Genome‐wide analysis and molecular dissection of the SPL gene family in Salvia miltiorrhiza

Abstract

SQUAMOSA promoter binding protein-likes (SPLs) are plant-specific transcription factors playing vital regulatory roles in plant growth and development. There is no information about SPLs in Salvia miltiorrhiza (Danshen), a significant medicinal plant widely used in Traditional Chinese medicine (TCM) for >1,700 years and an emerging model plant for TCM studies. Through genome-wide identification and subsequent molecular cloning, we identified a total 15 SmSPLs with divergent sequence features, gene structures, and motifs. Comparative analysis showed sequence conservation between SmSPLs and their Arabidopsis counterparts. A phylogenetic tree clusters SmSPLs into six groups. Many of the motifs identified commonly exist in a group/subgroup, implying their functional redundancy. Eight SmSPLs were predicted and experimentally validated to be targets of miR156/157. SmSPLs were differentially expressed in various tissues of S. milltiorrhiza. The expression of miR156/157-targeted SmSPLs was increased with the maturation of S. miltiorrhiza, whereas the expression of miR156/157 was decreased, confirming the regulatory roles of miR156/157 in SmSPLs and suggesting the functions of SmSPLs in S. miltiorrhiza development. The expression of miR156/157 was negatively correlated with miR172 during the maturation of S. miltiorrhiza. The results indicate the significance and complexity of SmSPL-, miR156-, and miR172-mediated regulation of developmental timing in S. miltiorrhiza.

Molecular characterization of the SPL gene family in Populus trichocarpa

“…The results showed that the 44 SPL proteins clustered into 6 groups (named G1–G6), each of which contained at least one AtSPL and one PtSPL (Figure 2). It is consistent with the results from SmSPLs in Salvia miltiorrhiza [41]. To further confirm that there are 6 groups of SPLs, we also constructed a phylogenetic tree for 28 PtSPLs, 16 AtSPLs, 18 rice OsSPLs and 15 SmSPLs.…”

Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza

“…All of them encode SQUAMOSA promoter binding protein-likes. It is consistent with previous results showing the cleavage of miR156 on S. miltiorrhiza SPL transcripts (Zhang et al 2014a). These results suggest that miR156 plays crucial regulatory roles in the development of S. miltiorrhiza and indicate that some mlncRNAs are important regulators in S. miltiorrhiza.…”

“…In this study, two primary transcripts of miR156 were identified from the 5446 S. miltiorrhiza mlncRNA candidates. miR156 regulates S. miltiorrhiza development through direct cleavage of SPL transcripts (Zhang et al 2014a). The results suggest that some mlncRNAs are important regulators in S. miltiorrhiza.…”

“…Members of a gene family can be derived from the same ancestors and exhibit similarity on structures and functions (Wu et al 2012a;Zhang et al 2014a). To obtain the first clue to the function of mlncRNAs, we classified the identified 5,444 S. miltiorrhiza mlnRNAs (two pri-miRNAs excluded) based on the sequence homology.…”

“…S. miltiorrhiza genes involved in secondary metabolism (Ma et al 2012;Li and Lu 2014;Zhang et al 2014a, b), stress response ) and miRNA pathway Lu 2013, 2014) have been intensively studied recently. However, there is no information available for S. miltiorrhiza mlncRNAs.…”