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Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato.

Huang W, Xian Z, Kang X, Tang N, Li Z - BMC Plant Biol. (2015)

Bottom Line: SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes.Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated.The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.

View Article: PubMed Central - PubMed

Affiliation: Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. huanghaowei1988@126.com.

ABSTRACT

Background: GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling, and abiotic/biotic stress. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species with fleshy fruits.

Results: In this study, 53 GRAS genes were identified and renamed based on tomato whole-genome sequence and their respective chromosome distribution except 19 members were kept as their already existed name. Multiple sequence alignment showed typical GRAS domain in these proteins. Phylogenetic analysis of GRAS proteins from tomato, Arabidopsis, Populus, P.mume, and Rice revealed that SlGRAS proteins could be divided into at least 13 subfamilies. SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes. Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated.

Conclusions: This study provides the first comprehensive analysis of GRAS gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.

No MeSH data available.


Related in: MedlinePlus

Multiple sequence alignment of the 48 GRAS domain from tomato GRAS genes obtained by ClustalX and manual correction. The most conserved motif of GRAS domain, VHIID, was underlined
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Fig3: Multiple sequence alignment of the 48 GRAS domain from tomato GRAS genes obtained by ClustalX and manual correction. The most conserved motif of GRAS domain, VHIID, was underlined

Mentions: From the alignment of predicted GRAS domain sequences we found members containing partial GRAS domains with missing motifs, some of which were severely truncated. In tomato, for instance, the GRAS domain of SlGRAS35 could be as short as 85 amino acids, while the typical GRAS domain had a minimum length of about 350 amino acids (e.g., At4g00150, SlGRAS38), thereby 5 non-canonical GRAS proteins (SlGRAS19, SlGRAS20, SlGRAS29, SlGRAS35, SlGRAS50) were excluded from some of the following analyses (multiple sequence alignment and phylogenetic analysis) because of the low reliability by incorporating these fragments. Furthermore, although the multiple sequence analysis showed a low overall identity among the 48 analyzed SlGRAS proteins, the 5 most prominent motifs, including leucine-rich region I (LR I), VHIID, leucine-rich region II (LR II), PFYRE, and SAW could be observed in their GRAS domains (Fig. 3 and Additional file 3).Fig. 3


Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato.

Huang W, Xian Z, Kang X, Tang N, Li Z - BMC Plant Biol. (2015)

Multiple sequence alignment of the 48 GRAS domain from tomato GRAS genes obtained by ClustalX and manual correction. The most conserved motif of GRAS domain, VHIID, was underlined
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4549011&req=5

Fig3: Multiple sequence alignment of the 48 GRAS domain from tomato GRAS genes obtained by ClustalX and manual correction. The most conserved motif of GRAS domain, VHIID, was underlined
Mentions: From the alignment of predicted GRAS domain sequences we found members containing partial GRAS domains with missing motifs, some of which were severely truncated. In tomato, for instance, the GRAS domain of SlGRAS35 could be as short as 85 amino acids, while the typical GRAS domain had a minimum length of about 350 amino acids (e.g., At4g00150, SlGRAS38), thereby 5 non-canonical GRAS proteins (SlGRAS19, SlGRAS20, SlGRAS29, SlGRAS35, SlGRAS50) were excluded from some of the following analyses (multiple sequence alignment and phylogenetic analysis) because of the low reliability by incorporating these fragments. Furthermore, although the multiple sequence analysis showed a low overall identity among the 48 analyzed SlGRAS proteins, the 5 most prominent motifs, including leucine-rich region I (LR I), VHIID, leucine-rich region II (LR II), PFYRE, and SAW could be observed in their GRAS domains (Fig. 3 and Additional file 3).Fig. 3

Bottom Line: SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes.Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated.The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.

View Article: PubMed Central - PubMed

Affiliation: Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China. huanghaowei1988@126.com.

ABSTRACT

Background: GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling, and abiotic/biotic stress. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species with fleshy fruits.

Results: In this study, 53 GRAS genes were identified and renamed based on tomato whole-genome sequence and their respective chromosome distribution except 19 members were kept as their already existed name. Multiple sequence alignment showed typical GRAS domain in these proteins. Phylogenetic analysis of GRAS proteins from tomato, Arabidopsis, Populus, P.mume, and Rice revealed that SlGRAS proteins could be divided into at least 13 subfamilies. SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes. Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated.

Conclusions: This study provides the first comprehensive analysis of GRAS gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.

No MeSH data available.


Related in: MedlinePlus