- Identification and expression analysis of GRAS transcription factors in the wild relative of sweet potato Ipomoea trifida. - Sweet potato is an important food, vegetable, industrial raw material, and biofuel crop in the world, which plays an essential role in food security in China . - However, the function of sweet potato GRAS genes remains unknown.. - Gene structure showed that most of the GRAS genes in I. - Conclusions: Our findings will further facilitate the functional study of GRAS gene and molecular breeding of sweet potato.. - The subfamily identifica- tion of GRAS genes has a slight difference among diverse species.. - In the recent 10 years, with increasing species having complete genome sequence, the genome-wide analyses of GRAS gene family were carried out in more than 30 species belonging to more than 20 genera, such as in A.. - Sweet potato [Ipomoea batatas (L.) Lam.] is an im- portant food crop, which ranks seventh in the world [20]. - Therefore, we performed the genome-wide identifica- tion of GRAS transcription factors in I. - We firstly investigated the phylogeny, chromosomal locations and exon/intron structure of GRAS transcription factors in I.. - Our work will provide evi- dence for further study of GRAS gene function and sweet potato breeding.. - Identification of GRAS genes in I. - Chromosomal location and exon – intron structures analysis of GRAS members in I. - We mapped the genetic linkage map of GRAS genes in the whole I. - Phylogenetic analysis of GRAS proteins. - The phylogenetic analysis of the aligned sequences was then carried out by using the Maximum-Likelihood method. - Analysis of Cis -acting elements in ItfGRAS promoters To determine cis-acting elements in the promoter regions of ItfGRASs, we first extracted the promoter sequences (2 kb) for every ItfGRAS gene from I. - Expression analysis of GRAS members. - We downloaded the original RNA sequencing data from the GT4SP Project Download page to investigate the ex- pression profiles of GRAS genes under abiotic stresses (drought, salt, heat and cold) and among various tissues (root, stem, leaf, flower and flower bud). - 1 Chromosomal locations of GRAS genes in I. - Identification and characterization analysis of GRAS genes in I. - To identify the number of GRAS members in I. - 2 Phylogenetic analysis of GRAS proteins in Arabidopsis , Oryza sativa L and I. - Chromosomal distributions of ItfGRAS genes. - The identified GRAS genes were mapped to 15 I. - 3 Gene structure of GRAS members in I. - while the number of genes located in the remaining chromosomes ranged from 3 to 7.. - Evolutionary relationships of GRAS genes among three species. - Figure 2 showed us that the ItfGRAS proteins were classified into 11 subfamilies, namely, HAM, DELLA, SCL3, DLT, SCR, LAS, SCL4/7, SHR, PAT1, Os19 and LISCL according to the previous classification of GRAS families. - The GRAS genes were very unevenly dis- tributed in different subfamilies. - Notably, only one GRAS gene in the DLT sub- family was found in those three species. - The number of Itf- GRAS genes was approximately 10 in the HAM, SHR and PAT1 subfamilies, whereas four and six were found in the SCL3 and DELLA subfamilies, respectively.. - To evaluate the likely diversity of GRAS transcription factors, we conducted an exon/intron analysis based on the sequence alignment between coding sequences and genomic sequences for each I. - trifida GRAS genes had 1–2 introns. - Furthermore, the majority of GRAS genes in the same clade generally presented similar gene structures.. - Nevertheless, some GRAS transcription factors had excep- tions in the same clade but with different gene structure, such as ItfGRAS46 and ItfGRAS57 in the clade SHR, and ItfGRAS7 and ItfGRAS53 in the clade SCL4/7.. - Figure 4 showed all pre- dicted different cis-elements in the promoter regions of ItfGRAS. - Expression profile of ItfGRAS among various tissues Increasing evidence of the key role of GRAS genes in plant development are available. - To investigate the biological functions of GRAS genes during different developmental stages, we analysed the transcript levels of GRAS genes in different tissues from the root, stem, leaf, flower and flower bud by using public data. - For instance, Itf- GRAS7 and ItfGRAS43 had a low expression in flower rela- tive to those detected in the other tissues. - Four GRAS genes (ItfGRAS12, ItfGRAS45 and ItfGRAS59) were expressed at higher levels in the leaf and stem than in the other tissues, except that ItfGRAS12 had no change in the flower. - In addition and GRAS genes were rela- tively highly expressed in the root and stem, respectively.. - The values of these GRAS genes are listed in Additional file 5: Table S4. - The expression levels for GRAS genes vary widely among different tissues. - ItfGRAS1 and ItfGRAS31 were weakly expressed in the flower but were highly expressed in other tissues. - ItfGRAS69 showed relatively higher expression levels in root and mature leaf than in the other tissues. - Finally, the expression levels of the selected four genes (ItfGRAS6, ItfGRAS21, ItfGRAS31 and ItfGRAS34) among these tissues were all higher than those of the other genes.. - Under salt stress treatment, five genes (ItfGRAS6, ItfGRAS37, ItfGRAS50, ItfGRAS68 and ItfGRAS69) were significantly up-regulated in the. - The FPKM values of abiotic stresses for GRAS genes are listed in Additional file 6: Table S5. - In the remaining genes, four genes (Itf- GRAS1, ItfGRAS21, ItfGRAS31 and ItfGRAS34) were clearly down-regulated in the root. - The expression of genes in leaves was basically the same as that in the roots under salt stress, except for the up-regulated ex- pression of ItfGRAS21 and down-regulated expression of ItfGRAS68 and the substantially unchanged expression level of ItfGRAS69 compared with that at 0 h. - For drought stress in the root, the expression of four GRAS members (ItfGRAS4, ItfGRAS31, ItfGRAS50 and Itf- GRAS69) were up-regulated and that of the other six genes were obviously down-regulated with the lowest expression level at 24 h. - Three other significantly up- regulated genes, namely ItfGRAS6, ItfGRAS21 and Itf- GRAS37, were found in the leaf compared with drought stress in root. - After heat treatment, five genes were up- regulated in the root, among which, ItfGRAS4, Itf- GRAS50 and ItfGRAS68 exhibited an obvious increase.. - The expression levels of almost all genes were up-regulated in the leaf with the highest expression levels at 48 h. - Only two genes, Itf- GRAS4 and ItfGRAS6, were down-regulated in the leaf.. - Under cold treatment, most genes were down-regulated either in the root or leaf. - ItfGRAS31) in the root increased at 24 h but decreased sharply at 48 h. - ItfGRAS21 and ItfGRAS37 in leaf) were markedly up-regulated under cold stress, whereas the expression level of another gene, ItfGRAS31, was only relatively high in the leaf.. - In recent years, with the rapid development of bioinformat- ics analysis, reports on the whole-genome identification of GRAS transcription factors in plants increased. - So far, the characteristics of GRAS transcription factors in I.. - Thus, we performed a compre- hensive analysis of GRAS transcription factors in I. - The number of GRAS genes in I. - Phylogenetic analysis of GRAS proteins in I. - trifida GRAS proteins are located in the same clade with that. - The overall pattern of intron position plays vital roles in the evolution of transcription factor families [32].. - Intronless genes are also found in the F-box transcription factor gene family [34] and DEAD box RNA helicase [35]. - In addition, most GRAS members have similar exon–intron structure, indicating that the structures of GRAS genes are highly conserved.. - The expression patterns of GRAS transcription factors differed across various tissues, consistent with those. - ItfGRAS60 belonging to the DLT subfamily has a relatively higher expression in the bud than the other tissues, suggesting the function of this gene in bud development. - All ItfGRAS genes in the PAT1 subfamily were highly expressed in the leaf except ItfGRAS4 and ItfGRAS5. - We also analysed the expression of the selected ItfGRAS genes under four abiotic stresses with qRT- PCR, which was similar to the result of RNA-seq data.. - For instance, ItfGRAS34 was expressed at low levels in salt, drought and cold treatments in the qRT-PCR results, but public data showed their high ex- pression under these stresses. - All ItfGRAS members in the PAT1 subfamily were highly expressed under at least one abiotic stress.. - In this study, we identified 70 GRAS genes from I. - the structures of GRAS gene were highly conserved. - Our findings will further facilitate the functional study of GRAS genes and molecular breeding of sweet potato.. - Detailed information of the ItfGRAS. - Arabidopsis and rice GRAS genes used for phylogenetic analysis. - The expression data of the ItfGRAS genes in various tissues. - The expression data of the GRAS genes under four abiotic stress conditions in I.trifida. - Gene-specific primers used for qRT-PCR analysis of the ItfGRAS genes. - The GRAS gene family in arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. - The role of GRAS proteins in plant signal transduction and development. - A functionally required unfoldome from the plant kingdom: intrinsically disordered N- terminal domains of GRAS proteins are involved in molecular recognition during plant development. - Genome-wide analysis of the GRAS gene family in rice and Arabidopsis . - Genome-wide analysis of the GRAS gene family in Chinese cabbage ( Brassica rapa ssp. - Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato. - Genome-wide analysis of the GRAS gene family in Prunus mume . - Genome-wide comparative analysis of the GRAS gene family in populus , Arabidopsis and rice. - Chapter 19-functional aspects of GRAS family proteins. - NtGRAS1 , a novel stress-induced member of the GRAS family in tobacco, localizes to the nucleus. - Reconciling conflicting phylogenies in the origin of sweet potato and dispersal to Polynesia. - Genome-wide analysis of the GRAS gene family in physic nut ( Jatropha curcas L. - Identification and expression of GRAS family genes in maize ( Zea mays L. - Origin and evolutionary analysis of the plant-specific TIFY transcription factor family. - Genome-wide characterization of GRAS family genes in Medicago truncatula reveals their evolutionary dynamics and functional diversification. - Structural and functional analysis of the GRAS gene family in grapevine indicates a role of GRAS proteins in the control of development and stress responses. - PAT1 , a new member of the GRAS family, is involved in phytochrome a signal transduction. - Genome-wide identification and characterization of GRAS transcription factors in tomato ( Solanum lycopersicum
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