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

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.

Genome-wide systematic characterization of the HAK/KUP/KT gene family and its expression profile during plant growth and in response to low-K+ stress in Saccharum

“…Analysis of the expression profiling of HAKs in Saccharum based on RNA-seq RNA preparation, cDNA libraries construction and RNA-seq libraries sequencing were performed as previously described [51,52]. Raw data were aligned to available S. spontaneum AP85-441 reference gene models using Trinity (https:// github.com/trinityrnaseq/trinityrnaseq/wiki).…”

“…Raw data were aligned to available S. spontaneum AP85-441 reference gene models using Trinity (https:// github.com/trinityrnaseq/trinityrnaseq/wiki). Fragments per kilobase per million mapped fragments (FPKM) values were calculated to represent gene expression levels as previously described [51,52].…”

“…(Additional file 10). The reaction program of reverse transcription, real-time PCR and the relative expression levels calculation were carried out as Wang et al described [52].…”

Genome-wide systematic characterization of HAK/KUP/KT gene family and their expression profiles during plant growth and in response to low K+ stress in Saccharum

“…The expression level of three HAK genes (HAK1, HAK7 and HAK20b) in the root of saccharum hybrid variety YT55 at 6 time points (0 h, 6 h, 12 h, 24 h, 48 h and 72 h) under K + -starvation were validated by RT-qPCR (Additional file 10). The reverse transcription, real time PCR program and method to calculate the relative expression levels was performed as previously described [52]. Phylogenetic relationships of HAK/KUP/KT families based on the current data for angiosperms.…”

Genome-wide systematic characterization of the HAK/KUP/KT gene family and its expression profile during plant growth and in response to low-K+ stress in Saccharum

“…(Additional file 10). The reverse transcription, realtime PCR program and method to calculate the relative expression levels were performed as previously described [52].…”