Genome-wide analysis of annexin gene family in Schrenkiella parvula and Eutrema salsugineum suggests their roles in salt stress response

Annexins (Anns) play an important role in plant development, growth and responses to various stresses. Although Ann genes have been characterized in some plants, their role in adaptation mechanisms and tolerance to environmental stresses have not been studied in extremophile plants. In this study, Ann genes in Schrenkiella parvula and Eutrema salsugineum were identified using a genome-wide method and phylogenetic relationships, subcellular distribution, gene structures, conserved residues and motifs and also promoter prediction have been studied through bioinformatics analysis. We identified ten and eight encoding putative Ann genes in S. parvula and E. salsugineum genome respectively, which were divided into six subfamilies according to phylogenetic relationships. By observing conservation in gene structures and protein motifs we found that the majority of Ann members in two extremophile plants are similar. Furthermore, promoter analysis revealed a greater number of GATA, Dof, bHLH and NAC transcription factor binding sites, as well as ABRE, ABRE3a, ABRE4, MYB and Myc cis-acting elements in compare to Arabidopsis thaliana. To gain additional insight into the putative roles of candidate Ann genes, the expression of SpAnn1, SpAnn2 and SpAnn6 in S. parvula was studied in response to salt stress, which indicated that their expression level in shoot increased. Similarly, salt stress induced expression of EsAnn1, 5 and 7, in roots and EsAnn1, 2 and 5 in leaves of E. salsugineum. Our comparative analysis implies that both halophytes have different regulatory mechanisms compared to A. thaliana and suggest SpAnn2 gene play important roles in mediating salt stress

List of <i>Ann</i> genes identified in <i>A</i>. <i>thaliana</i>, <i>S</i>. <i>parvula</i> and <i>E</i>. <i>salsugineum</i>.

List of Ann genes identified in A. thaliana, S. parvula and E. salsugineum.</p

RNA-seq data of expression levels of <i>E</i>. <i>salsugineum Anns</i> under salt stress treatments.

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Phylogenetic analysis of SpAnn and EsAnn sequences.

The six groupings are represented by the roman letters.</p

Gene structure of <i>Ann</i> genes in <i>A</i>. <i>thaliana</i>, <i>S</i>. <i>parvula</i> and <i>E</i>. <i>salsugineum</i>.

Gene structure of Ann genes in A. thaliana, S. parvula and E. salsugineum.</p

RNA-seq results comparing expression strengths of homologs between <i>S</i>. <i>parvula</i> (Sp) and <i>A</i>. <i>thaliana</i> (At).

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MSA of Ann deduced amino acid obtained by ClustalW in <i>A</i>. <i>thaliana</i>, <i>S</i>. <i>parvula</i> and <i>E</i>. <i>salsugineum</i>.

Sequence shading: similarity across groups: blue box; similarity in a group: red box and red character; strict identity: red box and white character. Features: GXGT-38-D/E Ca2+-binding sites: purple arrows; conserved tryptophan required for membrane binding: blue circle; His40 key peroxidase residue: green triangle; DXXG putative GTP-binding motif: yellow stars; IRI actin binding motif: blue squares.</p

Expression pattern of <i>E</i>. <i>salsugineum Anns</i> under salt stress treatments.

The gradient bar indicates the expression value of log2FC. Thirty days after germination, E. salsugineum seedlings were treated with 300 mM NaCl and after 24 h, leaves and roots were separately collected.</p

The identified cis-acting elements in <i>Ann</i> gene family promoters in <i>A</i>. <i>thaliana</i>, <i>E</i>. <i>salsugineum</i> and <i>S</i>. <i>parvula</i>.

The identified cis-acting elements in Ann gene family promoters in A. thaliana, E. salsugineum and S. parvula.</p

Ka/Ks ratios of the <i>Ann</i> genes.

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