Identification, evolution and expression analyses of the whole genome-wide PEBP gene family in Brassica napus L

Abstract

Background: With the release of genomic data for B.rapa, B.oleracea, and B.napus, research on the genetic and molecular functions of Brassica spp. has entered a new stage. PEBP genes in plants play an important role in the transition to flowering as well as seed development and germination. Molecular evolutionary and functional analyses of the PEBP gene family in B.napus based on molecular biology methods can provide a theoretical basis for subsequent investigations of related regulators.

Results: In this paper, we identified a total of 29 PEBP genes from B.napus that were located on 14 chromosomes and 3 random locations. Most members contained 4 exons and 3 introns; motif 1 and motif 2 were the characteristic motifs of PEBP members. On the basis of intraspecific and interspecific collinearity analyses, it is speculated that fragment replication and genomic replication are the main drivers of for the amplification and evolution of the PEBP gene in the B.napus genome. The results of promoter cis-elements prediction suggest that BnPEBP family genes are inducible promoters, which may directly or indirectly participate in multiple regulatory pathways of plant growth cycle. Furthermore, the tissue-specific expression results show that the expression levels of BnPEBP family genes in different tissues were quite different, but the gene expression organization and patterns of the same subgroup were basically the same. qRT‒PCR revealed certain spatiotemporal patterns in the expression of the PEBP subgroups in roots, stems, leaves, buds, and siliques, was tissue-specific, and related to function.

Conclusions: A systematic comparative analysis of the B.napus PEBP gene family was carried out at here. The results of gene identification, phylogenetic tree construction, structural analysis, gene duplication analysis, prediction of promoter cis-elements and interacting proteins, and expression analysis provide a reference for exploring the molecular mechanisms of BnPEBP family genes in future research.

Keywords: B.napus; Evolutionary analysis; Expression analysis; Gene duplication; PEBP.

Fig. 1

Phylogeny of the PEBP family in B.napus , B.rapa, B.oleracea, and A.thaliana. Note: The proteins are clustered into six subgroups. Yellow, light blue, orchid, light green, orange and pink sections indicate the subgroups of PEBP proteins. BnaPEBPs are marked with green dots, BraPEBPs are marked with purple dots, BolPEBPs are marked with blue stars, AtPEBPs are marked with red triangles, and 9 BnPEBPs core genes are marked with red stars

Fig. 2

Construction of a phylogenetic tree of 29 PEBP genes in B.napus with TBtools. Note: The visual display of the BnPEBP evolutionary tree, gene motifs (a), domains (b) and structure (c)

Fig. 3

Distribution of PEBP family genes on the chromosomes of B.napus

Fig. 4

Duplication of BnPEBP genes on the chromosomes of B.napus L.

Fig. 5

Synteny analysis of PEBP genes between B.napus and its progenitors. Note: The grey lines in the background indicate the collinear blocks within B.napus and its progenitor species. The purple-red lines highlight the syntenic PEBP gene pairs. (a) indicates the genome collinearity of B.napus (AACC) and B.rapa (AA), and (b) indicates the genome collinearity of B.napus (AACC) and B.oleracea (CC). (c) indicates B.napus (AACC) and A. thaliana genome collinearity. To show the completeness of the results, genes located in random regions are not shown in the figure

Fig. 6

Analysis of cis-acting elements in the BnPEBP gene promoter. Notes: The image does not contain any unannotated cis-acting elements

Fig. 7

Predicted BnPEBP gene family protein interaction network

Fig. 8

Tissue-specific expression analysis of PEBP gene members in B.napus

Fig. 9

Expression levels of 5 subgroups of PEBP genes in roots, stems, leaves, buds, siliques of B.napus by qRT-PCR