Abstract
BackgroundPolyploidization is a common event in the evolutionary history of angiosperms, and there will be some changes in the genomes of plants other than a simple genomic doubling after polyploidization. Allotetraploid Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are a good group for studying the problems associated with polyploidization. On the other hand, the EIN3/EIL gene family is an important gene family in plants, all members of which are key genes in the ethylene signaling pathway. Until now, the EIN3/EIL gene family in B. napus and its diploid progenitors have been largely unknown, so it is necessary to comprehensively identify and analyze this gene family.ResultsIn this study, 13, 7 and 7 EIN3/EIL genes were identified in B. napus (2n = 4x = 38, AnCn), B. rapa (2n = 2x = 20, Ar) and B. oleracea (2n = 2x = 18, Co). All of the identified EIN3/EIL proteins were divided into 3 clades and further divided into 8 sub-clades. Ka/Ks analysis showed that all identified EIN3/EIL genes underwent purifying selection after the duplication events. Moreover, gene structure analysis showed that some EIN3/EIL genes in B. napus acquired introns during polyploidization, and homolog expression bias analysis showed that B. napus was biased towards its diploid progenitor B. rapa. The promoters of the EIN3/EIL genes in B. napus contained more cis-acting elements, which were mainly involved in endosperm gene expression and light responsiveness, than its diploid progenitors. Thus, B. napus might have potential advantages in some biological aspects.ConclusionsThe results indicated allotetraploid B. napus might have potential advantages in some biological aspects. Moreover, our results can increase the understanding of the evolution of the EIN3/EIL gene family in B. napus, and provided more reference for future research about polyploidization.
Highlights
Polyploidization is a common event in the evolutionary history of angiosperms, and there will be some changes in the genomes of plants other than a simple genomic doubling after polyploidization
Our results can increase the understanding of the evolution of the ethylene-insensitive 3 (EIN3)/ethylene-insensitive 3-like (EIL) gene family in B. napus, and provided more reference for future research about polyploidization
Homolog expression of EIN3/EIL genes in B. napus is biased towards its diploid progenitor B. rapa B. napus, a young allotetraploid, formed only ~ 7500 years ago by the natural hybridization and polyploidization of B. rapa and B. oleracea [22]
Summary
Polyploidization is a common event in the evolutionary history of angiosperms, and there will be some changes in the genomes of plants other than a simple genomic doubling after polyploidization. The EIN3/EIL gene family is an important gene family in plants, all members of which are key genes in the ethylene signaling pathway. The EIN3/EIL gene family in B. napus and its diploid progenitors have been largely unknown, so it is necessary to comprehensively identify and analyze this gene family. The ethylene-insensitive 3 (EIN3)/ethylene-insensitive 3-like (EIL) gene family is a small transcription factor gene family in higher plants [8, 9]. The EIN3/EIL genes participate in ethylene signal transduction by activating downstream ethylene response genes [10, 11]. Ethylene can act as a signal molecule to regulate the expression of some genes [13]. The EIN3/EIL gene family plays an important role in plants
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