Comparative genome analysis of the SPL gene family reveals novel evolutionary features in maize

Abstract

SPLs are plant-specific transcription factors that play important regulatory roles in plant growth and development. Systematic analysis of the SPL family has been performed in numerous plants, such as Arabidopsis , rice, and Populus . However, no comparative analysis has been performed across different species to examine evolutionary features. In this study, we present a comparative analysis of SPLs in different species. The results showed that 84 SPLs of the four species can be divided into six groups according to phylogeny. We found that most of the SPL-containing regions in maize showed extensive conservation with duplicated regions of rice and sorghum. A gene duplication analysis in maize indicated that ZmSPLs showed a significant excess of segmental duplication. The Ka/Ks analysis indicated that 9 out of 18 duplicated pairs in maize experienced positive selection, while SPL gene pairs of rice and sorghum mainly evolved under purifying selection, suggesting novel evolutionary features for ZmSPLs . The 31 ZmSPLs were further analyzed by describing their gene structure, phylogenetic relationships, chromosomal location, and expression, Among the ZmSPLs, 13 were predicated to be targeted by miR156s and involved in drought stress response. These results provide the foundation for future functional analyses of ZmSPLs .

Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

“…In this study, we used comparative genomics methods to examine 56 TaSPLs , 13 TuSPLs , 17 AetSPLs , and 17 BdSPLs . The number of SPL genes in T.urartu , A. tauschii and B. distachyon is similar to that in A. thaliana (16) [ 10 ], and rice (19) [ 27 ] but lower than that in maize (31) [ 28 ] and buckwheat (24) [ 29 ]. However, the number of TaSPLs is higher than that of the above species; in particular, there are threefold as many TaSPLs than TuSPLs and AetSPLs .…”

“…The SPL genes encode plant-specific zinc finger proteins play critical roles in regulating plant growth and development. These genes have been identified in many green plants, such as rice [27], A. thaliana [10], maize [28], and buckwheat [29]. Wheat is a major crop, and the complete genome sequencing of Chinese Spring would provide detailed information to study SPL gene families.…”

Genome-wide identification and expression analysis of SBP-box gene family reveal their involvement in hormone response and abiotic stresses in Chrysanthemum nankingense

“…1 ). Compared with crops, cotton (83 GhSBPs ), maize (42 ZmSBPs ), oilseed rape (58 BnaSBP ) and wheat (50 TaSBPs ), C. nankingense contained much less SBP-box genes ( Zhang et al, 2015 ; Cheng et al, 2016 ; Peng et al, 2019 ; Li et al, 2020 ), but resembled the model plant Arabidopsis (17 AtSPLs ), flowering plants petunia (21 PhSPLs ), Prunus persica (17 PpSPLs ), Prunus mume (17 PmSPLs ) and Rosa rugosa (17 RcSPLs ), indicating that the SBP-box family genes endowed with more diversified and complicated functions with species specificity. It could be a consequence of the divergence of flowering responsive functions in SBP-box genes.…”

Genome-Wide Characterization and Expression Analysis of the SBP-Box Gene Family in Sweet Orange (Citrus sinensis)

“…SQUAMOSA promoter-binding-protein (SBP) gene family is exclusively found in plants, and the members of this family all share a highly conserved DNA-binding domain, which is composed of approximately 80 amino acid residues and contains C3H or C2HC zinc-finger structure [4]. Conserved domain structural analysis of SBP revealed that a highly conserved nuclear localization signal partially overlapped with the zinc-finger structure at the C-terminal region [5]. SPB genes are known to be associated with the transcriptional regulation of various physiological processes related to growth and development and can regulate multiple plant adaptational responses to biotic and abiotic stresses [6].…”