Genome-wide identification and expression analysis of detoxification efflux carriers (DTX) genes family under abiotic stresses in flax

Genome-wide identification and characterization of DTX family genes highlighting their locations, functions, and regulatory factors in banana (Musa acuminata)

The detoxification efflux carriers (DTX) are a significant group of multidrug efflux transporter family members that play diverse functions in all kingdoms of living organisms. However, genome-wide identification and characterization of DTX family transporters have not yet been performed in banana, despite its importance as an economic fruit plant. Therefore, a detailed genome-wide analysis of DTX family transporters in banana (Musa acuminata) was conducted using integrated bioinformatics and systems biology approaches. In this study, a total of 37 DTX transporters were identified in the banana genome and divided into four groups (I, II, III, and IV) based on phylogenetic analysis. The gene structures, as well as their proteins' domains and motifs, were found to be significantly conserved. Gene ontology (GO) annotation revealed that the predicted DTX genes might play a vital role in protecting cells and membrane-bound organelles through detoxification mechanisms and the removal of drug molecules from banana cells. Gene regulatory analyses identified key transcription factors (TFs), cis-acting elements, and post-transcriptional regulators (miRNAs) of DTX genes, suggesting their potential roles in banana. Furthermore, the changes in gene expression levels due to pathogenic infections and non-living factor indicate that banana DTX genes play a role in responses to both biotic and abiotic stresses. The results of this study could serve as valuable tools to improve banana quality by protecting them from a range of environmental stresses.

Glutamate Receptor-like (GLR) Family in Brassica napus: Genome-Wide Identification and Functional Analysis in Resistance to Sclerotinia sclerotiorum

Plant glutamate receptor-like channels (GLRs) are homologs of animal ionotropic glutamate receptors. GLRs are critical in various plant biological functions, yet their genomic features and functions in disease resistance remain largely unknown in many crop species. Here, we report the results on a thorough genome-wide study of the GLR family in oilseed rape (Brassica napus) and their role in resistance to the fungal pathogen Sclerotinia sclerotiorum. A total of 61 GLRs were identified in oilseed rape. They comprised three groups, as in Arabidopsis thaliana. Detailed computational analyses, including prediction of domain and motifs, cellular localization, cis-acting elements, PTM sites, and amino acid ligands and their binding pockets in BnGLR proteins, unveiled a set of group-specific characteristics of the BnGLR family, which included chromosomal distribution, motif composition, intron number and size, and methylation sites. Functional dissection employing virus-induced gene silencing of BnGLRs in oilseed rape and Arabidopsis mutants of BnGLR homologs demonstrated that BnGLR35/AtGLR2.5 positively, while BnGLR12/AtGLR1.2 and BnGLR53/AtGLR3.2 negatively, regulated plant resistance to S. sclerotiorum, indicating that GLR genes were differentially involved in this resistance. Our findings reveal the complex involvement of GLRs in B. napus resistance to S. sclerotiorum and provide clues for further functional characterization of BnGLRs.

Comparative transcriptome analysis and Arabidopsis thaliana overexpression reveal key genes associated with cadmium transport and distribution in root of two Capsicum annuum cultivars

The molecular mechanisms underlying high and low cadmium (Cd) accumulation in hot pepper cultivars remain unclear. In this study, comparative transcriptome analysis of root between high-Cd (J) and low-Cd (Z) cultivars was conducted under hydroponic cultivation with 0 and 0.4 mg/L Cd, respectively. The results showed that J enhanced the root uptake of Cd by elevating the expression of Nramp5 and counteracting Cd toxicity by increasing the expression of genes, such as NIR1, GLN1, and IAA9. Z reduced Cd accumulation by enhancing the cell wall lignin synthesis genes PAL, COMT, 4CL, LAC, and POD and the Cd transporters ABC, MTP1, and DTX1. Elevated expression of genes related to sulfur metabolism was observed in Z, potentially contributing to its ability to detoxify Cd. To investigate the function of CaCOMT1, an Arabidopsis thaliana overexpression line (OE-CaCOMT1) was constructed. The results revealed that OE-CaCOMT1 drastically increased the lignin content by 38-42% and reduced the translocation of Cd to the aboveground parts by 32%. This study provides comprehensive insights into the mechanisms underlying Cd accumulation in hot pepper cultivars using transcriptome analysis. Moreover, this study elucidates the critical function of CaCOMT1, providing a theoretical foundation for the production of low-Cd vegetables for food safety.

Genome-wide identification and expression pattern analysis of the MATE gene family in carmine radish (Raphanus sativus L.)

Carmine radish (Raphanus sativus L.) is famousforcontaininganaturalredpigment(redradishpigment) that grown in Fuling, Chongqing City, China. MATE (multidrug and toxic compound extrusion), as an integral member of the multidrug efflux transporter family, has various functions in plants. However, noinformationhasbeenavailableaboutcharacteristicsoftheMATEgenefamily in carmine radish. In this study, total of 85 candidate MATE gene family members classifiedinto 4 groups were identified and foundtobewidelyandrandomlydistributedindifferent genome. Synteny analysis revealed that twenty-one segmental and ten tandem duplications acted as important regulators for the expansion of RsMATE genes. The Ka/Ks ratios of RsMATE indicated that RsMATE may have undergone intense purification in the radish genome. Cis-acting element analysis of RsMATE in the promoter region indicated that RsMATE were mainly related to the abiotic stress response and phytohormone. Quantitative real-time polymerase chain reaction (qRT-PCR) showed that RsMATE40-b, RsMATE16-b and RsMATE13-a genes were significantly expressed under ABA (abscisic acid) and NaCl stress treatments respectively. In addition, the expression patterns of fifteen key RsMATE genes were investigated in 'XCB' (Xichangbai) and 'HX' (Hongxin) roots under Cadmium (Cd) stress for different treatment times using qRT-PCR, of those, RsMATE49-b, RsMATE33 and RsMATE26 transcripts were strongly altered at different time points in XCB responsive to Cd stress,compared to HX. This study will provide valuable insights for studying the functional characterization of the MATE gene in carmine radish and other plants.

Physiological and molecular mechanisms of boron in alleviating cadmium toxicity in Capsicum annuum

Soil cadmium (Cd) contamination threatens food safety and human health, particularly in developing countries. Previously, we have proposed that boron (B) could reduce Cd uptake and accumulation in hot peppers (Capsicum annuum) by regulating the expression of genes related to Cd transport in roots. However, only few studies have examined the role of B in plant leaves under Cd stress. It is unclear how B induces the expression of relevant genes and metabolites in hot pepper leaves and to what extent B is involved in leaf growth and Cd accumulation. The purpose of this study was to investigate the effects of B on growth and Cd accumulation in hot pepper leaves by determining physiological parameters and transcriptome sequencing. The results showed that B application significantly improved the concentration of chlorophyll a and intercellular CO2, stomatal conductance, and photosynthetic and transpiration rates by 18-41 % in Cd-stressed plants. Moreover, B enhanced Cd retention in the cell wall by upregulating the expression levels of pectin-, lignin-, and callose-related genes and improving the activity of pectin methylesterase by 30 %, resulting in an approximate 31 % increase in Cd retention in the cell wall. Furthermore, B application not only enhanced the expression levels of genes related to antioxidant enzymes (superoxide dismutase, catalase, and peroxidase) and their activities by 28-40 %, thereby counteracting Cd-induced oxidative stress, but also improved Cd chelation, sequestration, and exclusion by upregulating the expression levels of genes related to sulfur metabolism, heavy metal-associated isoprenylated plant protein (HIPP), and transporters such as vacuolar cation/proton exchanger (CAX3), metal-nicotianamine transporter (YSL), ATP-binding cassette (ABC), zinc/iron transporters (ZIP) and oxic-compound detoxification (DTX), ultimately reinforcing Cd tolerance. Together, our results suggest that B application reduces the negative effects of Cd on leaf growth, promotes photosynthesis, and decreases Cd transfer to fruits through its sequestration and retention.

Genome-wide identification and expression profile analysis of metal tolerance protein gene family in Eucalyptus grandis under metal stresses

Metal tolerance proteins (MTPs) as Me²⁺/H⁺(K⁺) antiporters participate in the transport of divalent cations, leading to heavy metal stress resistance and mineral utilization in plants. In the present study, to obtain better knowledge of the biological functions of the MTPs family, 20 potential EgMTPs genes were identified in Eucalyptus grandis and classified into seven groups belonging to three cation diffusion facilitator groups (Mn-CDFs, Zn/Fe-CDFs, and Zn-CDFs) and seven groups. EgMTP-encoded amino acids ranged from 315 to 884, and most of them contained 4-6 recognized transmembrane domains and were clearly prognosticated to localize into the cell vacuole. Almost all EgMTP genes experienced gene duplication events, in which some might be uniformly distributed in the genome. The numbers of cation efflux and the zinc transporter dimerization domain were highest in EgMTP proteins. The promoter regions of EgMTP genes have different cis-regulatory elements, indicating that the transcription rate of EgMTP genes can be a controlled response to different stimuli in multiple pathways. Our findings provide accurate perception on the role of the predicted miRNAs and the presence of SSR marker in the Eucalyptus genome and clarify their functions in metal tolerance regulation and marker-assisted selection, respectively. Gene expression profiling based on previous RNA-seq data indicates a probable function for EgMTP genes during development and responses to biotic stress. Additionally, the upregulation of EgMTP6, EgMTP5, and EgMTP11.1 to excess Cd²⁺ and Cu²⁺ exposure might be responsible for metal translocation from roots to leaves.

Salt Stress Tolerance in Casuarina glauca: Insights from the Branchlets Transcriptome

Climate change and the accelerated rate of population growth are imposing a progressive degradation of natural ecosystems worldwide. In this context, the use of pioneer trees represents a powerful approach to reverse the situation. Among others, N₂-fixing actinorhizal trees constitute important elements of plant communities and have been successfully used in land reclamation at a global scale. In this study, we have analyzed the transcriptome of the photosynthetic organs of Casuarina glauca (branchlets) to unravel the molecular mechanisms underlying salt stress tolerance. For that, C. glauca plants supplied either with chemical nitrogen (KNO₃⁺) or nodulated by Frankia (NOD⁺) were exposed to a gradient of salt concentrations (200, 400, and 600 mM NaCl) and RNA-Seq was performed. An average of ca. 25 million clean reads was obtained for each group of plants, corresponding to 86,202 unigenes. The patterns of differentially expressed genes (DEGs) clearly separate two groups: (i) control- and 200 mM NaCl-treated plants, and (ii) 400 and 600 mM NaCl-treated plants. Additionally, although the number of total transcripts was relatively high in both plant groups, the percentage of significant DEGs was very low, ranging from 6 (200 mM NaCl/NOD⁺) to 314 (600 mM NaCl/KNO₃⁺), mostly involving down-regulation. The vast majority of up-regulated genes was related to regulatory processes, reinforcing the hypothesis that some ecotypes of C. glauca have a strong stress-responsive system with an extensive set of constitutive defense mechanisms, complemented by a tight mechanism of transcriptional and post-transcriptional regulation. The results suggest that the robustness of the stress response system in C. glauca is regulated by a limited number of genes that tightly regulate detoxification and protein/enzyme stability, highlighting the complexity of the molecular interactions leading to salinity tolerance in this species.

Integrated omics approaches for flax improvement under abiotic and biotic stress: Current status and future prospects

Flax (Linum usitatissimum L.) or linseed is one of the important industrial crops grown all over the world for seed oil and fiber. Besides oil and fiber, flax offers a wide range of nutritional and therapeutic applications as a feed and food source owing to high amount of α-linolenic acid (omega-3 fatty acid), lignans, protein, minerals, and vitamins. Periodic losses caused by unpredictable environmental stresses such as drought, heat, salinity-alkalinity, and diseases pose a threat to meet the rising market demand. Furthermore, these abiotic and biotic stressors have a negative impact on biological diversity and quality of oil/fiber. Therefore, understanding the interaction of genetic and environmental factors in stress tolerance mechanism and identification of underlying genes for economically important traits is critical for flax improvement and sustainability. In recent technological era, numerous omics techniques such as genomics, transcriptomics, metabolomics, proteomics, phenomics, and ionomics have evolved. The advancements in sequencing technologies accelerated development of genomic resources which facilitated finer genetic mapping, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection in major cereal and oilseed crops including flax. Extensive studies in the area of genomics and transcriptomics have been conducted post flax genome sequencing. Interestingly, research has been focused more for abiotic stresses tolerance compared to disease resistance in flax through transcriptomics, while the other areas of omics such as metabolomics, proteomics, ionomics, and phenomics are in the initial stages in flax and several key questions remain unanswered. Little has been explored in the integration of omic-scale data to explain complex genetic, physiological and biochemical basis of stress tolerance in flax. In this review, the current status of various omics approaches for elucidation of molecular pathways underlying abiotic and biotic stress tolerance in flax have been presented and the importance of integrated omics technologies in future research and breeding have been emphasized to ensure sustainable yield in challenging environments.

Genome-Wide Analysis of Multidrug and Toxic Compound Extruction Transporters in Grape

Grape (Vitis vinifera L.) is an important fruit crop in the world. It is used as a table grape and is also used for raisin and wine production. Grape berries accumulate secondary metabolites, such as anthocyanins, tannins, and resveratrol, which are known as functional compounds for human health. Multidrug and toxic compound extrusion transporter (MATEs) transport secondary metabolites. MATEs also transport other solutes, including organic acids, and toxic xenobiotics, depending on cation gradient and play various roles in plants. MATE comprises 300-500 amino acid residues and possesses a MATE domain and 8-12 transmembrane domains. In the present study, 59 MATE genes were identified in the grape genome, and phylogenetic analysis revealed the presence of four groups of grape MATEs (Group 1-4). Their information, such as gene structures, protein motifs, predicted subcellular localizations, and gene IDs of four genome annotations, that is, CRIBI v1, CRIBI v2, Genoscope, and Vcost v3, were annotated. The transport substrates and physiological functions of grape MATEs were estimated based on their homology with the analyzed MATEs in other plant species. Group 1 may transport toxic compounds and alkaloids, Group 2 may transport polyphenolic compounds, Group 3 may transport organic acids, and Group 4 may transport plant hormones related to signal transduction. In addition to the known anthocyanin transporters, VvMATE37 and VvMATE39, a novel anthocyanin transporter, VvMATE38 in Group 2, was suggested as a key transporter for anthocyanin accumulation in grape berry skin. VvMATE46, VvMATE47, and VvMATE49 in Group 3 may contribute to Al³⁺ detoxification and Fe²⁺/Fe³⁺ translocation via organic acid transport. This study provides helpful and fundamental information for grape MATE studies and resolves the confusion of gene IDs in different genome annotations.

Comparative Transcriptomics Analysis of Roots and Leaves under Cd Stress in Calotropis gigantea L

Calotropis gigantea is often found in mining areas with heavy metal pollution. However, little is known about the physiological and molecular response mechanism of C. gigantea to Cd stress. In the present study, Cd tolerance characteristic of C. gigantea and the potential mechanisms were explored. Seed germination test results showed that C. gigantea had a certain Cd tolerance capacity. Biochemical and transcriptomic analysis indicated that the roots and leaves of C. gigantea had different responses to early Cd stress. A total of 176 and 1618 DEGs were identified in the roots and leaves of C. gigantea treated with Cd compared to the control samples, respectively. Results indicated that oxidative stress was mainly initiated in the roots of C. gigantea, whereas the leaves activated several Cd detoxification processes to cope with Cd, including the upregulation of genes involved in Cd transport (i.e., absorption, efflux, or compartmentalization), cell wall remodeling, antioxidant system, and chelation. This study provides preliminary information to understand how C. gigantea respond to Cd stress, which is useful for evaluating the potential of C. gigantea in the remediation of Cd-contaminated soils.

A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants

Multidrug and toxic compound extrusion (MATE) transporters comprise a multigene family that mediates multiple functions in plants through the efflux of diverse substrates including organic molecules, specialized metabolites, hormones, and xenobiotics. MATE classification based on genome-wide studies remains ambiguous, likely due to a lack of large-scale phylogenomic studies and/or reference sequence datasets. To resolve this, we established a phylogeny of the plant MATE gene family using a comprehensive kingdom-wide phylogenomic analysis of 74 diverse plant species. We identified more than 4,000 MATEs, which were classified into 14 subgroups based on a systematic bioinformatics pipeline using USEARCH, blast+ and synteny network tools. Our classification was performed using a four-step process, whereby MATEs sharing ≥ 60% protein sequence identity with a ≤ 1E-05 threshold at different sequence lengths (either full-length, ≥ 60% length, or ≥ 150 amino acids) or retaining in the similar synteny blocks were assigned to the same subgroup. In this way, we assigned subgroups to 95.8% of the identified MATEs, which we substantiated using synteny network clustering analysis. The subgroups were clustered under four major phylogenetic groups and named according to their clockwise appearance within each group. We then generated a reference sequence dataset, the usefulness of which was demonstrated in the classification of MATEs in additional species not included in the original analysis. Approximately 74% of the plant MATEs exhibited synteny relationships with angiosperm-wide or lineage-, order/family-, and species-specific conservation. Most subgroups evolved independently, and their distinct evolutionary trends were likely associated with the development of functional novelties or the maintenance of conserved functions. Together with the systematic classification and synteny network profiling analyses, we identified all the major evolutionary events experienced by the MATE gene family in plants. We believe that our findings and the reference dataset provide a valuable resource to guide future functional studies aiming to explore the key roles of MATEs in different aspects of plant physiology. Our classification framework can also be readily extendable to other (super) families.

Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress

Metal tolerance proteins (MTPs) encompass plant membrane divalent cation transporters to specifically participate in heavy metal stress resistance and mineral acquisition. However, the molecular behaviors and biological functions of this family in Medicago truncatula are scarcely known. A total of 12 potential MTP candidate genes in the M. truncatula genome were successfully identified and analyzed for a phylogenetic relationship, chromosomal distributions, gene structures, docking analysis, gene ontology, and previous gene expression. M. truncatula MTPs (MtMTPs) were further classified into three major cation diffusion facilitator (CDFs) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The structural analysis of MtMTPs displayed high gene similarity within the same group where all of them have cation_efflux domain or ZT_dimer. Cis-acting element analysis suggested that various abiotic stresses and phytohormones could induce the most MtMTP gene transcripts. Among all MTPs, PF16916 is the specific domain, whereas GLY, ILE, LEU, MET, ALA, SER, THR, VAL, ASN, and PHE amino acids were predicted to be the binding residues in the ligand-binding site of all these proteins. RNA-seq and gene ontology analysis revealed the significant role of MTP genes in the growth and development of M. truncatula. MtMTP genes displayed differential responses in plant leaves, stems, and roots under five divalent heavy metals (Cd²⁺, Co²⁺, Mn²⁺, Zn²⁺, and Fe²⁺). Ten, seven, and nine MtMTPs responded to at least one metal ion treatment in the leaves, stems, and roots, respectively. Additionally, MtMTP1.1, MtMTP1.2, and MtMTP4 exhibited the highest expression responses in most heavy metal treatments. Our results presented a standpoint on the evolution of MTPs in M. truncatula. Overall, our study provides a novel insight into the evolution of the MTP gene family in M. truncatula and paves the way for additional functional characterization of this gene family.

Genome-wide identification, characterization and expression analysis of MATE family genes in apple (Malus × domestica Borkh)

BACKGROUND

As an important group of the multidrug efflux transporter family, the multidrug and toxic compound extrusion (MATE) family has a wide range of functions and is distributed in all kingdoms of living organisms. However, only two MATE genes in apple have been analyzed and genome-wide comprehensive analysis of MATE family is needed.

RESULTS

In this study, a total of 66 MATE (MdMATE) candidates encoding putative MATE transporters were identified in the apple genome. These MdMATE genes were classified into four groups by phylogenetic analysis with MATE genes in Arabidopsis. Synteny analysis reveals that whole genome duplication (WGD) and segmental duplication events played a major role in the expansion of MATE gene family in apple. MdMATE genes show diverse expression patterns in different tissues/organs and developmental stages. Analysis of cis-regulatory elements in MdMATE promoter regions indicates that the function of MdMATE genes is mainly related to stress response. Besides, the changes of gene expression levels upon different pathogen infections reveal that MdMATE genes are involved in biotic stress response.

CONCLUSIONS

In this work, we systematically identified MdMATE genes in apple genome using a set of bioinformatics approaches. Our comprehensive analysis provided valuable resources for improving disease resistance in apple and further functional characterization of MATE genes in other species.

Non-glandular trichomes of sunflower are important in the absorption and translocation of foliar-applied Zn

Trichomes are potentially important for absorption of foliar fertilizers. A study has shown that the non-glandular trichromes (NGTs) of sunflower (Helianthus annuus) accumulated high concentrations of foliar-applied zinc (Zn); however, the mechanisms of Zn accumulation in the NGTs and the fate of this Zn are unclear. Here we investigated how foliar-applied Zn accumulates in the NGTs and the subsequent translocation of this Zn. Time-resolved synchrotron-based X-ray fluorescence microscopy and transcriptional analyses were used to probe the movement of Zn in the NGTs, with the cuticle composition of the NGTs examined using confocal Raman microscopy. The accumulation of Zn in the NGTs is both an initial preferential absorption process and a subsequent translocation process. This preferred absorption is likely because the NGT base has a higher hydrophilicity, whilst the subsequent translocation is due to the presence of plasmodesmata, Zn-chelating ligands, and Zn transporters in the NGTs. Furthermore, the Zn sequestered in the NGTs was eventually translocated out of the trichome once the leaf Zn concentration had decreased, suggesting that the NGTs are also important in maintaining leaf Zn homeostasis. This study demonstrates for the first time that trichomes have a key structural and functional role in the absorption and translocation of foliar-applied Zn.

Genome-Wide Identification of MATE Gene Family in Potato (Solanum tuberosum L.) and Expression Analysis in Heavy Metal Stress

A genome-wide identification and expression analysis of multidrug and toxic compound extrusion (MATE) gene family in potato was carried out to explore the response of MATE proteins to heavy meta stress. In this study, we identified 64 MATE genes from potato genome, which are located on 12 chromosomes, and are divided into I–IV subfamilies based on phylogenetic analysis. According to their order of appearance on the chromosomes, they were named from StMATE1–64. Subcellular location prediction showed that 98% of them are located on the plasma membrane as transporters. Synteny analysis showed that five pairs of collinearity gene pairs belonged to members of subfamily I and subfamily II had two pairs indicating that the duplication is of great significance to the evolution of genes in subfamilies I and II. Gene exon–intron structures and motif composition are more similar in the same subfamily. Every StMATE gene contained at least one cis-acting element associated with regulation of hormone transport. The relative expression levels of eight StMATE genes were significantly upregulated under Cu²⁺ stress compared with the non-stress condition (0 h). After Cd²⁺ stress for 24 h, the expression levels of StMATE33 in leaf tissue were significantly increased, indicating its crucial role in the process of Cd²⁺ stress. Additionally, StMATE18/60/40/33/5 were significantly induced by Cu²⁺ stress, while StMATE59 (II) was significantly induced by Ni²⁺ stress. Our study initially explores the biological functions of StMATE genes in the regulation of heavy metal stress, further providing a theoretical basis for studying the subsequent molecular mechanisms in detail.

Identification and Expression of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Capsicum annuum and Solanum tuberosum

Multidrug and Toxic Compound Extrusion (MATE) proteins are essential transporters that extrude metabolites and participate in plant development and the detoxification of toxins. Little is known about the MATE gene family in the Solanaceae, which includes species that produce a broad range of specialized metabolites. Here, we identified and analyzed the complement of MATE genes in pepper (Capsicum annuum) and potato (Solanum tuberosum). We classified all MATE genes into five groups based on their phylogenetic relationships and their gene and protein structures. Moreover, we discovered that tandem duplication contributed significantly to the expansion of the pepper MATE family, while both tandem and segmental duplications contributed to the expansion of the potato MATE family, indicating that MATEs took distinct evolutionary paths in these two Solanaceous species. Analysis of ω values showed that all potato and pepper MATE genes experienced purifying selection during evolution. In addition, collinearity analysis showed that MATE genes were highly conserved between pepper and potato. Analysis of cis-elements in MATE promoters and MATE expression patterns revealed that MATE proteins likely function in many stages of plant development, especially during fruit ripening, and when exposed to multiple stresses, consistent with the existence of functional differentiation between duplicated MATE genes. Together, our results lay the foundation for further characterization of pepper and potato MATE gene family members.

Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.)

Background

The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The ABC transporter and HMA gene families are important in the control of cadmium (Cd) accumulation in crops. To date, the genome-wide analysis of these two gene families has been successfully conducted in some plant species, but no systematic evolutionary analysis is available for the flax genome.

Results

Here we describe the ABC transporter and HMA gene families in flax to provide a comprehensive overview of its evolution and some support towards the functional annotation of its members. The 198 ABC transporter and 12 HMA genes identified in the flax genome were classified into eight ABC transporter and four HMA subfamilies based on their phylogenetic analysis and domains’ composition. Nine of these genes, i.e., LuABCC9, LuABCC10, LuABCG58, LuABCG59, LuABCG71, LuABCG72, LuABCG73, LuHMA3, and LuHMA4, were orthologous with the Cd associated genes in Arabidopsis, rice and maize. Ten motifs were identified from all ABC transporter and HMA genes. Also, several motifs were conserved among genes of similar length, but each subfamily each had their own motif structures. Both the ABC transporter and HMA gene families were highly conserved among subfamilies of flax and with those of Arabidopsis. While four types of gene duplication were observed at different frequencies, whole-genome or segmental duplications were the most frequent with 162 genes, followed by 29 dispersed, 14 tandem and 4 proximal duplications, suggesting that segmental duplications contributed the most to the expansion of both gene families in flax. The rates of non-synonymous to synonymous (Ka/Ks) mutations of paired duplicated genes were for the most part lower than one, indicative of a predominant purifying selection. Only five pairs of genes clearly exhibited positive selection with a Ka/Ks ratio greater than one. Gene ontology analyses suggested that most flax ABC transporter and HMA genes had a role in ATP binding, transport, catalytic activity, ATPase activity, and metal ion binding. The RNA-Seq analysis of eight different organs demonstrated diversified expression profiling patterns of the genes and revealed their functional or sub-functional conservation and neo-functionalization.

Conclusion

Characterization of the ABC transporter and HMA gene families will help in the functional analysis of candidate genes in flax and other crop species.