Evolutionary research on the expansin protein family during the plant transition to land provides new insights into the development of Tartary buckwheat fruit

- development of Tartary buckwheat fruit.
- We found that the expansion of the FtEXPA subfamily was caused by duplication events and that the functions of certain duplicated genes may have differentiated.
- Our study provides a blueprint for improving the agronomic traits of Tartary buckwheat and a reference for defining the evolutionary history of the expansin family during plant transitions to land..
- Keywords: Expansin, Terrestrialization, Phylogenetic, Evolutionary research, Tartary buckwheat.
- 1 College of Life Science, Sichuan Agricultural University, Ya ’ an 625014, China Full list of author information is available at the end of the article Sun et al.
- A recent study established a 3D model of the FaEXPA2 protein that was involved in strawberry fruit softening and determined that FaEXPA2 formed a more stable complex with cellulose than other ligands via the different residues present in the open groove surface of its two domains [18].
- The EXPA subfamily was the first subfamily to be identified that contains cell wall-loosening proteins, which can quickly induce relaxation of the cell wall without lytic activity [29].
- Tartary buckwheat (Fagopyrum tataricum) is a versatile pseudo- cereal that is known as the golden crop [36].
- There were fewer members of the algae EXPA subfamily and more members of the EXLB subfamily, which was in sharp contrast to higher plants (Fig.
- Interestingly, up to 32 members of the EXPA subfamily were found in M..
- The number of expansin proteins in each subfamily of Tartary buckwheat is very close to that in A.
- Two pairs of EXPA subfamily genes (FtPinG FtPinG and FtPinG FtPinG from chromosomes 3 and 8 are tandem duplications, which may have contributed to the expansion of the EXPA subfamily to some extent.
- We also investigated the exon-intron organizations of all identified FtEXPs for a deeper understanding of the evolution of this family in Tartary buckwheat (Fig.
- Among 37 FtEXPs, the number of introns ranged from 0 to 3, and most members of the EXPA subfamily con- tained 2 introns.
- Notably, the structure of several mem- bers of the EXPA subfamily is special.
- five introns, while its exon length is significantly different from those of the other genes (Fig.
- Analysis of the motifs was performed through the online MEME software to further study the characteristic regions of the FtEXP proteins (Fig.
- Most members of the EXPA subfamily contain motifs 1 to 8, while most members of the other subfamilies contain motifs and 10 (Fig.
- Overall, most genes from the same subfamily have similar motif composi- tions, and the expansin proteins of the other 11 plants also have conserved domains and general char- acteristics (Fig.
- For a deeper understanding of the evolution of expansin homologous copy genes, we conducted a syntenic analysis of the expansin proteins from four di- cotyledons (F.
- To explore the different selective constraints of the dupli- cated FtEXP pairs, we calculated the Ks values and Ka/.
- The Ka/Ks values of the majority of expansin homologous gene pairs were less than 1, especially for the EXPA sub- family, which indicated that expansin genes are highly conserved in evolution and can be important for plant growth and development (Fig.
- Syntenic expansin gene pairs are widely found among Tartary buckwheat and Arabidopsis (32 homologous gene pairs), C.
- The phylogenetic tree of the expansin protein sequences of Tartary buckwheat and A.
- Differential expression of EXPA subfamily genes in different tissues of Tartary buckwheat.
- Mem- bers of the EXPA subfamily are generally involved in the regulation of plant fruit development, which has been fully confirmed in previous studies [50]..
- 3 Schematic representations of the chromosomal distributions of the Tartary buckwheat expansin genes.
- correlation analysis of the 36 genes expressed in differ- ent tissues that there were positive correlations among the expression profiles of most genes, especially the six fruit-specific genes mentioned earlier, all of which were significantly positively correlated (Fig.
- 4 Phylogenetic relationships, gene structures, and architectures of the conserved protein motifs of the expansin genes from Tartary buckwheat.
- Prediction of the exon-intron structures of Tartary buckwheat expansin genes was performed using the online Gene Structure Display Service 2.0 (http://gsds.gao- lab.org/) and was visualized by TBtools v1.082.
- The number indicates the phases of the corresponding introns.
- b The motif compositions of the Tartary buckwheat expansin proteins.
- In general, there were close correlations among those genes of the EXPA family that were highly expressed in fruit (Fig.
- 5 Schematic representations of the interchromosomal relationships of the expansin genes from different plants.
- a Analysis of the interchromosomal relationships of the expansin genes from Tartary buckwheat was conducted by using multiple collinear scanning toolkits (MCScanX) and was visualized by TBtools v1.082.
- Gray lines in the background indicate collinear blocks within the Tartary buckwheat genome, while red lines highlight syntenic expansin gene pairs.
- b Analysis of the interchromosomal relationships of the expansin genes from A.
- c Analysis of the interchromosomal relationships of the expansin genes from Vitis vinifera was conducted by using multiple collinear scanning toolkits (MCScanX), and was visualized by TBtools v1.082.
- d Analysis of the interchromosomal relationships of the expansin genes from Oryza sativa was conducted by using multiple collinear scanning toolkits (MCScanX), and was visualized by TBtools v1.082.
- The results showed that there were sig- nificant differences in the expression of the other five genes except FtPinG in STB and BTB fruits.
- Among them, the expression of three genes (FtPinG FtPinG and FtPinG in STB fruits was higher than that in BTB fruits, and the expression of the other two genes (FtPinG and FtPinG in BTB fruits was higher than that in STB fruits.
- 6 Synteny analyses between the expansin genes of Tartary buckwheat and five angiosperms.
- The syntenic relationships among the expansin genes of Tartary buckwheat and five angiosperms were visualized by using Dual Synteny Plotter software.
- Gray lines in the background indicate collinear blocks within the Tartary buckwheat genome and other plant genomes, while red lines highlight syntenic expansin gene pairs.
- 7 Tissue-specific gene expression of Tartary buckwheat expansin genes and the correlation between the gene expression patterns of FtEXPs..
- a The expression patterns of Tartary buckwheat expansin genes in flower (FL), leaf (L), root (R), stem (S) and fruit (FR) were examined by qRT-PCR..
- b The correlation of expression patterns of Tartary buckwheat expansin genes in different tissues was visualized by TBTools v1.082.
- 8 Gene expression of Tartary buckwheat expansin genes during fruit development and the correlation between the gene expression patterns of FtEXPs during fruit development.
- a The expression patterns of Tartary buckwheat FtEXPs in the fruit developmental stages were examined using a qRT-PCR assay.
- b The correlation of expression patterns of Tartary buckwheat expansin genes in different fruit developmental stages was visualized by TBTools v1.082.
- 9 Gene expression of six FtEXPA genes in the BTB and STB at 13 DAP and 19 DAP and the expression patterns of five FtEXPA genes from 13 DAP and 19 DAP of the STB with IAA treatment.
- Our first key finding is that the Tartary buckwheat EXPA subfamily expanded after gene duplication, and the evolution direction of the members varied.
- This conclusion is further supported by the finding that most members of the Tartary buckwheat EXPA subfamily undergo tandem and segmental duplication (Fig.
- It has been reported that the expansion and contraction of gene families is a manifestation of the rapid adaptation of organisms to the environment [58]..
- Cell wall loosening is the direct cause of fruit organ enlargement [5], but ex- pansion of the cell wall also leads to an increase in the gaps between cells, which may make plants vulnerable to external pathogens.
- Of the two FtEXPA subfamily genes (FtPinG and FtPinG that were significantly downregulated after exogenous IAA treatment in our study (Fig.
- Collectively, our research not only identified all expansin family members in the 12 representative plants during terrestrial processes, but also from the perspective of evolution, a blueprint was drawn for the selection and cultivation of the important agro- nomic traits of Tartary buckwheat fruit develop- ment.
- Plant genome sequence acquisition and identification of the Expansin gene family.
- Then, the expansin proteins identified above were BLASTp searched in NCBI to analyze whether they were part of the expansin family.
- The sub- cellular localizations of the FtEXP proteins were pre- dicted with CELLO (http://cello.life.nctu.edu.tw/)..
- The phylogenetic tree of the expansin protein sequences in different plants was con- structed with Mega 7.0 by the maximum likelihood method and 1000 bootstrap replications.
- The phylogen- etic tree of Tartary buckwheat and A.
- The syntenic relationships between the expansin genes of Tartary buckwheat and five angiosperms were visualized by using Dual Synteny Plotter software and were visualized using TBtools v1.082.
- The big fruit Tartary buckwheat accessions (BTB, XIQIAO) and small fruit Tartary buckwheat accessions (STB, MIQIAO) were cultivated at the experimental farm of the College of Life Sciences, Sichuan Agricul- tural University, China.
- In previous studies of the regulation of fruit size by FtARF2, STB was sprayed at the budding stage with or 160 mg L − 1 IAA.
- Expression analysis of the FtEXPs.
- BTB: Big fruit Tartary buckwheat.
- STB: Small fruit Tartary buckwheat.
- TBGP: Tartary buckwheat genome project.
- Phylogenetic relationships and motif compositions of the expansin proteins from five different plant species..
- Inner layer: Distribution of the conserved motifs in expansin proteins.
- The conserved motifs of the expansin proteins were determined by the MEME online program (http://meme-suite.org/tools/.
- Protein motif model of the expansin protein family in representative species.
- (A) Motif model of the algal expansin protein family.
- The conserved motifs of the algal expansin proteins were determined by the MEME online program (http://meme- suite.org/tools/meme) and were visualized by TBtools v1.082.
- (B) Motif model of the bryophyta expansin protein family.
- The conserved motifs of the bryophyta expansin proteins were determined by the MEME online program (http://meme-suite.org/tools/meme), and were visualized by TBtools v1.082.
- (C) Motif model of the monocotyledon expansin protein family.
- The conserved motifs of the monocotyledon expansin proteins were determined by the MEME online program (http://meme-suite.org/.
- (D) Motif model of the dicotyledonous expansin protein family.
- Cis-acting element analysis of the expan- sin protein promoters from Tartary buckwheat.
- Table S3 List of the 37 FtEXP genes identified in this study.
- Table S4 List of the Tartary buckwheat 37 FtEXP genes identified in this study..
- Table S5 Analysis and distribution of conserved motifs in Tartary buckwheat expansin proteins.
- Table S7 Synteny expansin gene pairs between Tartary buckwheat and other angiosperms..
- Funds were used for the design of the study and collection, analysis, and interpretation of data and in writing the manuscript, as well as in the open access payment..
- The plant materials are maintained in accordance with the institutional guidelines of the College of Life Sciences, Sichuan Agricultural University, China.
- The role of the primary Cell Wall in plant morphogenesis.
- Study of the structure and binding site features of FaEXPA2, an α -expansin protein involved in strawberry fruit softening.
- Nomenclature for members of the expansin superfamily of genes and proteins.
- Genome-wide identification, characterization and expression analysis of the expansin gene family under drought stress in tea (Camellia sinensis L.
- Genome-wide identification and expression analysis of the expansin gene family in tomato.
- Genome-wide identification of the expansin gene family reveals that expansin genes are involved in fibre cell growth in cotton.
- Chemical composition and health effects of Tartary buckwheat.
- Diverged copies of the seed regulatory Opaque-2 gene by a segmental duplication in the progenitor genome of Rice, sorghum, and maize.
- Characterization and transcriptional expression of the alpha-expansin gene family in rice.
- Expansins abundant in secondary xylem belong to subgroup a of the -Expansin gene family.
- Activation of the Indole-3- acetic acid-Amido Synthetase GH3-8 suppresses Expansin expression and promotes salicylate- and Jasmonate-independent basal immunity in Rice..
- Genome-wide investigation of the Auxin response factor gene family in Tartary buckwheat (Fagopyrum tataricum).
- Genome-wide identification, expression analysis and functional study of the GRAS gene family in Tartary buckwheat (Fagopyrum tataricum)

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