2.1 Whole-genome identification and characteristics of PsSAURs
A total of 57 PsSAURs were identified in P. sibirica genome, which were randomly distributed on eight chromosomes (Fig. 1). Among them, the highest number (24) of PsSAURs was chromosome 8, with several genes forming clusters, and the other seven chromosomes each containing 1–10 PsSAURs. The PsSAURs were named PsSAUR1-PsSAUR57 according to their position on chromosome. The length PsSAURs were ranged from 70 to 236 amino acid (aa), the Mw and PIs ranging from 8.05 (PsSAUR53) to 27.03 (PsSAUR17) kDa and 5.11 (PsSAUR33) to 10.46 (PsSAUR19), respectively (Table 1). A total of forty-nine and 8 PsSAURs were hydrophilic and hydrophobic proteins. Protein instability index analysis showed that 17 PsSAURs were stable with an instability index less than 40. In addition, the protein subcellular localization prediction showed that PsSAURs were primarily located in the cytoplasm, nucleus, and mitochondria.
Table 1
Information related to PsSAURs in P. sibirica
Gene name | Accession | Chromosome location | Strand | Number of amino acids/aa | Molecular weight/kD | Theoretical pI | Instability index | Aliphatic index | Grand average of hydropathicity (GRAVY) | Predicted subcellular localization |
PsSAUR1 | PaF106G0100000780.01 | Chr1: 4851261–4851947 | + | 166 | 18.68785 | 9.9 | 59.13 | 90.42 | -0.005 | PlasmaMembrane/ Mitochondrial |
PsSAUR2 | PaF106G0100002700.01 | Chr1: 20203785–20204276 | + | 163 | 18.46055 | 9.37 | 56.43 | 69.26 | -0.452 | Nuclear |
PsSAUR3 | PaF106G0100004332.01 | Chr1: 29206302–29206619 | + | 105 | 12.08995 | 7.83 | 61.56 | 87.24 | -0.355 | Mitochondrial |
PsSAUR4 | PaF106G0100004336.01 | Chr1: 29228506–29229489 | - | 150 | 17.0335 | 9.79 | 62.65 | 82.53 | -0.28 | Mitochondrial/ Nuclear |
PsSAUR5 | PaF106G0100005296.01 | Chr1: 33845860–33846426 | + | 188 | 21.21526 | 8.74 | 56.44 | 74.15 | -0.414 | Nuclear |
PsSAUR6 | PaF106G0200006771.01 | Chr2 : 110636–111793 | + | 133 | 14.77948 | 5.17 | 44.96 | 57.22 | -0.714 | Nuclear |
PsSAUR7 | PaF106G0200006772.01 | Chr2 : 116535–116960 | + | 141 | 15.90597 | 6.9 | 40.75 | 73.97 | -0.671 | Nuclear |
PsSAUR8 | PaF106G0200008604.01 | Chr2: 15878329–15879323 | + | 172 | 19.42461 | 10.45 | 29.56 | 71.4 | -0.49 | Mitochondrial |
PsSAUR9 | PaF106G0200009291.01 | Chr2 : 19915629–19916397 | + | 124 | 14.43145 | 7.89 | 27.07 | 75.32 | -0.673 | Nuclear |
PsSAUR10 | PaF106G0200009494.01 | Chr2: 21116519–21116899 | + | 126 | 14.75434 | 8.75 | 34.76 | 88.17 | -0.107 | Extracellular |
PsSAUR11 | PaF106G0200010737.01 | Chr2: 27010514–27011408 | + | 132 | 15.73591 | 7.12 | 29.14 | 70.76 | -0.742 | Nuclear |
PsSAUR12 | PaF106G0300014330.01 | Chr3: 1769202–1769762 | + | 186 | 21.06221 | 9.22 | 40.42 | 78.06 | -0.409 | Nuclear |
PsSAUR13 | PaF106G0300014329.01 | Chr3: 1770375–1771793 | - | 177 | 20.16526 | 6.79 | 60.88 | 86.5 | -0.288 | Cytoplasmic/ Mitochondrial/ Nuclear |
PsSAUR14 | PaF106G0300014203.01 | Chr3: 2666558–2667170 | + | 117 | 13.1601 | 6.06 | 37.09 | 96.5 | -0.099 | Mitochondrial/ chloroplast/ Nuclear |
PsSAUR15 | PaF106G0400018086.01 | Chr4: 1700338–1701561 | + | 117 | 12.85694 | 5.7 | 55.59 | 90 | 0.104 | PlasmaMembrane/ chloroplast |
PsSAUR16 | PaF106G0400016888.01 | Chr4 : 8162844–8163143 | + | 99 | 11.12376 | 6.02 | 42.29 | 90.51 | -0.153 | Extracellular/ Mitochondrial/ Nuclear |
PsSAUR17 | PaF106G0400016886.01 | Chr4: 8164068–8166793 | - | 236 | 27.02566 | 7.65 | 40.32 | 75.59 | -0.398 | Nuclear |
PsSAUR18 | PaF106G0400016640.01 | Chr4 : 9687821–9688240 | - | 139 | 15.99332 | 9.38 | 80.52 | 95.25 | -0.408 | Mitochondrial/ Nuclear |
PsSAUR19 | PaF106G0500019384.01 | Chr5 : 7321462–7322312 | + | 166 | 19.46583 | 10.46 | 33.43 | 77.47 | -0.627 | Mitochondrial |
PsSAUR20 | PaF106G0600022654.01 | Chr6: 7496390–7497064 | + | 128 | 14.52475 | 6.9 | 43.44 | 88.28 | -0.501 | Nuclear |
PsSAUR21 | PaF106G0600022655.01 | Chr6 : 7500637–7501071 | + | 144 | 15.97596 | 5.65 | 51.05 | 68.4 | -0.583 | Nuclear |
PsSAUR22 | PaF106G0600022656.01 | Chr6 : 7505887–7506315 | + | 142 | 16.00309 | 6.9 | 41.36 | 73.45 | -0.677 | Nuclear |
PsSAUR23 | PaF106G0600024333.01 | Chr6: 22092133–22092647 | + | 170 | 19.37449 | 8.76 | 54.84 | 85.35 | -0.106 | Extracellular |
PsSAUR24 | PaF106G0700028558.01 | Chr7:7344400–7344855 | - | 151 | 17.02373 | 9.55 | 63.49 | 92.98 | -0.142 | PlasmaMembrane |
PsSAUR25 | PaF106G0700028555.01 | Chr7: 7361195–7361650 | - | 151 | 17.03777 | 9.55 | 69.5 | 90.4 | -0.165 | PlasmaMembrane/ Nuclear |
PsSAUR26 | PaF106G0700028553.01 | Chr7 : 7377830–7378284 | - | 135 | 15.23753 | 7.81 | 73.42 | 87.41 | -0.11 | Extracellular/ PlasmaMembrane |
PsSAUR27 | PaF106G0700028551.01 | Chr7 : 7383579–7383929 | - | 116 | 12.98013 | 5.7 | 51.53 | 99.14 | 0.241 | Extracellular/ PlasmaMembrane |
PsSAUR28 | PaF106G0700028552.01 | Chr7: 7383579–7384040 | - | 153 | 17.24314 | 9.58 | 52.95 | 91.76 | -0.092 | Extracellular/ PlasmaMembrane/ Nuclear |
PsSAUR29 | PaF106G0700028547.01 | Chr7 : 7429270–7429728 | - | 152 | 17.14089 | 9.3 | 59.34 | 92.43 | -0.148 | PlasmaMembrane/ Nuclear |
PsSAUR30 | PaF106G0700027893.01 | Chr7: 12353407–12353796 | - | 129 | 14.30748 | 6.83 | 39.07 | 76.28 | -0.188 | chloroplast |
PsSAUR31 | PaF106G0700027703.01 | Chr7 : 13383893–13384288 | - | 125 | 14.04426 | 8.78 | 53.76 | 87.36 | -0.3 | Nuclear |
PsSAUR32 | PaF106G0700027134.01 | Chr7 : 16479544–16480270 | - | 106 | 12.08287 | 8.6 | 53.09 | 77.26 | -0.446 | Mitochondrial |
PsSAUR33 | PaF106G0700026812.01 | Chr7 : 18024373–18025218 | + | 125 | 14.02486 | 5.11 | 59.04 | 82.56 | -0.371 | Mitochondrial/ Nuclear |
PsSAUR34 | PaF106G0800031625.01 | Chr8 : 11282676–11284223 | + | 158 | 17.77833 | 8.61 | 50.16 | 78.29 | -0.266 | Extracellular/ Nuclear |
PsSAUR35 | PaF106G0800031622.01 | Chr8 : 11300070–11300537 | + | 155 | 17.7714 | 6.88 | 45.6 | 84.26 | 0.059 | PlasmaMembrane |
PsSAUR36 | PaF106G0800031620.01 | Chr8 : 11310028–11310553 | + | 109 | 12.31222 | 6.07 | 36.93 | 89.36 | -0.143 | Extracellular/ Mitochondrial |
PsSAUR37 | PaF106G0800031618.01 | Chr8 : 11335417–11335943 | + | 145 | 16.30579 | 8.47 | 36.42 | 87.38 | -0.254 | Extracellular/ Mitochondrial |
PsSAUR38 | PaF106G0800031616.01 | Chr8 : 11349134–11349529 | + | 97 | 10.62313 | 6.71 | 36.13 | 76.29 | -0.228 | chloroplast/ Nuclear |
PsSAUR39 | PaF106G0800031609.01 | Chr8 : 11404246–11406526 | - | 120 | 13.21033 | 6.71 | 39.09 | 102.33 | 0.235 | PlasmaMembrane |
PsSAUR40 | PaF106G0800031605.01 | Chr8: 11432471–11433969 | + | 158 | 17.76854 | 9.2 | 31.21 | 83.86 | -0.046 | PlasmaMembrane |
PsSAUR41 | PaF106G0800031604.01 | Chr8 : 11436254–11436994 | + | 91 | 10.21372 | 6.55 | 39.31 | 85.71 | -0.202 | Mitochondrial |
PsSAUR42 | PaF106G0800031608.01 | Chr8: 11404246–11438414 | - | 186 | 20.61977 | 6.42 | 31.52 | 90.65 | -0.068 | Cytoplasmic |
PsSAUR43 | PaF106G0800031599.01 | Chr8 : 11491197–11498191 | - | 186 | 20.49061 | 6.9 | 32.59 | 88.55 | -0.062 | Cytoplasmic/ Mitochondrial |
PsSAUR44 | PaF106G0800031596.01 | Chr8 : 11506866–11507486 | - | 156 | 17.59013 | 5.94 | 49.6 | 90.58 | -0.315 | Mitochondrial/ Nuclear |
PsSAUR45 | PaF106G0800031595.01 | Chr8 : 11508605–11508910 | + | 101 | 11.33027 | 8.71 | 40.39 | 94.65 | 0.051 | PlasmaMembrane/ Mitochondrial/ chloroplast |
PsSAUR46 | PaF106G0800031594.01 | Chr8 : 11513969–11514385 | + | 101 | 11.25811 | 8.93 | 65.03 | 90.79 | -0.023 | Mitochondrial/ chloroplast |
PsSAUR47 | PaF106G0800031591.01 | Chr8 : 11521494–11522770 | + | 101 | 11.31822 | 9.36 | 64.39 | 88.91 | -0.027 | Mitochondrial/ chloroplast |
PsSAUR48 | PaF106G0800031590.01 | Chr8: 11524532–11524816 | + | 94 | 10.64937 | 8.85 | 53.16 | 99.47 | 0.055 | Mitochondrial/ chloroplast |
PsSAUR49 | PaF106G0800031588.01 | Chr8 : 11542778–11543299 | + | 171 | 19.52165 | 9.64 | 58.7 | 77.49 | -0.587 | Nuclear |
PsSAUR50 | PaF106G0800031587.01 | Chr8 : 11565588–11566287 | - | 150 | 16.86448 | 9.21 | 66.27 | 93.6 | -0.157 | Nuclear |
PsSAUR51 | PaF106G0800030701.01 | Chr8 : 16931768–16932043 | - | 91 | 10.14858 | 8.66 | 58.21 | 76.15 | -0.297 | Mitochondrial/ Nuclear |
PsSAUR52 | PaF106G0800030700.01 | Chr8: 16933274–16933676 | + | 94 | 10.49326 | 8.54 | 64.09 | 88.09 | 0.121 | PlasmaMembrane/ Mitochondrial |
PsSAUR53 | PaF106G0800030699.01 | Chr8: 16934478–16934909 | - | 70 | 8.05333 | 7.99 | 50.22 | 83.57 | -0.056 | Extracellular/ Mitochondrial |
PsSAUR54 | PaF106G0800030698.01 | Chr8 : 16936378–16936848 | + | 94 | 10.59748 | 8.52 | 61.73 | 89.15 | 0.122 | Extracellular/ Mitochondrial |
PsSAUR55 | PaF106G0800030697.01 | Chr8 : 16938188–16938499 | + | 103 | 11.42508 | 7.79 | 16.37 | 81.46 | -0.237 | Mitochondrial |
PsSAUR56 | PaF106G0800030696.01 | Chr8 : 16940616–16940909 | + | 97 | 11.22181 | 7.06 | 38.9 | 75.36 | -0.497 | Cytoplasmic/ Mitochondrial/ Nuclear |
PsSAUR57 | PaF106G0800030695.01 | Chr8: 16942827–16943126 | + | 99 | 11.17022 | 9.87 | 45.24 | 83.54 | -0.242 | Mitochondrial |
2.2 Phylogenetic of the PsSAURs
To study the phylogenetic relationships among PsSAURs, 78 AtSAUR protein sequences in Arabidopsis and 57 PsSAUR protein sequences in P. sibirica were used to construct a phylogenetic tree (Fig. 2). The PsSAURs were divided into five groups (Groups A-E). Among them, Group E had the largest number of PsSAURs, which contained 24 PsSAUR members, followed by Group A, which contained 14 PsSAUR members, Group B, Group C, and Group D consisted 9, 7, and 3 PsSAUR members, respectively. Most of PsSAURs with similar locations were distributed in the same group as follows: PsSAUR24, PsSAUR25, PsSAUR26, PsSAUR27, PsSAUR28, and PsSAUR29 from Group A were located on chromosome 7; PsSAUR6, PsSAUR7, PsSAUR8, PsSAUR9, and PsSAUR11 from Group B were located on chromosome 2; PsSAUR34, PsSAUR35, PsSAUR36, PsSAUR37, PsSAUR38, PsSAUR39, PsSAUR40, PsSAUR41, PsSAUR42, PsSAUR43, PsSAUR44, PsSAUR45, PsSAUR46, PsSAUR47, PsSAUR48, PsSAUR51, PsSAUR52, PsSAUR53, PsSAUR54, PsSAUR55, and PsSAUR56 from Group E were located on chromosome 8.
2.3 Gene structure and conserved motifs in PsSAURs
The exon-intron structure of PsSAURs and their conserved motifs were analyzed to understand their sequence characteristics (Fig. 3). Totally, 73.68% (42/57) of PsSAURs are none intron, ten PsSAURs contained one intron, only four PsSAURs including PsSAUR13, PsSAUR15, PsSAUR17, and PsSAUR23, contained two introns, and PsSAUR49 contained three introns. MEME was used to analyze the conserved motifs of 57 PsSAUR proteins. A total of five conserved motifs were obtained (Fig. 3), including Motif1 (RFVVPISYLNHPLFQDLLSQAEEEFGFDHPMG), motif2 (SSKSLDVPKGHFAVYVGESQK), motif3 (JTIPCSEETFE), motif4 (MGFRLPGIVHAKKNL), and motif5 (MNKIRSIVRLKQILKKWQKSA), at lengths of 32, 21, 11, 15, and 21 aa, respectively. 16 PsSAURs contained motif1, motif2, motif3, and motif4, 14 PsSAURs contained motif1, motif2, motif3, and motif5, and 19 contained motif1, motif2, and motif3. However, two PsSAURs (PsSAUR36, PsSAUR37) contained motif1, motif2 and motif4, two PsSAURs (PsSAUR28, PsSAUR29) contained motif1, motif3, and motif5, and PsSAUR33 contained motif2, motif3, and motif5. Gerenally, some PsSAURs in the same group had similar conserved structures. For example, PsSAURs in Group D contained motif1, motif2, motif3, and motif5, and most PsSAURs in Group E contained motif1, motif2, motif3, and motif4.
2.4 Gene duplication in PsSAURs
The gene duplication of PsSAURs was analyzed, and even segmental duplications and ten tandem duplications of PsSAURs were obtained (Table 2). These include 21 PsSAURs located on chromosomes 1, 3, 4, 6, 7, and 8, respectively. Taken together with the phylogenetic relationship of PsSAURs, the result showed that most of the gene pairs for segmental duplication (6/7) and tandem duplication (9/10) were located in the same group, including the segmental duplication PsSAUR3/PsSAUR46 and the tandem duplication PsSAUR12/PsSAUR13.
Table 2
PsSAUR gene duplication of in P. siberia
Type | Chromosome | Gene ID |
Segmental duplication | Chr1&Chr7 | PsSAUR3/PsSAUR32 |
Chr1&Chr8 | PsSAUR3/PsSAUR46 |
Chr1&Chr8 | PsSAUR4/PsSAUR50 |
Chr2&Chr6 | PsSAUR6/PsSAUR20 |
Chr2&Chr2 | PsSAUR9/PsSAUR11 |
Chr2&Chr6 | PsSAUR10/PsSAUR23 |
Chr3&Chr7 | PsSAUR14/PsSAUR33 |
Tandem duplication | Chr1 | PsSAUR6/PsSAUR7 |
Chr3 | PsSAUR12/PsSAUR13 |
Chr4 | PsSAUR16/PsSAUR17 |
Chr6 | PsSAUR20/PsSAUR21/PsSAUR22 |
Chr7 | PsSAUR27/PsSAUR28 |
Chr8 | PsSAUR39/PsSAUR42 |
Chr8 | PsSAUR40/PsSAUR41 |
Chr8 | PsSAUR45/PsSAUR46 |
Chr8 | PsSAUR47/PsSAUR48 |
Chr8 | PsSAUR55/PsSAUR56 |
2.5 Promoter analysis of PsSAURs
The cis-acting elements of promoter regions (1,000 bp from the start codon) were analyzed (Fig. 4). The results revealed that the promoters of the 11 PsSAURs contain the auxin signaling transduction related cis-elements, including PsSAUR6, PsSAUR15, PsSAUR30, PsSAUR36, PsSAUR37, PsSAUR38, PsSAUR39, PsSAUR44, PsSAUR45, PsSAUR48, and PsSAUR49. and 11 PsSAURs, including PsSAUR9, PsSAUR11, PsSAUR17, PsSAUR29, PsSAUR33,PsSAUR34,PsSAUR57, and PsSAUR55, contain cis-acting element involved in defense and stress responsiveness. Cis-responsive elements were also involved in hormonal response, and primarily included 84 methyl jasmonate (MeJA), 25 zein, 65 abscisic acid (ABA), 17 salicylic acid (SA), and 8 gibberellin (GA) responsive elements. In addition, PsSAUR promoters also contained 11 low-temperature responsiveness elements, six endosperm expression cis-responsive elements, and two wound-responsive elements.
2.6 Expression patterns of PsSAURs in different floral organs
The expression patterns of PsSAURs in pistil, stamen, petal, and sepal were analyzed (Fig. 5). A total of 34 PsSAURs had an average expression level of FPKM > 1, which were used in subsequent analyses. PsSAUR4, PsSAUR8, PsSAUR19, and PsSAUR22 were highly expressed in pistil, PsSAUR13 was highly expressed in stamen, PsSAUR30, PsSAUR32, PsSAUR33, PsSAUR38, PsSAUR41, PsSAUR42, PsSAUR43, PsSAUR44, PsSAUR45, PsSAUR46, PsSAUR48, PsSAUR51, and PsSAUR52 were highly expressed in petal, PsSAUR9 and PsSAUR11 were highly expressed in sepal.
2.7 Expression patterns of PsSAURs in kernals at different developmental stages
To analyze the function of PsSAURs in kernel development, the expression patterns of PsSAURs in kernel during six different developmental stages (S1-S6) were analyzed (Fig. 6). The results showed that the average expression level of 17 PsSAURs revealed an FPKM of > 1, and the expression patterns of PsSAURs in kernel were differences during different developmental stages, such as PsSAUR49 was downregulation during the development. PsSAUR9 and PsSAUR11, PsSAUR5 and PsSAUR14, and PsSAUR42 and PsSAUR43 were high expressed at S1, S2, and S3 respectively, which were the rapidly growth stage, whereas the expression of PsSAUR8 was higher at the S5 and S6, which were the mature stage.