Evolutionary History, Transcriptome Expression Profiles, and Abiotic Stress Responses of the SBP Family Genes in the Three Endangered Medicinal Notopterygium Species

Squamosa promoter binding protein (SBP) plays a vital role in plant growth, development, and responses to abiotic stresses. The genus <i>Notopterygium</i> is an endangered perennial herbaceous plant mainly distributed in the high-altitude Qinghai-Tibet Plateau and adjacent areas, which possibly occurred the adaptive evolution to the extreme environmental conditions. In this study, we firstly determined the genome-wide structural characteristics, evolutionary history, and expression profiles of the <i>SBP</i> family genes in <i>Notopterygium</i> species by using genome, transcriptome, and DNA resequencing data. We have also investigated the response patterns of <i>SBPs</i> of <i>N. franchetii</i> to the drought and high-temperature stresses. The 21, 18, and 18 <i>SBP</i> family genes of three <i>Notopterygium</i> species, <i>N. incisum</i>, <i>N. franchetii</i>, and <i>N. forrestii</i>, were, respectively, identified and classified into eight subfamilies, with four subfamily members regulated by miR156. The structure analysis showed that the members of the same <i>SBP</i> subfamily had similar structures and conserved motif composition. <i>Cis</i>-element analysis suggested that those <i>SBP</i> genes may have been essential to the growth and environmental adaptation of <i>Notopterygium</i>. The expansion of the <i>SBP</i> gene family was mainly caused by the whole genome duplication/segmental duplication and transposable element duplication. Evolutionary analysis showed the <i>SBP</i> gene family experienced severe contraction events and most of the gene copies underwent purification selection. Population genetics analysis based on <i>SBPs</i> variations suggested that the genus <i>Notopterygium</i> species have obvious genetic structure and interspecific differentiation. RNA-seq and qRT-PCR experiments demonstrated that the expressions of <i>SBPs</i> genes in <i>Notopterygium</i> were not species-specific, but tissue-specific. <i>NinSBP08</i> and <i>NinSBP10/12</i> may have played the key roles in heat tolerance and drought resistance, respectively. These results provided novel insights into the evolutionary history of the <i>SBP</i> gene family in the endangered herb <i>Notopterygium</i> species in the high-altitude Qinghai-Tibet Plateau and adjacent areas.