Genome-wide identification and expression analysis of the expansin gene family in tomato

Abstract

Plant expansins are capable of inducing pH-dependent cell wall extension and stress relaxation. They may be useful as targets for crop improvement to enhance fruit development and stress resistance. Tomato is a major agricultural crop and a model plant for studying fruit development. Because only some tomato expansins have been studied, a genome-wide analysis of the tomato expansin family is necessary. In this study, we identified 25 SlEXPAs, eight SlEXPBs, one SlEXLA, four SlEXLBs, and five short homologs in the tomato genome. 25 of these genes were identified as being expressed. Bioinformatic analysis showed that although tomato expansins share similarities with those from other plants, they also exhibit specific features regarding genetic structure and amino acid sequences, which indicates a unique evolutionary process. Segmental and tandem duplication events have played important roles in expanding the tomato expansin family. Additionally, the 3-exon/2-intron structure may form the basic organization of expansin genes. We identified new expansin genes preferentially expressed in fruits (SlEXPA8, SlEXPB8, and SlEXLB1), roots (SlEXPA9, SlEXLB2, and SlEXLB4), and floral organs. Among the analyzed genes those that were inducible by hormone or stress treatments, including SlEXPA3, SlEXPA7, SlEXPB1-B2, SlEXPB8, SlEXLB1-LB2, and SlEXLB4. Our findings may further clarify the biological activities of tomato expansins, especially those related to fruit development and stress resistance, and contribute to the genetic modification of tomato plants to improve crop quality and yield.

Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum)

“…In plants, the expression of expansins are regulated by both internal and external factors, resulting in their involvement in a variety of developmental processes, such as seed germination , fruit growth and/or ripening (Rose et al 1997;Brummell et al 1999;Ishimaru et al 2007), as well as in nutrient uptake and efficiency (Zhou et al 2014), and stress tolerance Zhao et al 2011;Lü et al 2013), which are conjured to be regulated by the corresponding cis-acting elements they contain. Plant hormones can regulate the expression of expansin genes and the regulation of expansin activity by plant hormones is well documented (Zhao et al 2012;Li et al 2014;Lu et al 2016). For example, cytokinin and auxin act synergistically to induce the accumulation and proteolytic processing of Cim1/GmEXPB1, a cytokinin-inducible β-expansin from soybean (Downes et al 2001;Li et al 2014); the Arabidopsis LBD18 up-regulates a subset of expansin genes, including EXPA4, EXPA14 and EXPA17, to enhance cell separation thus promoting lateral root emergence, the effects of which were promoted by exogenous application of auxin (Lee and Kim 2013); the rice OsMPS, whose expression is induced by ABA and cytokinin, but is repressed by auxin, GA and brassinolide (BR), is a direct negative upstream regulator of OsEXPA4/8 and OsEXPB2/3/6, illustrating an indirect regulation of these plant hormones to EXPs (Schmidt et al 2013).…”

“…Two tobacco expansin genes, NtEXPA1 and NtEXPA4, were induced by auxin in young leaves located near the terminal bud, whereas in the lower leaves BR could inhibit NtEXPA1 but up-regulate NtEXPA4 expression (Kuluev et al 2014). The regulation of plant architecture by expansins to adapt to certain external environmental changes, such as drought, heat, low phosphorus (P), is also well studied (Cosgrove 2015;Lu et al 2016). Some examples include the wheat (Triticum aestivum) TaEXPB23, Poa pratens PpEXPA1, soybean GmEXPB2 and rose (Rosa hybrida) RhEXPA4, the transgenic plants with which gained tolerance to drought (Li et al , 2013, tolerance to heat (Xu et al 2014), improved P efficiency Zhou et al 2014) and tolerance to drought and salt (Lü et al 2013;Yan et al 2014), respectively.…”

“…Expansins which are encoded by a multi-gene family have been reported in many plant species and organs, including Arabidopsis and rice (Lee et al 2001), maize (Zhang et al 2014a, b), soybean (Zhu et al 2014), tomato (Lu et al 2016), apple (Zhang et al 2014a, b) to mention but a few. They have also been reported in bacteria and fungi, most of which colonize plant surfaces (Georgelis et al 2015).…”

Expansin gene loss is a common occurrence during adaptation to an aquatic environment

“…Interestingly, SppEXPA10 branches as a sister to poplar and Arabidopsis EXPA‐XII genes with strong support (PP‐1, ML‐86 and NJ‐82). Although EXPA‐XII members have been identified in multiple eudicot species, none have been positively identified for any other angiosperm, leaving doubt as to whether this clade arose before or after the split of monocots and eudicots (Sampedro et al , ; Sampedro et al , ; Dal Santo et al , ; Zhu et al , ; Zhang et al , ; Krishnamurthy et al , ; Lu et al , ). To confidently place SppEXPA10 as a member of EXPA‐XII, we searched for EXPA‐XII genes in other monocots and identified members among both grass and non‐grass species (Figure S3a,b).…”

“…Phylogenetic analysis of monocots and eudicots has further subdivided expansins into 17 orthologous clades, of which at least 16 are shared with the basal angiosperm Amborella trichopoda (Sampedro and Cosgrove, ; Seader et al , ) . Expansin superfamilies tend to be large in angiosperm species, maintained predominantly through whole‐genome duplications, and the retention of such large superfamilies would suggest an advantage for numerous paralogs (Sampedro et al , ; Cosgrove, ; Lu et al , ; Ding et al , ; Seader et al , ). One possible explanation for this observation is that individual expansin genes, or perhaps entire clades, have unique and non‐redundant functions.…”