- ADHs participate in growth, development, and adaptation in many plant species, but the evolution and function of the ADH gene family in sugarcane is still unclear.. - Phylogenetic analysis demonstrated two groups of ADH genes and suggested that these genes underwent duplication during angiosperm evolution. - Conclusions: This study depicted the size and composition of the ADH gene family in 17 species, and investigated their evolution pattern. - These findings will facilitate research on evolutionary and functional aspects of the ADH genes in sugarcane, especially for the understanding of ScADH3 under cold stress.. - Full list of author information is available at the end of the article Su et al. - Expression of the ADH gene is induced by different environmental stresses [14], such as low temperature [9, 15], osmotic [16], drought [8], salt [10], mechanical damage [17], and the exogenous hormone abscisic acid (ABA) [18]. - The ADH gene is one of the most common cold-induced genes in cereal crops and Arabidopsis [9]. - Few studies have investigated the ADH genes in sugar- cane. - However, the functions of sugarcane ADH genes are unknown. - Phylogenetic analysis was used to study the evolutionary history and the origin of ADH genes in plants. - We used bioinformatics to analyze the ADH genes in two sugarcane genomes for comparative analysis. - These were the haploid genome of the modern sugarcane cultivar R570 [26] and the haploid genome version of the sugarcane ancestor S. - The ADH genes in the Sorghum bicolor gen- ome, a common reference for comparative analysis of sugarcane [31], were also analyzed. - These findings increase our un- derstanding of the evolution and functional divergence of the ADH gene family in sugarcane and also the physiological mechanism and regulatory function of ScADH3. - Identification of ADH genes in plant genomes. - The largest number of ADH genes (32) was found in S. - In the basal an- giosperms, seven copies of ADH genes were identified in Amborella trichopoda. - Therefore, these Class III ADH genes were reserved for subsequent phylogenetic analysis.. - The results of the grand average of hydropathicity (GRAVY) suggested that 43 of 169 were hydrophilic and the instability index showed that 13 of 151 ADH proteins were unstable. - Phylogenetic classification of ADH gene family. - To study the evolution of the ADH gene family, a total of 153 ADHs from 17 plant species and three Class III ADHs from Rhodophyta as outgroups were used to con- struct a phylogenetic tree using the Maximum Likeli- hood (ML) method (Fig. - Topology of the ML tree showed that ADH genes clearly cluster into two major groups in plants (Fig. - b The number of identified ADH genes in these 20 species. - The Rhodophyta are separated from other embryophytes according to the topology of the ML tree. - The generation of four subgroups of the ADH gene family among plants may have been caused by the duplication event.. - These results suggest that gene expansion appeared in these plants during the evolution of the ADH gene family.. - The pattern of exon–intron distribution and position of the ADH genes from 17 species were analyzed to study the structural characteristics and evolution of the ADH gene family (Fig. - 2 Phylogenetic classification of ADH genes in plants. - The topology of the ML tree showed that ADH genes in plants can be classified into two major groups, which are designed as Groups A and B.. - There was no cor- relation between chromosome length and the number of ADH genes.. - The types of ADH genes in S. - 4 Chromosomal distribution of the ADH gene family in S. - expansion because more than half of the SbADHs were related to tandem duplication. - Al- though the rates of the four duplicated types in the three species varied, the dispersed and tandem duplications appear to be the most common mechanisms for ADH family gene expansion.. - bicolor may be regarded as an outcome of the strategy adopted to assemble Saccharum BAC clones.. - These results suggest that these genes may have been involved in the evolution of the ADH gene family.. - The Ka/Ks ratios of the ADH gene pairs were calcu- lated to study the evolutionary constraints acting on the ADH gene family (Supplemental Table S3). - The length of the ORF in ScADH3 was 1137 bp, and it encoded polypep- tide of 379 amino acids (Fig. - The protein primary structure analysis showed that MW, pI, GRAVY, and in- stability index (II) of the ScADH3 protein were 40.82 kDa, 6.03. - 5 Expansion mechanisms of the ADH gene family in S. - The effects of dispersed, proximal, tandem, and WGD/segmental duplications on the expansion of ADH genes in S. - 6 Synteny analysis of ADH genes in S. - a Synteny analysis of ADH genes in S. - b Synteny analysis of ADH genes in S. - c Synteny analysis of ADH genes in R570 and S. - Histochemical staining showed that the WT leaves showed deeper staining by DAB than those of the transgenic plants (Fig. - To study the molecular mecha- nisms underlying the enhanced cold tolerance by overexpressing ScADH3, qRT-PCR was used to detect the mRNA abundance of the ROS-related genes NtSOD, NtPOD, and NtCAT in the WT and transgenic lines. - 10c–e), indicating that overexpression of ScADH3 led to an up-regulation of the ROS-related genes. - These results demonstrated that overexpression of ScADH3 im- proved cold tolerance of the transgenic tobacco plants.. - Evolution of ADH gene family in plants. - 7 Complete cDNA and deduced amino acid sequences of the ScADH3 gene. - The copy num- ber of the ADH gene in plants varies widely but mostly ranges from 6 to 10. - The phylogenetic tree suggests that the origin of the ADH gene can be traced back to a com- mon ancestor of lower plants and higher plants before. - 8 qRT-PCR expression analysis of the ScADH3 gene in sugarcane ROC22 plantlets after treatment with Sporisorium scitamineum, 100 μ M ABA, 25% polyethylene glycol (PEG mM NaCl, and 4 °C. - As the phylogenetic tree of the examined plants indi- cated, the ADH gene families were phylogenetically clus- tered into four groups (Groups A-1, A-2, B-1, and B-2).. - Some WGDs, as- sociated with the origin of the recent common ancestor of extant angiosperms (ε), pan-core eudicots (γ), and monocots (ρ), have been revealed by integrated synteny, age estimates of gene duplication, and phylogenomic analysis [43, 44]. - trichopoda is strongly supported as the single living representative species of the sister lineage to all other extant flowering plants. - genome content and structure of the most recent com- mon ancestor of living angiosperms [46]. - trichopoda, indicating that all these ADH genes experienced duplication. - Comparative genomics of ADH gene family in S. - spontaneum and R570), the genomic features of the pre- dicted ADHs specifically with regard to their motif, gene structure, chromosomal arrangement, duplicated types, and synteny were investigated.. - the gene structures were analyzed to study the structural characteristics and evolution of the ADH genes (Fig. - spontaneum and R570, the intron number of ADH genes ranged from 0 to 16, and 26 of the 47 ADH genes had nine introns. - Dispersed, tandem, proximal, and WGD/segmental duplications were identified among the ADH genes within the three focal genomic references. - About 67% of the ShADHs in R570 were expanded by dispersed duplication. - The results showed that tandem duplication, dispersed duplication, and WGD/segmental duplication were the main driving forces for the expansion of the ADH gene family in S. - Infection by pathogenic bacteria can possibly induce the expression of ADH genes and increase ADH enzyme activity. - We also found that ScADH3 was induced by ABA, and its expression pattern was similar to that of the ADH gene in Arabi- dopsis [14]. - The ADH gene is one of the most common cold- induced genes in cereals and Arabidopsis [9]. - The level of ROS is an indicator of the magnitude of stress severity and stress tolerance. - Phylogenetic analysis showed that ADH genes subfamilies of ADH genes underwent dis- tinct gene duplication patterns during angiosperm evolu- tion. - Function analysis implied that ScADH3 is involved in cold tolerance, which involved modulation of the homeostasis of react- ive oxygen species (ROS) by regulating ROS-related genes. - These findings reveal evolutionary and functional aspects of the ADH genes in sugarcane and identify genes that may be useful for genetic manipulation.. - To study the expression of the sugarcane ScADH3 gene in response to ABA, abiotic, and biotic stress, uniform four-month-old tissue cultured plantlets of sugarcane were grown in water for 1 week at 28 °C with a 16:8 h (L:D) photoperiod. - All of the harvested plant tissues were fro- zen in liquid nitrogen and stored at − 80 °C until total RNA extraction.. - Twenty sequenced plant genomes were collected and screened for ADH genes to obtain a representation of the major plant lineage (Supplementary Table S7).. - in/mg2c_v2.1/) was applied to map the chromosomal positions of the ADH genes in S. - Gel-purification of the production of RT-PCR and cloning into pMD19-T vec- tor (TaKaRa, Dalian, China) was then conducted. - Each of the samples had three biological replicates. - After continuous growth at 37 °C for 12 h, we adjusted the concentration of the culture to OD 600 of 0.6 and used LB medium to dilute the samples by 10 − 3 - and 10 − 4 -fold. - Finally, 10 μL from each of the 10 − 3 - and 10 − 4 -fold dilutions of the sample was spotted on LB agar plates. - Transcript analyses of the three tobacco hydrogen peroxide-related genes (NtPOD, NtSOD, and NtCAT) were conducted on the treated N.. - Each of the samples had three bio- logical replicates. - The detailed information of ADH genes included in this study. - The gene type of ADH genes in S.. - Sources of ADH genes from sequenced plant included in this study.. - Revised the final version of the paper: LPX, YCS, KM and YXQ. - The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.. - The plant ADH gene family. - Differential interactions of promoter elements in stress responses of the Arabidopsis Adh gene. - Analysis of the grasspea proteome and identification of stress-responsive proteins upon exposure to high salinity, low temperature, and abscisic acid treatment. - Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut- resistant genotype. - Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. - Molecular cloning and DNA sequence of the Arabidopsis thaliana alcohol dehydrogenase gene. - Selective recruitment of Adh genes for distinct enzymatic functions in Petunia hybrida. - Evolution of the 3R- MYB gene family in plants. - Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium). - A complex interplay of tandem- and whole-genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae. - Homologues of the Cf-9 disease resistance gene (Hcr9s) are present at multiple loci on the short arm of tomato chromosome 1. - The evolution of the genome pp
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