Genome-wide identification of the SPL gene family in Dichanthelium oligosanthes

SQUAMOSA promoter-binding protein-like (SPL) transcription factors play vital roles in various plant physiological processes. Although, the identification of the SPL gene family has been done in C4 grass plants, including rice and maize, the same has not been characterized in the C3 grass species Dichanthelium oligosanthes. In this study, 14 SPL genes were identified in the genome of D. oligosanthes. Gene structure analysis of the identified DoSPLs revealed the similarity and redundancy in their exon/intron organizations. Sequence comparisons within the DoSPLs and along with rice SPLs revealed the putative paralogs and orthologs in D. oligosanthes SPL genes. Phylogenetic analysis clustered the DoSPLs into eight groups along with other plant SPLs. Identification of the conserved SBP motifs in all 14 DoSPLs suggested them to be putative SPLs. In addition, the prediction of sub-cellular localization and associated functions for DoSPLs further supported to be SPL genes. The outcome of this study can serve as a framework for the isolation and functional validation of SPL genes in D. oligosanthes

the promoter of the SQUAMOSA floral meristem identity gene [6]. Since then, many studies have reported the identification and characterization of the SPL genes in the model plant Arabidopsis involved in numerous plant physiological processes, including development of shoot [7], leaves [8], and flowers [9], nutrient balances [10,11], phytohormone signalling [12,13], and plant fertility and reproduction [13,14].
Genome-wide identification of the TF families provides extensive information about their occurrence, structural organization, and functional attributes in a specific plant genome. In recent years, the genome-wide identification of the SPL gene families has been performed in several model and non-model plants, the SPL gene family in the perennial and frost tolerant grass species Dichantheliumo ligosanthes, also known as the Heller's rosette grass or few-flowered panicgrass. D. oligosanthes is a C3 plant from the grass family, and therefore offers a great potential to be a model species being used to be compared with its important C4 relatives, including rice, wheat, and maize. Recently, the draft genome of D. oligosanthes has been sequenced and made available in the NCBI genome database [28]. Thus, the available genome sequence has provided an opportunity to perform the genome-wide analysis of the SPL genes in D. oligosanthes. In the current study, the genomewide analysis of the SPL genes in D. oligosanthes has been carried out. In total, 14 numbers of putative DoSPL TF genes have been identified. Further, their structural organizations depicting exonintron arrangements and the 5'/3' untranslated regions (UTRs), and associated regulatory cis-elements have been determined. Additionally, the conserved motifs present in the identified DoSPLs have been identified by in silico analysis. A bootstrapped phylogenetic tree has been constructed to reveal the ancestral relationship of the identified DoSPLs amongst other plant SPL proteins. In addition, the paralogous and orthologous pairs of SPLs in D. oligosanthes, and in between D. oligosanthes and rice, respectively, have been reported. Moreover, the functional attributes of the identified DoSPLs have been predicted by peptide properties and gene ontology (GO) analysis.

Subcellular localization prediction and gene ontology (GO)
The subcellular localizations of the identified DoSPLs were predicted by using the mGOASVM (Plant V2) server [43]. Further, the subcellular localizations and the localization signature motif sequences were predicted by using the LocSigDB database [44]. The DoSPL protein functions were predicted by DeepGO protein function prediction tool with the protein GO classes [45].

Results & Discussion:
To identify the SPL transcription factor genes in D. oligosanthes, the SBP domain (PF03110) was used to search protein databases by HMMER.   contained a conserved SBP domain (Figure2B). Additionally, the identified conserved SBP domain had a signature zinc finger-like motif (Znf) and a highly conserved nuclear localization signal (NLS), which is partially overlapped with the Znf ( Figure 2B). Thus, possession of the conserved Znf motif and an overlapping NLS, which are the key features of a SPL protein further support the functionality of the identified putative DoSPLs [27,46]. were also associated to some of the other DoSPLs as identified by the DeepGO analysis (Table 2).

Conclusion:
The current study represents the genome-wide analysis of the SPL gene family in the frost tolerant C3 grass species D. oligosanthes. Further, the systematic in silico analysis resulted in the identification of 14 SPL genes in D. oligosanthes. The gene structure analysis suggested the variations in the gene structures of DoSPLs. Phylogenetic analysis indicated that the DoSPLs can be clustered into eight groups along with their orthologs. Structural analysis confirmed the presence of the signature SBP motifs with the Znf and NLS sequences in all 14 DoSPLs. Putative cis-elements identified in this study suggest their potential roles in regulating the expressions of DoSPLs under different stimuli, drought in particular. Prediction of the sub-cellular localization and associated functions further supported them to belong to the SPL transcription factor family. Moreover, this study can act as the framework for the future functional characterizations of the SPL genes in D. oligosanthes.