Complex Interplay of Tandem, Segmental, Whole Genome Duplication, and Re-organization Drives Expansion of SAUR Gene Family in Brassicaceae

Abstract

Members of the SAUR, small auxin upregulated RNA, gene family initially identified as auxin inducible, mediate diverse developmental and adaptive processes in plants. Inspite of their importance, identification and analysis of homologs from Brassica juncea, a major oilseed crop, is lacking. Additionally, investigations into organisational complexity and evolutionary past across Brassicaceae remain to be investigated. The present study was therefore designed to identify members of the SAUR gene family in B. juncea, reconstruct phylogenetic relationship, and analyse the history of expansion of the SAUR gene family across Brassicaceae. Genome-wide in-silico analysis allowed us to identify 237 SAUR genes in the allotetraploid B. juncea (AABB genome), which are distributed in a clustered manner among all 18 chromosomes of the B. juncea genome. Comparative analysis with the diploid parents- B. rapa (AA) and B. nigra (BB) revealed conserved organisation pattern. A striking feature of SAUR genes is intronless nature of most members. Comparative analysis revealed ten clusters of tandemly arrayed genes (TAGs) in Arabidopsis thaliana; two of these clusters were lost, and 33 clusters that are orthologous to the rest of A. thaliana clusters were identified from B. juncea genome. Organisational complexity revealed the presence of putative bidirectional promoters between some SAUR genes. Phylogenetic reconstruction shows several SAUR genes of A. thaliana and B. juncea forming separate clades, indicating lineage-specific expansion. Inclusion of homologs from across Brassicaceae allowed us to perform comparative synteny analysis and hypothesize local duplications being responsible for the tandem organisation, and segmental duplications as driving mechanism for large-scale expansion. The present study allowed us to catalog homologs of the SAUR gene family in B. juncea. This study thus forms the foundation for functional characterization involving transcriptional regulation, generation, and analysis of reverse genetic models toward understanding their role in plant growth and development.

Keywords: Brassica; Brassicaceae; Local tandem duplication; SAUR; Synteny; Tandemly arrayed genes (TAG).