Comparative Genomic Analysis of SAUR Gene Family, Cloning and Functional Characterization of Two Genes (PbrSAUR13 and PbrSAUR52) in Pyrus bretschneideri

Abstract

The SAUR (small auxin-up RNA) gene family is the biggest family of early auxin response genes in higher plants and has been associated with the control of a variety of biological processes. Although SAUR genes had been identified in several genomes, no systematic analysis of the SAUR gene family has been reported in Chinese white pear. In this study, comparative and systematic genomic analysis has been performed in the SAUR gene family and identified a total of 116 genes from the Chinese white pear. A phylogeny analysis revealed that the SAUR family could be classified into four groups. Further analysis of gene structure (introns/exons) and conserved motifs showed that they are diverse functions and SAUR-specific domains. The most frequent mechanisms are whole-genome duplication (WGD) and dispersed duplication (DSD), both of which may be important in the growth of the SAUR gene family in Chinese white pear. Moreover, cis-acting elements of the PbrSAUR genes were found in promoter regions associated with the auxin-responsive elements that existed in most of the upstream sequences. Remarkably, the qRT-PCR and transcriptomic data indicated that PbrSAUR13 and PbrSAUR52 were significantly expressed in fruit ripening. Subsequently, subcellular localization experiments revealed that PbrSAUR13 and PbrSAUR52 were localized in the nucleus. Moreover, PbrSAUR13 and PbrSAUR52 were screened for functional verification, and Dangshan pear and frandi strawberry were transiently transformed. Finally, the effects of these two genes on stone cells and lignin were analyzed by phloroglucinol staining, Fourier infrared spectroscopy, and qRT-PCR. It was found that PbrSAUR13 promoted the synthesis and accumulation of stone cells and lignin, PbrSAUR52 inhibited the synthesis and accumulation of stone cells and lignin. In conclusion, these results indicate that PbrSAUR13 and PbrSAUR52 are predominantly responsible for lignin inhibit synthesis, which provides a basic mechanism for further study of PbrSAUR gene functions.

Genome-wide identification, characterization, and expression analysis of the small auxin-up RNA gene family during zygotic and somatic embryo maturation of the cacao tree (Theobroma cacao)

“…Previous studies also revealed 52, 60, 62, and 68 SAUR proteins in pineapple, grape, cucumber, and wax gourd [17,23,25,27]. Meanwhile, a total of 98, 105, and 116 putative SAUR proteins was found in apple, poplar and Chinese white pear [16,20,47]. Our comparisons suggested that the SAUR families in higher plant species were large groups, with greatly variable members.…”

“…Interestingly, the chromosomal distributions of the SAUR gene family in the genomes of other higher plant species, such as coffea [19], melon [21], and wax gourd [23] also confirmed our finding. Previously, the SAUR family is being explored in various higher plant species, such as potato [12], tomato [12], watermelon [13], cotton [14], moso bamboo [15], poplar [16], grape [17], apple [18], coffea [19], Chinese white pear [20], melon [21], loquat [22], wax gourd [23], peanut [24], pineapple [25], foxtail millet [26], cucumber [27], and longan [28]. More specifically, 31 and 38 members of the SAUR families have been recorded in coffea and moso bamboo [15,19].…”

“…Ten remaining TcSAUR proteins, including TcSAUR18, TcSAUR26, TcSAUR27, TcSAUR34, TcSAUR38, TcSAUR40, TcSAUR44, TcSAUR49, TcSAUR67, and TcSAUR89, had plus GRAVY scores (Table 1), suggested that they were hydrophobic. Previously, the general features of the SAUR proteins in higher plant species were discussed [20]. For example, the pI scores of the SAUR proteins in Chinese white pear ranged from 5.10 to 10.28, of which 63 (out of 116) SAUR proteins shared pI scores greater than 7.00 [20].…”

“…Previously, the general features of the SAUR proteins in higher plant species were discussed [20]. For example, the pI scores of the SAUR proteins in Chinese white pear ranged from 5.10 to 10.28, of which 63 (out of 116) SAUR proteins shared pI scores greater than 7.00 [20]. The mW values of the SAUR proteins in Chinese white pear have been reported to vary greatly, with the minimum mW and maximum mW of 7.47 and 122.22 kDa, respectively [20].…”

“…To gain an insight into their functions, previous studies have been performed to analyze the SAUR families in many important crop species, including potato (Solanum tuberosum) and tomato (Solanum lycopersicum) [12], watermelon (Citrullus lanatus) [13], cotton (Gossypium spp.) [14], moso bamboo (Phyllostachys edulis) [15], poplar (Populus trichocarpa) [16], grape (Vitis vinifera) [17], apple (Malus domestica) [18], coffea (Coffea canephora) [19], Chinese white pear (Pyrus bretschneideri) [20], melon (Cucumis melo) [21], loquat (Eriobotrya japonica) [22], wax gourd (Benincasa hispida) [23], peanut (Arachis hypogaea) [24], pineapple (Ananas comosus) [25], foxtail millet (Setaria italica) [26], cucumber (Cucumis sativus) [27], and longan (Dimocarpus longan) [28]. However, this important gene family in cacao has not been recorded, even though the assembly of cacao was released [29].…”