Chin Bull Bot ›› 2015, Vol. 50 ›› Issue (6): 683-690.doi: 10.11983/CBB14147

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Sequence Divergence and Expression Specificity of the Starch Synthase Gene Family in Oryza officinalis Leaf

Ying Bao*, Jiaxiao Du, Xiang Jing, Si Xu   

  1. School of Life Sciences, Qufu Normal University, Qufu 273165, China
  • Received:2014-08-07 Accepted:2015-01-05 Online:2015-09-06 Published:2015-11-01
  • Contact: Bao Ying E-mail:baoyingus@126.com
  • About author:

    ? These authors contributed equally to this paper

Abstract:

Starch is produced by most green plants as an energy store and is also a major carbohydrate source in human diet. There are two stages of starch synthesis in most plants. In the first stage, transient starch is produced during photosynthesis, and in the second, the nutrition accumulation stage, starch is deposited for storage purposes. Although the first stage of starch synthesis plays a critical role in carbohydrate metabolism, starch biosynthesis in photosynthetic organs has received less attention. To detect the evolutionary patterns associated with starch synthase, the enzyme involved in the biosynthesis of starch, in plant photosynthetic organs, we used leaf transcriptome resequencing to investigate the genotype and expression divergence of the gene family in Oryza officinalis. Eight complete starch synthase genes were identified, and phylogenetic analyses confirmed that the genes were SSI, SSII, SIII, SSIV, SSV, and GSBBII. Comparison of sequences and expression quantities showed that the evolutionary patterns of the starch synthase family in O. officinalis were highly consistent with those of cultivated rice. The homologous sequence identities between the two species were 95% to 98% at the mRNA level. Further statistical tests based on the ratio of nonsynonymous to synonymous substitutions indicated that all eight genes were under significant purifying selection. In addition, three genes specifically expressed in the endosperm of cultivated rice were not found in the leaf transcriptome of O. officinalis. However, four genes with predominant expression in the leaves of cultivated rice showed relatively higher expression in the O. officinalis leaf transcriptome.

Table 1

Starch synthase genes in leaf transcriptome of Oryza officinalis"

Gene SSI SSII1 SSII2 SSII3 SSIII1 SSIII2 SSIV1 SSIV2 SSV GBSSI GBSSII
Mapped reads 1 216 419 3 035 82 3 365 280 20 249 252 31 9 779
Gene length (bp) 1 883 2 256 2 073 - 3 663 4 653 - 2 754 2 115 - 1 827

Table 2

Homologous comparisons of the starch synthase genes between Oryza officinalis and O. sativa"

Gene SSI SSII1 SSII2 SSIII1 SSIII2 SSIV2 SSV GBSSII
mRNA identities 96.4% 95.2% 95.5% 97.1% 96.4% 95.4% 95.2% 98.1%
Amino acid identities 96.9% 94.5% 93.1% 96.3% 94.1% 94.7% 93.6% 97.0%

Table 3

Amino acid sequence identities among the starch synthase genes in Oryza officinalis"

SSI SSII1 SSII2 SSIII1 SSIII2 SSIV2 SSV
SSII1 41.3% - - - - - -
SSII2 41.8% 58.1% - - - - -
SSIII1 28.7% 23.6% 25.6% - - - -
SSIII2 28.1% 23.4% 26.0% 61.9% - - -
SSIV2 28.0% 24.2% 27.6% 28.9% 29.8% - -
SSV 20.4% 18.8% 20.6% 24.1% 24.3% 27.7% -
GBSSII 31.6% 34.4% 33.5% 26.9% 27.1% 28.6% 17.8%

Table 4

Gene substitutions between Oryza officinalis and O. sativa"

Sequence Method Ka Ks Ka/Ks P-value (Fisher)
SSI GY-HKY 0.009 0.079 0.112 6.75E-14**
SSII1 GY-HKY 0.026 0.114 0.225 1.46E-14**
SSII2 GY-HKY 0.035 0.062 0.560 6.95E-03**
SSIII1 GY-HKY 0.015 0.068 0.219 5.50E-14**
SSIII2 GY-HKY 0.027 0.076 0.358 2.37E-11**
SSIV2 GY-HKY 0.029 0.100 0.289 9.13E-12**
SSV GY-HKY 0.025 0.087 0.289 1.71E-08**
GBSSII GY-HKY 0.014 0.038 0.361 3.07E-03**
SSI NG 0.009 0.085 0.108 1.54E-13**
SSII1 NG 0.024 0.128 0.189 2.83E-16**
SSII2 NG 0.034 0.065 0.526 5.94E-03**
SSIII1 NG 0.015 0.069 0.215 3.33E-13**
SSIII2 NG 0.026 0.080 0.329 5.39E-12**
SSIV2 NG 0.029 0.101 0.285 6.06E-11**
SSV NG 0.024 0.095 0.255 2.00E-09**
GBSSII NG 0.013 0.041 0.315 8.70E-04**
SSI YN 0.009 0.076 0.116 1.54E-12**
SSII1 YN 0.026 0.110 0.233 1.18E-12**
SSII2 YN 0.034 0.062 0.558 1.47E-02**
SSIII1 YN 0.015 0.062 0.245 1.11E-11**
SSIII2 YN 0.027 0.070 0.389 4.50E-09**
SSIV2 YN 0.029 0.096 0.302 2.61E-10**
SSV YN 0.025 0.087 0.289 5.49E-08**
GBSSII YN 0.013 0.038 0.357 2.95E-03**

Figure 1

Phylogenetic relationships and relative expression level of the starch synthase gene family(A) The maximum likelihood tree of the starch synthase gene family based on amino acid homologous sequences of Arabidopsis thaliana, Oryza officinalis, O. sativa, and Zea mays (Numbers near the branches indicate bootstrap values); (B) Relative expression level of the starch synthase genes in O. officinalis."

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