Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

Genome-Wide Identification and Gene Expression Analysis of Sweet Cherry Aquaporins (Prunus avium L.) under Abiotic Stresses

Aquaporins (AQPs) are integral transmembrane proteins well known as channels involved in the mobilization of water, small uncharged molecules and gases. In this work, the main objective was to carry out a comprehensive study of AQP encoding genes in Prunus avium (cv. Mazzard F12/1) on a genome-wide scale and describe their transcriptional behaviors in organs and in response to different abiotic stresses. A total of 28 non-redundant AQP genes were identified in Prunus spp. Genomes, which were phylogenetically grouped into five subfamilies (seven PIPs, eight NIPs, eight TIPs, three SIPs and two XIPs). Bioinformatic analyses revealed a high synteny and remarkable conservation of structural features among orthologs of different Prunus genomes. Several cis-acting regulatory elements (CREs) related to stress regulation were detected (ARE, WRE3, WUN, STRE, LTR, MBS, DRE, AT-rich and TC-rich). The above could be accounting for the expression variations associated with plant organs and, especially, each abiotic stress analyzed. Gene expressions of different PruavAQPs were shown to be preferentially associated with different stresses. PruavXIP2;1 and PruavXIP1;1 were up-regulated in roots at 6 h and 72 h of hypoxia, and in PruavXIP2;1 a slight induction of expression was also detected in leaves. Drought treatment strongly down-regulated PruavTIP4;1 but only in roots. Salt stress exhibited little or no variation in roots, except for PruavNIP4;1 and PruavNIP7;1, which showed remarkable gene repression and induction, respectively. Interestingly, PruavNIP4;1, the AQP most expressed in cherry roots subjected to cold temperatures, also showed this pattern in roots under high salinity. Similarly, PruavNIP4;2 consistently was up-regulated at 72 h of heat and drought treatments. From our evidence is possible to propose candidate genes for the development of molecular markers for selection processes in breeding programs for rootstocks and/or varieties of cherry.

Pearl Millet Aquaporin Gene PgPIP2;6 Improves Abiotic Stress Tolerance in Transgenic Tobacco

Pearl millet [Pennisetum glaucum (L) R. Br.] is an important cereal crop of the semiarid tropics, which can withstand prolonged drought and heat stress. Considering an active involvement of the aquaporin (AQP) genes in water transport and desiccation tolerance besides several basic functions, their potential role in abiotic stress tolerance was systematically characterized and functionally validated. A total of 34 AQP genes from P. glaucum were identified and categorized into four subfamilies, viz., plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin-26-like intrinsic proteins (NIPs), and small basic intrinsic proteins (SIPs). Sequence analysis revealed that PgAQPs have conserved characters of AQP genes with a closer relationship to sorghum. The PgAQPs were expressed differentially under high vapor pressure deficit (VPD) and progressive drought stresses where the PgPIP2;6 gene showed significant expression under high VPD and drought stress. Transgenic tobacco plants were developed by heterologous expression of the PgPIP2;6 gene and functionally characterized under different abiotic stresses to further unravel their role. Transgenic tobacco plants in the T2 generations displayed restricted transpiration and low root exudation rates in low- and high-VPD conditions. Under progressive drought stress, wild-type (WT) plants showed a quick or faster decline of soil moisture than transgenics. While under heat stress, PgPIP2;6 transgenics showed better adaptation to heat (40°C) with high canopy temperature depression (CTD) and low transpiration; under low-temperature stress, they displayed lower transpiration than their non-transgenic counterparts. Cumulatively, lower transpiration rate (Tr), low root exudation rate, declined transpiration, elevated CTD, and lower transpiration indicate that PgPIP2;6 plays a role under abiotic stress tolerance. Since the PgPIP2;6 transgenic plants exhibited better adaptation against major abiotic stresses such as drought, high VPD, heat, and cold stresses by virtue of enhanced transpiration efficiency, it has the potential to engineer abiotic stress tolerance for sustained growth and productivity of crops.

Genome-Wide Identification and Function of Aquaporin Genes During Dormancy and Sprouting Periods of Kernel-Using Apricot (Prunus armeniaca L.)

Aquaporins (AQPs) are essential channel proteins that play a major role in plant growth and development, regulate plant water homeostasis, and transport uncharged solutes across biological membranes. In this study, 33 AQP genes were systematically identified from the kernel-using apricot (Prunus armeniaca L.) genome and divided into five subfamilies based on phylogenetic analyses. A total of 14 collinear blocks containing AQP genes between P. armeniaca and Arabidopsis thaliana were identified by synteny analysis, and 30 collinear blocks were identified between P. armeniaca and P. persica. Gene structure and conserved functional motif analyses indicated that the PaAQPs exhibit a conserved exon-intron pattern and that conserved motifs are present within members of each subfamily. Physiological mechanism prediction based on the aromatic/arginine selectivity filter, Froger's positions, and three-dimensional (3D) protein model construction revealed marked differences in substrate specificity between the members of the five subfamilies of PaAQPs. Promoter analysis of the PaAQP genes for conserved regulatory elements suggested a greater abundance of cis-elements involved in light, hormone, and stress responses, which may reflect the differences in expression patterns of PaAQPs and their various functions associated with plant development and abiotic stress responses. Gene expression patterns of PaAQPs showed that PaPIP1-3, PaPIP2-1, and PaTIP1-1 were highly expressed in flower buds during the dormancy and sprouting stages of P. armeniaca. A PaAQP coexpression network showed that PaAQPs were coexpressed with 14 cold resistance genes and with 16 cold stress-associated genes. The expression pattern of 70% of the PaAQPs coexpressed with cold stress resistance genes was consistent with the four periods [Physiological dormancy (PD), ecological dormancy (ED), sprouting period (SP), and germination stage (GS)] of flower buds of P. armeniaca. Detection of the transient expression of GFP-tagged PaPIP1-1, PaPIP2-3, PaSIP1-3, PaXIP1-2, PaNIP6-1, and PaTIP1-1 revealed that the fusion proteins localized to the plasma membrane. Predictions of an A. thaliana ortholog-based protein-protein interaction network indicated that PaAQP proteins had complex relationships with the cold tolerance pathway, PaNIP6-1 could interact with WRKY6, PaTIP1-1 could interact with TSPO, and PaPIP2-1 could interact with ATHATPLC1G. Interestingly, overexpression of PaPIP1-3 and PaTIP1-1 increased the cold tolerance of and protein accumulation in yeast. Compared with wild-type plants, PaPIP1-3- and PaTIP1-1-overexpressing (OE) Arabidopsis plants exhibited greater tolerance to cold stress, as evidenced by better growth and greater antioxidative enzyme activities. Overall, our study provides insights into the interaction networks, expression patterns, and functional analysis of PaAQP genes in P. armeniaca L. and contributes to the further functional characterization of PaAQPs.

Genome-Wide Identification and Analysis of the Metallothionein Genes in Oryza Genus

Metallothionein (MT) proteins are low molecular mass, cysteine-rich, and metal-binding proteins that play an important role in maintaining metal homeostasis and stress response. However, the evolutionary relationships and functional differentiation of MT in the Oryza genus remain unclear. Here we identified 53 MT genes from six Oryza genera, including O. sativa ssp. japonica, O. rufipogon, O. sativa ssp. indica, O. nivara, O. glumaepatula, and O. barthii. The MT genes were clustered into four groups based on phylogenetic analysis. MT genes are unevenly distributed on chromosomes; almost half of the MT genes were clustered on chromosome 12, which may result from a fragment duplication containing the MT genes on chromosome 12. Five pairs of segmental duplication events and ten pairs of tandem duplication events were found in the rice MT family. The Ka/Ks values of the fifteen duplicated MT genes indicated that the duplicated MT genes were under a strong negative selection during evolution. Next, combining the promoter activity assay with gene expression analysis revealed different expression patterns of MT genes. In addition, the expression of OsMT genes was induced under different stresses, including NaCl, CdCl₂, ABA, and MeJ treatments. Additionally, we found that OsMT genes were mainly located in chloroplasts. These results imply that OsMT genes play different roles in response to these stresses. All results provide important insights into the evolution of the MT gene family in the Oryza genus, and will be helpful to further study the function of MT genes.

Genome-Wide Identification of Aquaporin Gene Family in Pitaya Reveals an HuNIP6;1 Involved in Flowering Process

Aquaporins (AQPs) are essential membrane proteins involved in seed maturation and germination, stomata movement, photosynthesis, and regulation of plant flowering processes. Pitaya flowers are open at night and wither at daybreak, which shows an obvious circadian rhythm. In this study, a comprehensive genome-wide analysis of AQPs in Hylocereus undantus was conducted to screen key genes associated with flowering processes. A total of 33 HuAQP genes were identified from the H. undantus genome. The 33 HuAQPs were grouped into four subfamilies: 10 PIPs, 13 TIPs, 8 NIPs, and 2 SIPs, which were distributed on 9 out of 11 pitaya chromosomes (Chr) (except for Chr7 and Chr10). Results from expression profiles showed that HuNIP6;1 may be involved in pitaya's floral opening. HuNIP6;1 was localized exclusively in the cell membrane. Overexpression of HuNIP6;1 in Arabidopsis thaliana significantly promoted early flowering through regulating negative flowering regulators of MJM30, COL9, and PRR5, suggesting that HuNIP6;1 plays key roles in regulating flowering time. The present study provides the first genome-wide analysis of the AQP gene family in pitaya and valuable information for utilization of HuAQPs.

Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula

Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 33 putative genes encoding full-length AQP sequences (BpeAQPs). They are grouped into five subfamilies, representing ten plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). The BpeAQP gene structure is conserved within each subfamily, with exon numbers ranging from one to five. The predictions of the aromatic/arginine selectivity filter (ar/R), Froger's positions, specificity-determining positions, and 2D and 3D biochemical properties indicate noticeable transport specificities to various non-aqueous substrates between members and/or subfamilies. Nevertheless, overall, the BpePIPs display mostly hydrophilic ar/R selective filter and lining-pore residues, whereas the BpeTIP, BpeNIP, BpeSIP, and BpeXIP subfamilies mostly contain hydrophobic permeation signatures. Transcriptional expression analyses indicate that 23 BpeAQP genes are transcribed, including five organ-related expressions. Surprisingly, no significant transcriptional expression is monitored in leaves in response to cold stress (6 °C), although interesting trends can be distinguished and will be discussed, notably in relation to the plasticity of this pioneer species, B. pendula. The current study presents the first detailed genome-wide analysis of the AQP gene family in a Betulaceae species, and our results lay a foundation for a better understanding of the specific functions of the BpeAQP genes in the responses of the silver birch trees to cold stress.

Aquaporins in regulation of plant protective responses to drought

Plasmolemma permeability is an integral indicator of the functional state of plant cells under stress. Aquaporins (AQPs), specialized transmembrane proteins that form water channels and play an important role in the adaptation of plants to adverse conditions and, in particular, to lack or excess of water, are involved in the formation of the response to drought. The main function of AQPs is to facilitate the movement of water across cell membranes and maintain aqueous cell homeostasis. Under stressful conditions, there is both an increase and decrease in the expression of individual aquaporin genes. Analysis of the data revealed differences in the expression of AQPs genes in stable and sensitive plant genotypes. It turned out that aquaporins in different stress-resistant varieties of the same species also respond differently to drought. The review provides brief information on the history of the discovery of aquaporins, the structure and function of these proteins, summarizes the latest information on the role of aquaporins in the regulation of metabolism and the response of plants to stressors, with particular emphasis on aquaporins in drought protection. The discovery and study of AQPs expands the possibilities of using genetic engineering methods for the selection of new plant species, in particular, more resistant to drought and salinization of the soil, as well as to increase their productivity. The use of aquaporins in biotechnology to improve drought resistance of various species has many prospects.

Integrated RNA-Seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots

Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice’s cold–stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold–stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold–stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.

Micro-Evolution Analysis Reveals Diverged Patterns of Polyol Transporters in Seven Gramineae Crops

Polyol transporters (PLTs), also called polyol/monosaccharide transporters, is of significance in determining plant development and sugar transportation. However, the diverged evolutionary patterns of the PLT gene family in Gramineae crops are still unclear. Here a micro-evolution analysis was performed among the seven Gramineae representative crops using whole-genome sequences, i.e., Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Oryza rufipogon (Or), Oryza sativa (Os), Sorghum bicolor (Sb), Setaria italica (Si), and Zea mays (Zm), leading to the identification of 12, 11, 12, 15, 20, 24, and 20 PLT genes, respectively. In this study, all PLT genes were divided into nine orthogroups (OGs). However, the number of PLT genes and the distribution of PLT OGs were not the same in these seven Gramineae species, and different OGs were also subject to different purification selection pressures. These results indicated that the PLT OGs of the PLT gene family have been expanded or lost unevenly in all tested species. Then, our results of gene duplication events confirmed that gene duplication events promoted the expansion of the PLT gene family in some Gramineous plants, namely, Bd, Or, Os, Si, Sb, and Zm, but the degree of gene family expansion, the type of PLT gene duplication, and the differentiation time of duplicate gene pairs varied greatly among these species. In addition, the sequence alignment and the internal repeat analysis of all PLTs protein sequences implied that the PLT protein sequences may originate from an internal repeat duplication of an ancestral six transmembrane helical units. Besides that, the protein motifs result highlighted that the PLT protein sequences were highly conserved, whereas the functional differentiation of the PLT genes was characterized by different gene structures, upstream elements, as well as co-expression analysis. The gene expression analysis of rice and maize showed that the PLT genes have a wide range of expression patterns, suggesting diverse biological functions. Taken together, our finding provided a perspective on the evolution differences and the functional characterizations of PLT genes in Gramineae representative crops.

The Tonoplast Intrinsic Protein Gene KvTIP3 is Responsive to Different Abiotic Stresses in Kosteletzkya virginica

In higher plants, aquaporin proteins (AQPs) play important roles in the uptake of water across cell membranes. However, their functions in halophytes are still largely unknown. In this work, we isolated, cloned, and identified KvTIP3, a tonoplast intrinsic protein gene from Kosteletzkya virginica. Bioinformatic analyses demonstrated that KvTIP3 encoded a tonoplast protein with the common properties of AQPs. Further multiple sequence alignment and phylogenetic analyses showed that KvTIP3 shared 65%–82% homology with other AQPs from Arabidopsis, cotton, polar, and cocoa. Quantitative real-time PCR (qPCR) analyses revealed that KvTIP3 was ubiquitously expressed in various tissues such as leaves, stems, and roots, with a predominant expression in roots. In addition, KvTIP3 transcript was strongly induced by NaCl, low temperature, and ABA in K. virginica. Our findings suggest that KvTIP3 encodes a new AQP possibly involved in multiple abiotic stress responses in K. virginica, and KvTIP3 could be used as a potential candidate gene for the improvement of plants resistant to various abiotic stresses.

Plant Aquaporins: Diversity, Evolution and Biotechnological Applications

The plasma membrane forms a permeable barrier that separates the cytoplasm from the external environment, defining the physical and chemical limits in each cell in all organisms. The movement of molecules and ions into and out of cells is controlled by the plasma membrane as a critical process for cell stability and survival, maintaining essential differences between the composition of the extracellular fluid and the cytosol. In this process aquaporins (AQPs) figure as important actors, comprising highly conserved membrane proteins that carry water, glycerol and other hydrophilic molecules through biomembranes, including the cell wall and membranes of cytoplasmic organelles. While mammals have 15 types of AQPs described so far (displaying 18 paralogs), a single plant species can present more than 120 isoforms, providing transport of different types of solutes. Such aquaporins may be present in the whole plant or can be associated with different tissues or situations, including biotic and especially abiotic stresses, such as drought, salinity or tolerance to soils rich in heavy metals, for instance. The present review addresses several aspects of plant aquaporins, from their structure, classification, and function, to in silico methodologies for their analysis and identification in transcriptomes and genomes. Aspects of evolution and diversification of AQPs (with a focus on plants) are approached for the first time with the aid of the LCA (Last Common Ancestor) analysis. Finally, the main practical applications involving the use of AQPs are discussed, including patents and future perspectives involving this important protein family.

Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum)

Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioning in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play a critical role in abiotic stress response pathways of plants. As a species closely related to Arabidopsis thaliana, Eutrema salsugineum has been proposed as a model for studying salt resistance in plants. Here we surveyed 35 full-length AQP genes in E. salsugineum, which could be grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), nine NOD-like intrinsic proteins (NIPs), and three small basic intrinsic proteins (SIPs) by phylogenetic analysis. EsAQPs were comprised of 237-323 amino acids, with a theoretical molecular weight (MW) of 24.31-31.80 kDa and an isoelectric point (pI) value of 4.73-10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger's position and specificity-determining position suggested quite differences in substrate specificities of EsAQPs. EsAQPs exhibited global expressions in all organs as shown by gene expression profiles and should be play important roles in response to salt, cold and drought stresses. This study provides comprehensive bioinformation on AQPs in E. salsugineum, which would be helpful for gene function analysis for further studies.

Crystal structure of the Siderophore-interacting protein SIP from Aeromonas hydrophila

Siderophores acquire iron from hosts under iron-limiting conditions and play an essential role in the survival of microorganisms. Siderophore-interacting proteins (SIPs) from microbes release iron from the siderophore complex by reducing ferric iron to ferrous iron, but the molecular mechanism of iron reduction remains unclear. To better understand the molecular mechanism of SIPs, we herein report the crystal structure of Aeromonas hydrophila SIP (AhSIP) in complex with flavin adenine dinucleotide (FAD) as a cofactor. AhSIP consists of an N-terminal FAD binding domain and a C-terminal NADH binding domain, which are connected by a linker region. AhSIP showed unique structural differences in the orientation of the cofactor binding lobes when compared with SIP homologs. This study identified a cluster of three basic residues (Lys48, His259 and Arg262) in AhSIP distributed around a potential substrate binding pocket. In addition, AhSIP, containing the NADH binding motif E(L)VL-X₃-GE, belongs to the group I subfamily. Our results show the diverse cofactor and substrate binding sites of the SIP family.

Genome-wide identification and expression analysis of aquaporin gene family related to abiotic stress in watermelon

The plant aquaporins (AQPs) are highly conserved integral membrane proteins that participate in multiple developmental processes and responses to various stresses. In this study, a total of 35 AQP genes were identified in the watermelon genome. The phylogenetic analysis showed that these AQPs can be divided into five types, including 16 plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight nodulin 26-like intrinsic proteins (NIPs), two small basic intrinsic proteins (SIPs), and one uncategorized X intrinsic protein (XIP). A number of cis-elements related to plant responses to hormones and stresses were detected in the promoter sequences of ClAQP genes. Chromosome distribution analysis revealed that the genes are unevenly distributed on eight chromosomes, with chromosomes 1 and 4 possessing the most genes. Expression analysis at different developmental stages in flesh and rind indicated that most of ClAQPs have tissue-specific expression. Meanwhile, some other AQP genes showed differential expression in response to cold, salt, and ABA treatments, which is consistent with the organization of the stress-responsive cis-elements detected in the promoter regions. Our results lay a foundation for understanding the specific functions of ClAQP genes to help the genetic improvement of watermelon.

Genome-Wide Identification of Na+/H+ Antiporter (NHX) Genes in Sugar Beet (Beta vulgaris L.) and Their Regulated Expression under Salt Stress

Salinity is one of the major environment factors that limits the growth of plants and the productivity of crops worldwide. It has been shown that Na+ transporters play a central role in salt tolerance and development of plants. The objective of this study was to identify Na+/H+ antiporter (NHX) genes and investigate their expression patterns in sugar beet (Beta vulgaris L.) subjected to various concentrations of NaCl. A total of five putative NHX genes were identified and distributed on four chromosomes in sugar beet. Phylogenetic analysis revealed that these BvNHX genes are grouped into three major classes, viz Vac- (BvNHX1, -2 and -3), Endo- (BvNHX4), and PM-class NHX (BvNHX5/BvSOS1), and within each class the exon/intron structures are conserved. The amiloride-binding site is found in TM3 at N-terminus of Vac-class NHX proteins. Protein-protein interaction (PPI) prediction suggested that only BvNHX5 putatively interacts with calcineurin B-like proteins (CBL) and CBL-interacting protein kinases (CIPK), implying it might be the primary NHX involved in CBL-CIPK pathway under saline condition. It was also found that BvNHX5 contains one abscisic acid (ABA)-responsive element (ABRE), suggesting that BvNHX5 might be involved in ABA signal responsiveness. Additionally, the qRT-PCR analysis showed that all the BvNHX genes in both roots and leaves are significantly up-regulated by salt, and the transcription levels under high salinity are significantly higher than those under either low or moderate salinity. Taken together, this work gives a detailed overview of the BvNHX genes and their expression patterns under salt stress. Our findings also provide useful information for elucidating the molecular mechanisms of Na+ homeostasis and further functional identification of the BvNHX genes in sugar beet.

Expansion and Evolutionary Patterns of Glycosyltransferase Family 8 in Gramineae Crop Genomes and Their Expression under Salt and Cold Stresses in Oryza sativa ssp. japonica

Plant cell walls play a fundamental role in several ways, providing structural support for cells, resistance against pathogens and facilitating the communication between cells. The glycosyltransferase family 8 (GT8) is involved in the formation of the plant cell wall. However, the evolutionary relationship and the functional differentiation of this important gene family remain obscure in Gramineae crop genomes. In the present investigation, we identified 269 GT8 genes in the seven Gramineae representative crop genomes, namely, 33 in Hordeum vulgare, 37 in Brachypodium distachyon, 40 in Oryza sativa ssp. japonica, 41 in Oryza rufipogon, 36 in Setaria italica, 37 in Sorghum bicolor, and 45 in Zea mays. Phylogenetic analysis suggested that all identified GT8 proteins belonged to seven subfamilies: galacturonosyltransferase (GAUT), galacturonosyltransferase-like (GATL), GATL-related (GATR), galactinol synthase (GolS), and plant glycogenin-like starch initiation proteins A (PGSIP-A), PGSIP-B, and PGSIP-C. We estimated that the GAUT subfamily might be further divided into four subgroups (I–IV) due to differentiation of gene structures and expression patterns. Our orthogroup analysis identified 22 orthogroups with different sizes. Of these orthogroups, several orthogroups were lost in some species, such as S. italica and Z. mays. Moreover, lots of duplicate pairs and collinear pairs were discovered among these species. These results indicated that multiple duplication modes led to the expansion of this important gene family and unequal loss of orthogroups and subfamilies might have happened during the evolutionary process. RNA-seq, microarray analysis, and qRT-PCR analyses indicated that GT8 genes are critical for plant growth and development, and for stresses responses. We found that OsGolS1 was significantly up-regulated under salt stress, while OsGAUT21, OsGATL2, and OsGATL5 had remarkable up-regulation under cold stress. The current study highlighted the expansion and evolutionary patterns of the GT8 gene family in these seven Gramineae crop genomes and provided potential candidate genes for future salt- and cold- resistant molecular breeding studies in O. sativa.

Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as "photosynthesis" and "starch and sucrose metabolism," were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.

Integrated approaches to study the drought tolerance mechanism in hot pepper (Capsicum annuum L.)

Drought is one of the predominant abiotic stresses which have phenomenal impact on crop productivity. Alterations in aquaporin gene expressions are part of complex molecular responses by plant in response to drought. To better understand the role of aquaporins in economically important crop chilli (Capsicum annuum), drought induced gene expression of twelve aquaporins was determined in drought tolerant-KCa-4884 and drought susceptible-G-4 genotypes. Conjointly, the effect of drought on leaf water status and photosynthetic parameters were evaluated. Gene expression of all examined 12 aquaporins was up-regulated in KCa-4884 and in contrast, all the aquaporin genes were down-regulated in G-4 under drought stress. Significant variations among two chilli genotypes have been recorded in photosynthetic rate (P _n ), stomatal conductance (G _s ), and relative water content (RWC), sub-stomatal CO₂ concentration (C _i ). KCa-4884 revealed significantly high rates of P _n and RWC and decreased G _s under water deficit conditions providing evidence for superior drought adaptive strategies. Differences in physiological parameters illustrate prevention of water loss during drought. Up-regulation of aquaporins in drought tolerant genotype implicates their possible role in water relations and photosynthetic performance even under extended drought conditions.

A Novel Insight into Functional Divergence of the MST Gene Family in Rice Based on Comprehensive Expression Patterns

Sugars are critical for plant growth and development as suppliers of carbon and energy, as signal molecules, or as solute molecules for osmotic homeostasis. Monosaccharide transporter (MST) genes are involved in various processes of plant growth and development as well as in response to abiotic stresses. However, the evolution and their roles of MST genes in growth and development and in coping with abiotic stresses in rice are poorly known. Here, we identified 64 MST genes in rice genome, which are classified into seven subfamilies: STP, PLT, AZT, ERD, pGlcT, INT, and XTPH. MST genes are not evenly distributed between chromosomes (Chrs) with a bias to Chr 3, 4, 7, and 11, which could be a result of duplication of fragments harboring MST genes. In total, 12 duplication events were found in the rice MST family, among which, two pairs were derived from fragmental duplications and ten pairs were from tandem duplications. The synonymous and nonsynonymous substitution rates of duplicate gene pairs demonstrated that the MST family was under a strong negative selection during the evolution process. Furthermore, a comprehensive expression analysis conducted in 11 different tissues, three abiotic stresses, five hormone treatments, and three sugar treatments revealed different expression patterns of MST genes and indicated diversified functions of them. Our results suggest that MST genes play important roles not only in various abiotic stresses but also in hormone and sugar responses. The present results will provide a vital insight into the functional divergence of the MST family in the future study.

Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica

Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were identified in O. sativa ssp. japonica, O. sativa ssp. indica, Oryza rufipogon, Oryza nivara, Oryza punctata, and Oryza glumaepatula, respectively. Gene duplication events, structural features, conserved motifs, a phylogenetic analysis, chromosome locations, and Ka/Ks ratios of this important family were found to be strictly conservative across these six Oryza species/subspecies, suggesting that the expansion of the GH3 gene family in Oryza species might be attributed to duplication events, and this expansion could occur in the common ancestor of Oryza species, even in common ancestor of rice tribe (Oryzeae) (23.07~31.01 Mya). The RNA-seq results of different tissues displayed that OsGH3 genes had significantly different expression profiles. Remarkably, the qRT-PCR result after NaCl treatment indicated that the majority of OsGH3 genes play important roles in salinity stress, especially OsGH3-2 and OsGH3-8. This study provides important insights into the evolution of the GH3 gene family in Oryza species and will assist with further investigation of OsGH3 genes’ functions under salinity stress.

Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family in Oryza Genus

The SPL (SQUAMOSA promoter binding protein-like) gene family is one of the plant-specific transcription factor families and controls a considerable number of biological functions, including floral development, phytohormone signaling, and toxin resistance. However, the evolutionary patterns and driving forces of SPL genes in the Oryza genus are still not well-characterized. In this study, we investigated a total of 105 SPL genes from six AA genome Oryza representative species (O. barthii, O. glumipatula, O. nivara, O. rufipogon, O. glaberrima, and O. sativa). Phylogenetic and motif analyses indicated that SPL proteins could be divided into two distinct lineages (I and II), and further studies showed lineage II consisted of three clades (IIA, IIB, and IIC). We found that clade I had comparable structural features with clade IIA, whereas genes in clade IIC displayed intrinsic differences, such as lower exon numbers and the presence of miR156 regulation elements. Nineteen orthologous groups of OsSPLs in Oryza were also identified, and most exons within those genes maintained constant length, whereas length of intron changed relatively. All groups were constrained by stronger purifying selection and diversified continually including alterative gene number, intron length, and miR156 regulation. Subsequently, cis-acting element analyses revealed the potential role of SPLs in wild rice, which might participate in light-responsive, phytohormone response, and plant growth and development. Our results shed light on that different evolutionary rates and duplication events might result in divergent evolutionary patterns in each lineage of SPL genes, providing a guide in exploring diverse function in the rice gene family among six closely related Oryza species.

Genome-Wide Identification and Characterization of Aquaporins and Their Role in the Flower Opening Processes in Carnation (Dianthus caryophyllus)

Aquaporins (AQPs) are associated with the transport of water and other small solutes across biological membranes. Genome-wide identification and characterization will pave the way for further insights into the AQPs’ roles in the commercial carnation (Dianthus caryophyllus). This study focuses on the analysis of AQPs in carnation (DcaAQPs) involved in flower opening processes. Thirty DcaAQPs were identified and grouped to five subfamilies: nine PIPs, 11 TIPs, six NIPs, three SIPs, and one XIP. Subsequently, gene structure, protein motifs, and co-expression network of DcaAQPs were analyzed and substrate specificity of DcaAQPs was predicted. qRT-PCR, RNA-seq, and semi-qRTRCR were used for DcaAQP genes expression analysis. The analysis results indicated that DcaAQPs were relatively conserved in gene structure and protein motifs, that DcaAQPs had significant differences in substrate specificity among different subfamilies, and that DcaAQP genes’ expressions were significantly different in roots, stems, leaves and flowers. Five DcaAQP genes (DcaPIP1;3, DcaPIP2;2, DcaPIP2;5, DcaTIP1;4, and DcaTIP2;2) might play important roles in flower opening process. However, the roles they play are different in flower organs, namely, sepals, petals, stamens, and pistils. Overall, this study provides a theoretical basis for further functional analysis of DcaAQPs.