Abstract
The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear (Pyrus bretschneideri), mei (Prunus mume), peach (Prunus persica) and strawberry (Fragaria vesca), respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny) analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.
Highlights
Rosaceae species such as pear (Pyrus bretschneideri), mei (Prunus mume), peach (Prunus persica) and strawberry (Fragaria vesca) are important perennial trees cultivated for the commercial production of fruits available worldwide
In total 24 of EIN3/EIL genes were identified, including ten in pear, four in peach, five in mei and five in strawberry, and named as PbEIL1-PbEIL10, PpEIL1-PpEIL4, PmEIL1-PmEIL5 and FvEIL1-FvEIL5, according to their locations in chromosome, respectively (Table 1 and Fig. 1). This result suggested that EIN3/EIL gene family was relatively small compared to other gene families in the studied species
Similar indication was reported by the previous studies in which six, five, four, six and 17 EIN3/EIL genes were found in Arabidopsis thaliana (Chao et al, 1997; Guo & Ecker, 2004), tobacco (Kosugi & Ohashi, 2000; Rieu, Mariani & Weterings, 2003), tomato (Tieman et al, 2001; Yokotani et al, 2003), rice (Hiraga et al, 2009; Mao et al, 2006) and banana (Jourda et al, 2014), respectively
Summary
Rosaceae species such as pear (Pyrus bretschneideri), mei (Prunus mume), peach (Prunus persica) and strawberry (Fragaria vesca) are important perennial trees cultivated for the commercial production of fruits available worldwide. The genomes of strawberry (X = 7), mei (X = 8), peach (X = 8), and pear (X = 17) shared an ancestor, which had nine pairs of chromosomes (Shulaev et al, 2011; Verde et al, 2013; Wu et al, 2012; Zhang et al, 2012). Some extant ‘‘diploid’’ species of Rosaceae family are originated from their polyploid ancestors, others are thought to be true polyploids (Wendel, 2000). These studies indicate that the diploid species in Rosaceae have evolved with a complex history. The EIL/EIN3 gene family was selected to investigate the specific evolutionary relationships among the related species of family Rosaceae
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