Genome-wide identification, phylogeny, evolutionary expansion and expression analyses of bZIP transcription factor family in tartary buckwheat

Abstract

Background In reported plants, the bZIP family is one of the largest transcription factor families. bZIP genes play roles in the light signal, seed maturation, flower development, cell elongation, seed accumulation protein, abiotic and biological stress and other biological processes. While, no detailed identification and genome-wide analysis of bZIP family genes in Fagopyum talaricum (tartary buckwheat) has previously been published. The recently reported genome sequence of tartary buckwheat provides theoretical basis for us to study and discuss the characteristics and expression of bZIP genes in tartary buckwheat based on the whole genome. Results In this study, 96 FtbZIP genes named from FtbZIP1 to FtbZIP96 were identified and divided into 11 subfamilies according to their genetic relationship with 70 bZIPs of A. thaliana . FtbZIP genes are not evenly distributed on the chromosomes, and we found tandem and segmental duplication events of FtbZIP genes on 8 tartary buckwheat chromosomes. According to the results of gene and motif composition, FtbZIP located in the same group contained analogous intron/exon organizations and motif composition. By qRT-PCR, we quantified the expression of FtbZIP members in stem, root, leaf, fruit, and flower and during fruit development. Exogenous ABA treatment increased the weight of tartary buckwheat fruit and changed the expressions of FtbZIP genes in group A. Conclusions Through our study, we identified 96 FtbZIP genes in tartary buckwheat and synthetically further analyzed the structure composition, evolution analysis and expression pattern of FtbZIP proteins. The expression pattern indicates that FtbZIP is important in the course of plant growth and development of tartary buckwheat. Through comprehensively analyzing fruit weight and FtbZIP genes expression after ABA treatment and endogenous ABA content of tartary buckwheat fruit, ABA may regulate downstream gene expression by regulating the expression of FtPinG0003523300.01 and FtPinG0003196200.01 , thus indirectly affecting the fruit development of tartary buckwheat. This will help us to further study the function of FtbZIP genes in the tartary buckwheat growth and improve the fruit of tartary buckwheat. Electronic supplementary material The online version of this article (10.1186/s12864-019-5882-z) contains supplementary material, which i...

Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.)

“…The contribution of gene duplication events to the amplification of gene families was significantly different among different species. In addition, by comparing the quantity of the tandem repeats, i.e., 4 pairs of olive, 1 pair of soybean [31], 2 pairs of tartary buckwheat [54], 0 pairs of grape, we concluded that the contribution of tandem repeats during the evolution of OebZIP genes was limited, which is consistent with reports on grape, soybean, and tartary buckwheat. Therefore, segment gene duplication plays an important role in bZIP gene family expansion in olive.…”

“…With respect to numbers and aa length, compared to other plants, Arabidopsis (78, 321 aa) [38], rice (89, 311 aa) [29], sesame (63, 339 aa) [30], soybean (160, 343 aa) [31], grape (47, 336 aa) [32], and apple (114, 411 aa) [35], the number of bZIP family members in olive is larger and similar to apple, while the coding sequence length of the genes is clearly different. Several studies [53,54] have found that there is no positive correlation between the numbers of bZIP genes and the genome size. The differences in the number of bZIP members in plants might be due to whole-genome duplication (WGD) events [37].…”

“…The two main reasons for the expansion of plant gene families are tandem repeats and segment repeats. Twenty-two olive, 119 soybean, 8 tartary buckwheat, and 28 grape bZIP genes are involved in gene duplication events (Figure 4), accounting for around 21.4% (olive), 86.2% (soybean) [31], 8.3% (tartary buckwheat) [54], 59.6% (grape) [32]. The contribution of gene duplication events to the amplification of gene families was significantly different among different species.…”

“…Therefore, segment gene duplication plays an important role in bZIP gene family expansion in olive. Soybean had the most bZIP genes that were colinear with olive bZIP genes ( Figure 5) and tartary buckwheat bZIP genes [54], which may be due to the large genome of soybean and the large number of GmbZIP genes.…”

Genome-wide investigation of the heat shock transcription factor (Hsf) gene family in Tartary buckwheat (Fagopyrum tataricum)

“…The cDNA was produced by 1 mg RNA sample with a Prime Script RT Reagent Kit with gDNA Eraser (TaKaRa) with SYBR Premix Ex Taq II (TaKaRa). Expression pattern of FtHsf genes identified in different tissues (stems, roots, leave, fruits and flowers) and fruits at three different stages (13, 19 and 25 DAP) from five strains of Tartary buckwheat were analyzed with qRT-PCR, and each Tartary buckwheat was analyzed three times [35]. The qRT-PCR primers of FtHsf genes listed in Additional file 4: Table S4 were obtained by Primer3 software (Additional file 4).…”