Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum

Yongjun Wang, Xiuting Hua, Jingsheng Xu, Zhichang Chen, Tianqu Fan, Zhaohui Zeng, Hengbo Wang, Ai Ling Hour, Qingyi Yu, Ray R Ming, Jisen Zhang

Research output: Contribution to journalArticle

Abstract

Background: Sugarcane served as the model plant for discovery of the C 4 photosynthetic pathway. Magnesium is the central atom of chlorophyll, and thus is considered as a critical nutrient for plant development and photosynthesis. In plants, the magnesium transporter (MGT) family is composed of a number of membrane proteins, which play crucial roles in maintaining Mg homeostasis. However, to date there is no information available on the genomics of MGTs in sugarcane due to the complexity of the Saccharum genome. Results: Here, we identified 10 MGTs from the Saccharum spontaneum genome. Phylogenetic analysis of MGTs suggested that the MGTs contained at least 5 last common ancestors before the origin of angiosperms. Gene structure analysis suggested that MGTs family of dicotyledon may be accompanied by intron loss and pseudoexon phenomena during evolution. The pairwise synonymous substitution rates corresponding to a divergence time ranged from 142.3 to 236.6 Mya, demonstrating that the MGTs are an ancient gene family in plants. Both the phylogeny and Ks analyses indicated that SsMGT1/SsMGT2 originated from the recent ρWGD, and SsMGT7/SsMGT8 originated from the recent σ WGD. These 4 recently duplicated genes were shown low expression levels and assumed to be functionally redundant. MGT6, MGT9 and MGT10 weredominant genes in the MGT family and werepredicted to be located inthe chloroplast. Of the 3 dominant MGTs, SsMGT6 expression levels were found to be induced in the light period, while SsMGT9 and SsMTG10 displayed high expression levels in the dark period. These results suggested that SsMGT6 may have a function complementary to SsMGT9 and SsMTG10 that follows thecircadian clock for MGT in the leaf tissues of S. spontaneum. MGT3, MGT7 and MGT10 had higher expression levels Insaccharum officinarum than in S. spontaneum, suggesting their functional divergence after the split of S. spontaneum and S. officinarum. Conclusions: This study of gene evolution and expression of MGTs in S. spontaneum provided basis for the comprehensive genomic study of the entire MGT genes family in Saccharum. The results are valuable for further functional analyses of MGT genes and utilization of the MGTs for Saccharum genetic improvement.

Original languageEnglish (US)
Article number5437
JournalBMC genomics
Volume20
Issue number1
DOIs
StatePublished - Jan 24 2019

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Saccharum
Genomics
Magnesium
Genes
Mya
Genome
Angiosperms
Plant Development
Photosynthesis
Chloroplasts
Chlorophyll
Phylogeny
Introns
Membrane Proteins
Homeostasis
Gene Expression
Light
Food

Keywords

  • Gene evolution
  • Gene expression
  • Magnesium transporter
  • Saccharum

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum. / Wang, Yongjun; Hua, Xiuting; Xu, Jingsheng; Chen, Zhichang; Fan, Tianqu; Zeng, Zhaohui; Wang, Hengbo; Hour, Ai Ling; Yu, Qingyi; Ming, Ray R; Zhang, Jisen.

In: BMC genomics, Vol. 20, No. 1, 5437, 24.01.2019.

Research output: Contribution to journalArticle

Wang, Yongjun ; Hua, Xiuting ; Xu, Jingsheng ; Chen, Zhichang ; Fan, Tianqu ; Zeng, Zhaohui ; Wang, Hengbo ; Hour, Ai Ling ; Yu, Qingyi ; Ming, Ray R ; Zhang, Jisen. / Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum. In: BMC genomics. 2019 ; Vol. 20, No. 1.
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AU - Hua, Xiuting

AU - Xu, Jingsheng

AU - Chen, Zhichang

AU - Fan, Tianqu

AU - Zeng, Zhaohui

AU - Wang, Hengbo

AU - Hour, Ai Ling

AU - Yu, Qingyi

AU - Ming, Ray R

AU - Zhang, Jisen

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N2 - Background: Sugarcane served as the model plant for discovery of the C 4 photosynthetic pathway. Magnesium is the central atom of chlorophyll, and thus is considered as a critical nutrient for plant development and photosynthesis. In plants, the magnesium transporter (MGT) family is composed of a number of membrane proteins, which play crucial roles in maintaining Mg homeostasis. However, to date there is no information available on the genomics of MGTs in sugarcane due to the complexity of the Saccharum genome. Results: Here, we identified 10 MGTs from the Saccharum spontaneum genome. Phylogenetic analysis of MGTs suggested that the MGTs contained at least 5 last common ancestors before the origin of angiosperms. Gene structure analysis suggested that MGTs family of dicotyledon may be accompanied by intron loss and pseudoexon phenomena during evolution. The pairwise synonymous substitution rates corresponding to a divergence time ranged from 142.3 to 236.6 Mya, demonstrating that the MGTs are an ancient gene family in plants. Both the phylogeny and Ks analyses indicated that SsMGT1/SsMGT2 originated from the recent ρWGD, and SsMGT7/SsMGT8 originated from the recent σ WGD. These 4 recently duplicated genes were shown low expression levels and assumed to be functionally redundant. MGT6, MGT9 and MGT10 weredominant genes in the MGT family and werepredicted to be located inthe chloroplast. Of the 3 dominant MGTs, SsMGT6 expression levels were found to be induced in the light period, while SsMGT9 and SsMTG10 displayed high expression levels in the dark period. These results suggested that SsMGT6 may have a function complementary to SsMGT9 and SsMTG10 that follows thecircadian clock for MGT in the leaf tissues of S. spontaneum. MGT3, MGT7 and MGT10 had higher expression levels Insaccharum officinarum than in S. spontaneum, suggesting their functional divergence after the split of S. spontaneum and S. officinarum. Conclusions: This study of gene evolution and expression of MGTs in S. spontaneum provided basis for the comprehensive genomic study of the entire MGT genes family in Saccharum. The results are valuable for further functional analyses of MGT genes and utilization of the MGTs for Saccharum genetic improvement.

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