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Sucrose metabolism gene families and their biological functions.

Jiang SY, Chi YH, Wang JZ, Zhou JX, Cheng YS, Zhang BL, Ma A, Vanitha J, Ramachandran S - Sci Rep (2015)

Bottom Line: Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions.They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion.Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses.

View Article: PubMed Central - PubMed

Affiliation: Genome Structural Biology Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604.

ABSTRACT
Sucrose, as the main product of photosynthesis, plays crucial roles in plant development. Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions. We focused on four sucrose metabolism related gene families including sucrose synthase, sucrose phosphate synthase, sucrose phosphate phosphatase and UDP-glucose pyrophosphorylase. These gene families exhibited different expansion and evolutionary history as their host genomes experienced differentiated rates of the whole genome duplication, tandem and segmental duplication, or mobile element mediated gene gain and loss. They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion. However, we have detected recent positive selection during intra-species divergence. Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses. Our studies uncovered the molecular mechanisms of gene expansion and evolution and also provided new insight into the role of positive selection in intra-species divergence. Overexpression data revealed novel biological functions of these genes in flowering time control and seed germination under normal and stress conditions.

No MeSH data available.


Related in: MedlinePlus

Genomic variations and expression divergence of the SuSy, SPS, SPP and UDPGP families between grain and sweet sorghum.(A) Detected SNP, Indel and SV between grain (BT × 623) and sweet (Keller) sorghum lines and their Ka/Ks analysis. (B,C) Screening for amino acid sites with purifying/positive selection for the gene Sobic.006G213100 by the SLR program. (B) No positive selection was detected among 15 species (inter-species). (C) Positive selection was detected among 44 sorghum lines, which belong to the same species (intra-species). (D–G) Comparative expression analysis of SuSy, SPS, SPP and UDPGP family members between grain (blue column) and sweet (green column) sorghum lines, respectively, by qRT-PCR. The prefix “Sobic.” was omitted in each locus name. (H) Expression divergence of the SuSy, SPS, SPP and UDPGP gene families between grain and sweet sorghum lines under sucrose treatment. Red, black, and green colors indicated the normalized expression values with >0, = 0, and < 0, respectively, in the matrix. The stars “*” indicated the statistical difference in their expression level between these two genes at P < 0.05.
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f5: Genomic variations and expression divergence of the SuSy, SPS, SPP and UDPGP families between grain and sweet sorghum.(A) Detected SNP, Indel and SV between grain (BT × 623) and sweet (Keller) sorghum lines and their Ka/Ks analysis. (B,C) Screening for amino acid sites with purifying/positive selection for the gene Sobic.006G213100 by the SLR program. (B) No positive selection was detected among 15 species (inter-species). (C) Positive selection was detected among 44 sorghum lines, which belong to the same species (intra-species). (D–G) Comparative expression analysis of SuSy, SPS, SPP and UDPGP family members between grain (blue column) and sweet (green column) sorghum lines, respectively, by qRT-PCR. The prefix “Sobic.” was omitted in each locus name. (H) Expression divergence of the SuSy, SPS, SPP and UDPGP gene families between grain and sweet sorghum lines under sucrose treatment. Red, black, and green colors indicated the normalized expression values with >0, = 0, and < 0, respectively, in the matrix. The stars “*” indicated the statistical difference in their expression level between these two genes at P < 0.05.

Mentions: BT × 623 and Keller belong to the same species S. bicolor. However, they exhibited obviously different phenotypes41. The former is grain sorghum and the latter is sweet sorghum with higher sucrose content in its stem. Genome sequences for these two cultivars were publicly available42. Our HMM searches identified the same numbers of SuSy, SPS, SPP and UDPGP families in these two cultivars. Genome-wide variation analysis identified one SuSy, two SPS, one SPP and two UDPGP genes showed 100% homology in their genome sequences with no single nucleotide polymorphism (SNP), no insertion/deletion (Indel) and no structural variation (SV) (Fig. 5A). The other 11 genes contained either SNP or Indel and only one gene Sobic.002G291200 has been detected with SV (Fig. 5A). The Ka/Ks analysis showed that up to 12 out of 18 genes from the four gene families showed no non-synonymous substitution with Ka/Ks = 0. Most of the remaining genes showed low ratios (0.043–0.562). Only one gene Sobic.006G213100 exhibited Ka/Ks > 1 (1.574) (Fig. 5A), suggesting the positive selection for this locus in these two varieties. As our data have showed that no positive selection occurred for all the four gene families among 15 species (Fig. 3D–G), we were interested in whether the positive selection could be detected in other sorghum lines within the species. We have further confirmed that the gene Sobic.006G213100 showed no positive selection among 15 different species (Fig. 5B). We then analyzed the selection force of this gene among 45 intra-species lines, which belong to the same species S. bicolor. As these lines are from the same species, we could align the full-length amino acid sequences instead of domain sequences for the Ka/Ks analysis. Our data showed that a total of 7 sites were under positive selection with Ka/Ks ratios larger than 1(P < 0.05) (Fig. 5C). Three of them were located on domain region and the remaining 4 sites were out of the domain (Fig. 5C). The Ka/Ks ratios in the remaining sites were zero with no nonsynonymous substitution. The data suggested that mutation occurred only in limited sites and positive selection of the gene Sobic.006G213100 occurred during the divergence of intra-species.


Sucrose metabolism gene families and their biological functions.

Jiang SY, Chi YH, Wang JZ, Zhou JX, Cheng YS, Zhang BL, Ma A, Vanitha J, Ramachandran S - Sci Rep (2015)

Genomic variations and expression divergence of the SuSy, SPS, SPP and UDPGP families between grain and sweet sorghum.(A) Detected SNP, Indel and SV between grain (BT × 623) and sweet (Keller) sorghum lines and their Ka/Ks analysis. (B,C) Screening for amino acid sites with purifying/positive selection for the gene Sobic.006G213100 by the SLR program. (B) No positive selection was detected among 15 species (inter-species). (C) Positive selection was detected among 44 sorghum lines, which belong to the same species (intra-species). (D–G) Comparative expression analysis of SuSy, SPS, SPP and UDPGP family members between grain (blue column) and sweet (green column) sorghum lines, respectively, by qRT-PCR. The prefix “Sobic.” was omitted in each locus name. (H) Expression divergence of the SuSy, SPS, SPP and UDPGP gene families between grain and sweet sorghum lines under sucrose treatment. Red, black, and green colors indicated the normalized expression values with >0, = 0, and < 0, respectively, in the matrix. The stars “*” indicated the statistical difference in their expression level between these two genes at P < 0.05.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4663468&req=5

f5: Genomic variations and expression divergence of the SuSy, SPS, SPP and UDPGP families between grain and sweet sorghum.(A) Detected SNP, Indel and SV between grain (BT × 623) and sweet (Keller) sorghum lines and their Ka/Ks analysis. (B,C) Screening for amino acid sites with purifying/positive selection for the gene Sobic.006G213100 by the SLR program. (B) No positive selection was detected among 15 species (inter-species). (C) Positive selection was detected among 44 sorghum lines, which belong to the same species (intra-species). (D–G) Comparative expression analysis of SuSy, SPS, SPP and UDPGP family members between grain (blue column) and sweet (green column) sorghum lines, respectively, by qRT-PCR. The prefix “Sobic.” was omitted in each locus name. (H) Expression divergence of the SuSy, SPS, SPP and UDPGP gene families between grain and sweet sorghum lines under sucrose treatment. Red, black, and green colors indicated the normalized expression values with >0, = 0, and < 0, respectively, in the matrix. The stars “*” indicated the statistical difference in their expression level between these two genes at P < 0.05.
Mentions: BT × 623 and Keller belong to the same species S. bicolor. However, they exhibited obviously different phenotypes41. The former is grain sorghum and the latter is sweet sorghum with higher sucrose content in its stem. Genome sequences for these two cultivars were publicly available42. Our HMM searches identified the same numbers of SuSy, SPS, SPP and UDPGP families in these two cultivars. Genome-wide variation analysis identified one SuSy, two SPS, one SPP and two UDPGP genes showed 100% homology in their genome sequences with no single nucleotide polymorphism (SNP), no insertion/deletion (Indel) and no structural variation (SV) (Fig. 5A). The other 11 genes contained either SNP or Indel and only one gene Sobic.002G291200 has been detected with SV (Fig. 5A). The Ka/Ks analysis showed that up to 12 out of 18 genes from the four gene families showed no non-synonymous substitution with Ka/Ks = 0. Most of the remaining genes showed low ratios (0.043–0.562). Only one gene Sobic.006G213100 exhibited Ka/Ks > 1 (1.574) (Fig. 5A), suggesting the positive selection for this locus in these two varieties. As our data have showed that no positive selection occurred for all the four gene families among 15 species (Fig. 3D–G), we were interested in whether the positive selection could be detected in other sorghum lines within the species. We have further confirmed that the gene Sobic.006G213100 showed no positive selection among 15 different species (Fig. 5B). We then analyzed the selection force of this gene among 45 intra-species lines, which belong to the same species S. bicolor. As these lines are from the same species, we could align the full-length amino acid sequences instead of domain sequences for the Ka/Ks analysis. Our data showed that a total of 7 sites were under positive selection with Ka/Ks ratios larger than 1(P < 0.05) (Fig. 5C). Three of them were located on domain region and the remaining 4 sites were out of the domain (Fig. 5C). The Ka/Ks ratios in the remaining sites were zero with no nonsynonymous substitution. The data suggested that mutation occurred only in limited sites and positive selection of the gene Sobic.006G213100 occurred during the divergence of intra-species.

Bottom Line: Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions.They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion.Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses.

View Article: PubMed Central - PubMed

Affiliation: Genome Structural Biology Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604.

ABSTRACT
Sucrose, as the main product of photosynthesis, plays crucial roles in plant development. Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions. We focused on four sucrose metabolism related gene families including sucrose synthase, sucrose phosphate synthase, sucrose phosphate phosphatase and UDP-glucose pyrophosphorylase. These gene families exhibited different expansion and evolutionary history as their host genomes experienced differentiated rates of the whole genome duplication, tandem and segmental duplication, or mobile element mediated gene gain and loss. They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion. However, we have detected recent positive selection during intra-species divergence. Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses. Our studies uncovered the molecular mechanisms of gene expansion and evolution and also provided new insight into the role of positive selection in intra-species divergence. Overexpression data revealed novel biological functions of these genes in flowering time control and seed germination under normal and stress conditions.

No MeSH data available.


Related in: MedlinePlus