysis revealed that these genes were divided into five groups (groups 1-5). Further, exon/intron structure and motif composition revealed that the GmSPL genes are conserved within their same group. The N-terminal zinc finger 1 (Zn1) of the SBP domain was a CCCH (Cys3His1) and the C terminus zinc finger 2 (Zn2) was a CCHC (Cys2HisCys) type. The 41 GmSPL genes were distributed unevenly on 17 of the 20 chromosomes, with tandem and segmental duplication events. We found that segmental duplication has made an important contribution to soybean SPL gene family expansion. The Ka/Ks ratios revealed that the duplicated GmSPL genes evolved under the effect of purifying selection. In addition, 17 of the 41 GmSPLs were found as targets of miR156; these might be involved in their posttranscriptional regulation through miR156. Importantly, RLM-RACE analysis confirmed the GmmiR156-mediated cleavage of GmSPL2a transcript in 2-4 mm stage of soybean seed. Alternative splicing events in 9 GmSPLs were detected which produces transcripts and proteins of different lengths that may modulate protein signaling, binding, localization, stability, and other properties. Expression analysis of the soybean SPL genes in various tissues and different developmental stages of seed suggested distinct spatiotemporal patterns. Differences in the expression patterns of miR156-targeted and miR156-non-targeted soybean SPL genes suggest that miR156 plays key functions in soybean development. Our results provide an important foundation for further uncovering the crucial roles of GmSPLs in the development of soybean and other biological processes.
authors.affiliation: Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India. rajeevqualish2007@yahoo.co.in.|Department of Plant Science, McGill University, 21111 Rue Lakeshore, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada. rajeevqualish2007@yahoo.co.in.
authors.forename: Rajiv K
authors.initials: RK
authors.lastname: Tripathi
authors.affiliation: Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, India.
authors.forename: Ridhi
authors.initials: R
authors.lastname: Goel
authors.affiliation: Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India.
authors.forename: Sweta
authors.initials: S
authors.lastname: Kumari
authors.affiliation: Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India.
authors.forename: Anil
authors.initials: A
authors.lastname: Dahuja
mesh_terms: D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D013025:Glycine max / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D014157:Transcription Factors
keywords: G. max; RLM-RACE; SPL genes; miR156