Gene Duplication Events Research Articles

A newborn F-box gene blocks gene flow by selectively degrading phosphoglucomutase in species hybrids

The establishment of reproductive barriers such as postzygotic h ybrid i ncompatibility (HI) remains the key to speciation. Gene duplication followed by differential functionalization has long been proposed as a major model underlying HI, but little supporting evidence exists. Here, we demonstrate that a newborn F-box gene, Cni-neib-1 , of the nematode Caenorhabditis nigoni specifically inactivates an essential phosphoglucomutase encoded by Cbr-shls-1 in its sister species Caenorhabditis briggsae and their hybrids. Zygotic expression of Cni-neib-1 specifically depletes Cbr- SHLS-1, but not Cni- SHLS-1, in approximately 40 min starting from gastrulation, causing embryonic death. Cni-neib-1 is one of thirty-three paralogues emerging from a recent surge in F-box gene duplication events within C. nigoni , all of which are evolving under positive selection. Cni-neib-1 undergoes turnover even among C. nigoni populations. Differential expansion of F-box genes between the two species could reflect their distinctive innate immune responses. Collectively, we demonstrate how recent duplication of genes involved in protein degradation can cause incidental destruction of targets in hybrids that leads to HI, providing an invaluable insight into mechanisms of speciation.

Analysis of bZIP transcription factors in Rhododendron simsii and functional study of RsbZIP6 in regulating anthocyanin biosynthesis

The basic leucine zipper (bZIP) transcription factors play a critical role in various plant biological processes, including anthocyanin biosynthesis. This study focuses on Rhododendron simsii, a notable ornamental species with insufficiently explored bZIP transcription factors. We identified 66 bZIP transcription factors in the R. simsii genome and conducted comprehensive bioinformatics analyses to determine their gene localization, phylogenetic relationships, grouping, gene/protein structure, duplication events, synteny, and expression profiles. Our analysis identified RsbZIP6, a homolog of HY5 known to influence anthocyanin biosynthesis in many plants, as a potential regulator of this pathway. We cloned the complete coding sequence of RsbZIP6, which encodes a 170-amino acid protein spanning 510 bp. Subcellular localization analysis verified the nuclear presence of the RsbZIP6 protein. RT-qPCR analysis revealed the highest expression of RsbZIP6 in petals, which correlated with anthocyanin accumulation. Transgenic experiments indicated that overexpressing RsbZIP6 in Arabidopsis enhanced anthocyanin accumulation by upregulating genes involved in anthocyanin biosynthesis (4CL, CHS, CHI, DFR, F3H, F3’H, ANS and UF3GT). Our findings enhance understanding of the bZIP transcription factor family in R. simsii and underscore the vital role of RsbZIP6 in anthocyanin biosynthesis, providing insights for future genetic enhancement strategies.

Genome-wide analysis and expression profile of the bZIP gene family in Neopyropia yezoensis.

The basic leucine zipper (bZIP) family consists of conserved transcription factors which are widely present in eukaryotes and play important regulatory roles in plant growth, development, and stress responses. Neopyropia yezoensis is a red marine macroalga of significant economic importance; however, their bZIP family members and functions have not been systematically identified and analyzed. In the present study, the bZIP gene family in Ny. yezoensis was characterized by investigating gene structures, conserved motifs, phylogenetic relationships, chromosomal localizations, gene duplication events, cis-regulatory elements, and expression profiles. Twenty-three Ny. yezoensis bZIP (NyybZIP) genes were identified and sorted into 13 out of 30 groups, which were classified based on the bZIPs of Ny. yezoensis and 15 other red algae species. Phylogenetic analysis revealed that bZIP genes may have a complex evolutionary pattern in red algae. Cross-species collinearity analysis indicated that the bZIP genes in Ny. yezoensis, Neoporphyra haitanensis, and Porphyra umbilicalis are highly evolutionarily conserved. In addition, we identified four main categories of cis-elements, including development-related, light-responsive, phytohormone-responsive and stress-responsive promoter sequences in NyybZIP genes. Finally, RNA sequencing data and quantitative real-time PCR (qRT-PCR) showed that NyybZIP genes exhibited different expression patterns depending on the life stage. NyybZIP genes were also found to be involved in the nitrogen stress response. We thought that bZIP genes may be involved in Ny. yezoensis growth and development, and play a significant role in nitrogen deficiency response. Taken together, our findings provide new insights into the roles of the bZIP gene family and provide a basis for additional research into its evolutionary history and biological functions.

Genome-wide identification of AP2/ERF gene family in Coptis Chinensis Franch reveals its role in tissue-specific accumulation of benzylisoquinoline alkaloids

BackgroundThe Plant-specific AP2/ERF gene family encodes proteins involved in various biological and physiological processes. Although the genome of Coptis chinensis Franch, a plant producing benzylisoquinoline alkaloids (BIAs), has been sequenced at the chromosome level, studies on the AP2/ERF gene family in C. chinensis are lacking. Thus, a genome-wide identification of AP2/ERF gene family in C. chinensis was conducted to explore its role in BIAs biosynthesis.ResultsA total of 96 CcAP2/ERF genes were identified and categorized into five subfamilies, including 43 ERFs, 32 DREBs, 17 AP2s, 3 RAVs, and 1 Soloist, based on their structural domains. These CcAP2/ERF genes were unevenly distributed across nine chromosomes. Analysis of gene duplication events identified 17 CcAP2/ERF gene pairs in the genome, with 7 involved in tandem duplication events and 10 involved in segmental duplicate events, indicating that both types of duplications contributed to the expansion of the AP2/ERF gene family. The Ka/Ks ratio analysis suggested that the CcAP2/ERF gene family underwent strong purifying selection. Two phytohormones, methyl jasmonate and abscisic acid, were identified as potential key inducers of BIAs biosynthesis due to the cis-acting element prediction. Analysis of the spatial transcriptomic data revealed that 28 differentially expressed AP2/ERF genes had the highest or relatively higher expression levels in the rhizome, 17 of which positively correlated with the tissue-specific accumulation of BIAs. Further real-time PCR verification and protein-protein interaction analysis indicated that DREB1B might be one of the central regulators in a highly complex BIAs biosynthesis network.ConclusionThese findings provide significant insight into the function of AP2/ERF genes in C. chinensis, particularly in the regulatory network of BIAs biosynthesis in C. chinensis. This study also identifies candidate genes for metabolic engineering to increase BIAs content in C. chinensis.

Expression analysis of the apple HSP70 gene family in abiotic stress and phytohormones and expression validation of candidate MdHSP70 genes

Heat shock protein 70 (HSP70) is one kind of molecular chaperones which are widely found in organisms, and its members are highly conserved among each other, with important roles in plant growth and development. In this study, 56 HSP70 genes were identified from the apple genome database. Analysis of gene duplication events showed that tandem and segmental duplication events play an important role in promoting the amplification of the MdHSP70 gene family. Collinearity analysis showed that HSP70 family members of apple were more closely related to HSP70 family members of Arabidopsis, tomato and soybean. The promoter region of the apple HSP70 genes contains a large number of cis-acting elements in response to hormones and stress. Tissue-specific expression analysis showed that some of the genes were associated with various stages of the apple growth process. Codon preference analysis showed small differences between codon bases 1 and 3 in the apple HSP70 genome, and the codon base composition had a small effect on codon usage preference. The multiple expression patterns of the MdHSP70 gene suggested that MdHSP70 gene members play important roles in growth and development and in response to hormonal and abiotic stresses. The yeast two-hybrid (Y2H) demonstrated that MdHSP70-53 interacts with MdDVH24_032563. The qRT-PCR analysis showed that most MdHSP70 members’ hormonal and abiotic stresses (MdHSP70-6, MdHSP70-26 and MdHSP70-45) appeared to be highly expressed. To further elucidate the function of MdHSP70 (6, 26, 45), we introduced them into tobacco to confirm subcellular locations and noted that these genes are located in the cytoplasm and cell membrane. This study serves as a theoretical basis for further studies of the MdHSP70 gene and helps to further investigate the functional characterization of MdHSP70 gene.

Genome-wide identification and analysis of anthocyanin synthesis-related R2R3-MYB genes in Fragaria pentaphylla

BackgroundMYB transcription factors regulate anthocyanin biosynthesis across numerous plant species. However, comprehensive genome-wide investigations regarding the R2R3-MYB gene family and its involvement in regulating anthocyanin biosynthesis in the red and white fruit color morphs of Fragaria pentaphylla remain scarce.ResultsA total of 101 FpR2R3-MYB genes were identified from the F. pentaphylla genome and were divided into 34 subgroups based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were particularly conserved among the FpR2R3-MYB genes, especially members within the same subgroup. The FpR2R3-MYB genes were distributed over seven F. pentaphylla chromosomes. Analysis of gene duplication events revealed five pairs of tandem duplication genes and 16 pairs of segmental duplication genes, suggesting that segmental duplications are the major pattern for expansion of the FpR2R3-MYB gene family expansion in F. pentaphylla. Cis-regulatory elements of the FpR2R3-MYB promoters were involved in cellular development, phytohormones, environmental stress and photoresponse. Based on the analysis of the FpR2R3-MYB gene family and transcriptome sequencing (RNA-seq) data, FpMYB9 was identified as a key transcription factor involved in the regulation of anthocyanin synthesis in F. pentaphylla fruits. The expression of FpMYB9 increases significantly during the ripening stage of red fruits, as confirmed by reverse transcription quantitative real-time PCR. In addition, subcellular localization experiments further confirmed the nuclear presence of FpMYB9, supporting its role as a transcription factor involved in anthocyanin biosynthesis.ConclusionOur results showed that the FpR2R3-MYB genes are highly conserved and play important roles in the anthocyanin biosynthesis in F. pentaphylla fruits. Our results also provide a compelling basis for further understanding of the regulatory mechanism underlying the role of FpMYB9 in anthocyanin formation in F. pentaphylla fruits.

Odorant receptors tuned to isothiocyanates in Drosophila melanogaster and their evolutionary expansion in herbivorous relatives.

Plants release complex volatile compounds to attract mutualists, deter herbivores, and deceive pollinators. Here, we used herbivorous specialist flies that feed on mustard plants ( Scaptomyza spp.) and microbe-feeding species ( Drosophila melanogaster and Scaptomyza spp.) to investigate how plant-derived electrophilic toxins such as isothiocyanates (ITCs) affect insects, and how flies detect these compounds through olfaction. In survival assays, D. melanogaster exposed to volatile allyl isothiocyanate (AITC), a toxin derived from many Brassicales plants, were acutely intoxicated, demonstrating the high toxicity of this volatile compound to non-specialized insects. Through single sensillum recordings (SSR) from olfactory organs and behavioral assays, we found that the Odorant receptor 42a (Or42a) is necessary for AITC detection and behavioral aversion. Comparative transcriptome and RNA FISH studies across the drosophilid genus Scaptomyza revealed lineage-specific triplication of Or42a in the Brassicales specialists and a doubling of Or42a -positive-olfactory sensory neurons. Heterologous expression experiments showed that Or42a paralogs in Brassicales-specialists exhibited broadened sensitivity to ITCs in a paralog-specific manner. Finally, AlphaFold2 modeling followed by site-directed mutagenesis and SSR identified two critical amino acid substitutions that conferred Or42a heighten sensitivity to Brassicales-derived ITCs. Our findings suggest that ITCs, which are toxic to most insects, can be detected and avoided by non-specialists like D. melanogaster through olfaction. In Brassicales specialists, these same Ors experienced gene duplication events that resulted in an expanded sensitivity to ITC compounds. Thus, the insect's olfactory system can rapidly adapt to toxic ecological niches provided by chemically-defended host plants through co-option of chemosensory capabilities already present in their ancestors.

Dosage constraint of the ribosome-associated molecular chaperone drives the evolution and fates of its duplicates in bacteria.

Gene duplication events presumably occur in tig, which encodes the ribosome-associated molecular chaperone trigger factor (TF). However, TF is singly copied in virtually every bacterium, and these exceptions with multiple TF homologs always retain only one complete copy while other homologs lack the N-terminal domain. Here, we reveal the manner and mechanism underlying the evolution and fates of TF duplicates in bacteria. We discovered that the mutation-to-loss or retention-to-sub/neofunctionalization of TF duplicates is associated with the dosage constraint of N-terminal complete TF. The dosage constraint of TF is attributed to its characteristic ribosome binding and substrate-holding activities, causing a decrease in protein productivity and profile changes in cellular proteome.

Genome-Wide Identification and Expression Analysis of the BTB Gene Superfamily Provides Insight into Sex Determination and Early Gonadal Development of Alligator sinensis.

The BTB gene superfamily is widely distributed among higher eukaryotes and plays a significant role in numerous biological processes. However, there is limited knowledge about the structure and function of BTB genes in the critically endangered species Alligator sinensis, which is endemic to China. A total of 170 BTB genes were identified from the A. sinensis genome, classified into 13 families, and unevenly distributed across 16 chromosomes. Analysis of gene duplication events yielded eight pairs of tandem duplication genes and six pairs of segmental duplication genes. Phylogenetics shows that the AsBTB genes are evolutionarily conserved. The cis-regulatory elements in the AsBTB family promoter region reveal their involvement in multiple biological processes. Protein interaction network analysis indicates that the protein interactions of the AsBTB genes are centered around CLU-3, mainly participating in the regulation of biological processes through the ubiquitination pathway. The expression profile and protein interaction network analysis of AsBTB genes during sex differentiation and early gonadal development indicate that AsBTB genes are widely expressed in this process and involves numerous genes and pathways for regulation. This study provides a basis for further investigation of the role of the BTB gene in sex differentiation and gonadal development in A. sinensis.

Genome-Wide Analysis of Potato CCT Family Genes and Its Response to Auxin Substances

The control of flowering time plays an important role in the growth and development of potato tubers. The CCT (CO, COL and TOC1) gene family is involved in the flowering process of plants. In this study, a total of 32 StCCT family genes were identified and further classified into five subfamilies, including COL (17 members), PRR (4 members), ZIM (3 members), ASML2 (6 members) and TCR1 (2 members), based on their phylogenetic relationship. An analysis of the gene structure, motif compositions and conserved domain provided support for this classification. The StCCT genes were unevenly distributed on 12 chromosomes of the potato plant. In total, six gene duplication events were observed, which played a crucial role in the expansion of the StCCT family genes in the potato. The expression profiles exhibited diverse expression patterns of the StCCT genes in six tissues (leaf, shoot, root, tuber, stolon, and flower), StCCT32 is only expressed in flowers, while StCCT19 and StCCT8 are highly expressed in flowers and tubers, respectively. The StCCT genes exhibit different expression patterns in response to IAA and TIBA treatments at different concentrations across three tissues (leaf, stem, and tuber). After IAA and TIBA treatments, it was found that the expression level of StCCT7 was low in leaves and stems but significantly increased in tubers. Collectively, this study provided valuable information for the further study of potato formation and development and provided candidate genes for molecular breeding in the potato.

Retinoblastoma protein activity revealed by CRISPRi study of divergent Rbf1 and Rbf2 paralogs.

Retinoblastoma tumor suppressor proteins (Rb) are highly conserved metazoan transcriptional corepressors involved in regulating the expression of thousands of genes. The vertebrate lineage and the Drosophila genus independently experienced an Rb gene duplication event, leading to the expression of several Rb paralogs whose unique and redundant roles in gene regulation remain to be fully explored. Here, we used a novel CRISPRi system in Drosophila to identify the significance of paralogy in the Rb family. We engineered dCas9 fusions to the fly Rbf1 and Rbf2 paralogs and deployed them to gene promoters in vivo, studying them in their native chromatin context. By directly querying the in vivo response of dozens of genes to Rbf1 and Rbf2 targeting, using both transcriptional as well as sensitive developmental readouts, we find that Rb paralogs function as "soft repressors" and have highly context-specific activities. Our comparison of targeting endogenous genes to reporter genes in cell culture identified striking differences in activity, underlining the importance of using CRISPRi effectors in a physiologically relevant context to identify paralog-specific activities. Our study uncovers the complexity of Rb-mediated transcriptional regulation in a living organism, and serves as a stepping stone for future CRISPRi development in Drosophila.

The evolution of flavonoid biosynthesis.

The flavonoid pathway is characteristic of land plants and a central biosynthetic component enabling life in a terrestrial environment. Flavonoids provide tolerance to both abiotic and biotic stresses and facilitate beneficial relationships, such as signalling to symbiont microorganisms, or attracting pollinators and seed dispersal agents. The biosynthetic pathway shows great diversity across species, resulting principally from repeated biosynthetic gene duplication and neofunctionalization events during evolution. Such events may reflect a selection for new flavonoid structures with novel functions that enable occupancy of varied ecological niches. However, the biochemical and genetic diversity of the pathway also likely resulted from evolution along parallel trends across land plant lineages, producing variant compounds with similar biological functions. Analyses of the wide range of whole-plant genome sequences now available, particularly for archegoniate plants, have enabled proposals on which genes were ancestral to land plants and which arose within the land plant lineages. In this review, we discuss the emerging proposals for how the flavonoid pathway may have evolved and diversified. This article is part of the theme issue 'The evolution of plant metabolism'.

Aquaporin (AQP) gene family in Buffalo and Goat: Molecular characterization and their expression analysis

Aquaporins (AQPs) are essential membrane proteins facilitating water and small solute transport across cell membranes. Mammals have approximately 13 paralogs of AQPs that may have evolved through gene duplication events. These genes are present in two separate clusters within the genome. In the present study, comprehensive 13 AQP genes (AQP0–12) were cloned and characterized in buffalo and goat. The protein coding region of AQPs in both species ranged from 729 to 990 bps, corresponding to 263–330 amino acid residues. Two important residues including NPA motifs and ar/R selectivity filter were found conserved in all AQPs, except for AQP7, 11 and 12. AQP0, 2, 4, 5, 7, 9, 12 showed tissue-restricted expression, whereas AQP1, 3, 8, and 11 exhibited ubiquitous expression across several tissues. AQP10 was identified as a pseudogene in all artiodactyls. Transcript variants were identified in buffalo and goat, where some variants of goat AQP5 and 6 lacked important motifs. Evolutionary analysis indicated positive selection at or near the NPA motifs and ar/R selectivity filter of AQP0, 3, 6, 7, and 10 that may alter its structure and function. This study is crucial for future investigations aiming to study the molecular mechanisms of AQPs in response to various physiological conditions.

Characterization, Evolution, Expression and Functional Divergence of the DMP Gene Family in Plants.

The DMP (DOMAIN OF UNKNOWN FUNCTION 679 membrane protein) domain, containing a family of membrane proteins specific to green plants, is involved in numerous biological functions including physiological processes, reproductive development and senescence in Arabidopsis, but their evolutionary relationship and biological function in most crops remains unknown. In this study, we scrutinized phylogenetic relationships, gene structure, conserved domains and motifs, promoter regions, gene loss/duplication events and expression patterns. Overall, 240 DMPs were identified and analyzed in 24 plant species selected from lower plants to angiosperms. Comprehensive evolutionary analysis revealed that these DMPs underwent purifying selection and could be divided into five groups (I-V). DMP gene structure showed that it may have undergone an intron loss event during evolution. The five DMP groups had the same domains, which were distinct from each other in terms of the number of DMPs; group III was the largest, closely followed by group V. The DMP promotor region with various cis-regulatory elements was predicted to have a potential role in development, hormone induction and abiotic stresses. Based on transcriptomic data, expression profiling revealed that DMPs were primarily expressed in reproductive organs and were moderately expressed in other tissues. Evolutionary analysis suggested that gene loss events occurred more frequently than gene duplication events among all groups. Overall, this genome-wide study elucidates the potential function of the DMP gene family in selected plant species, but further research is needed in many crops to validate their biological roles.

Diverse signatures of convergent evolution in cactus-associated yeasts.

Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently approximately 17 times. Using a machine learning-based approach, we further found that cactophily can be predicted with 76% accuracy from both functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which we found to be likely associated with altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved independently through disparate molecular mechanisms. Notably, we found that multiple cactophilic species and their close relatives have been reported as emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-might preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high-throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.

Genome-wide analysis of two repeats containing MYB transcription factors in groundnut identifies drought-inducible genes involved as a negative regulator of root nodulation

The MYB gene superfamily encompasses a group of related genes found in all eukaryotes. In contrast to animals, higher plants contain large numbers of two-repeat MYB genes, which have been established in regulating crucial developmental, biotic, and abiotic stress responses that profoundly affect the plant's yield. However, a comprehensive analysis of the two-repeat MYB gene family in groundnut and its progenitors, especially the role of two-repeat MYB genes in response to drought stress, and the effect of those genes in nodulation have not been reported so far. Our recent analysis of the groundnut genome has identified 79 (Arachis duranensis), 84 (Arachis ipaensis), and 161 (Arachis hypogaea) two-repeat MYB genes, which belong to multiple distinct subgroups based on their architecture. Here, we provided a complete overview of the gene structure, protein motif organization, chromosome localization, gene duplication events, and synteny analysis to clarify evolutionary perspectives. Members of the same subgroup showed highly conserved structure and motif compositions. The whole-genome duplication and segmental duplication likely contributed to the expansion of two-repeat MYB genes in Arachis hypogaea. The upstream sequences of most genes contained phytohormone-responsive, stress-responsive, light-responsive, and plant growth-related elements. The genes not only have diverse expression profiles across different development stages but as shown in our experimental findings, most of them were induced by ABA and drought-related stress. Further gene silencing experiments demonstrated that two drought-inducible MYB genes, homologs of Arabidopsis MYB96 and MYB94, function as a negative regulator of root nodulation. The results of this study can serve as a strong foundation for further elucidation of the physiological and molecular function of two-repeat MYB genes in groundnut.

Tapping into haloalkaliphilic bacteria for sustainable agriculture in treated wastewater: insights into genomic fitness and environmental adaptation.

The increasing salinity and alkalinity of soils pose a global challenge, particularly in arid regions such as Tunisia, where about 50% of lands are sensitive to soil salinization. Anthropogenic activities, including the use of treated wastewater (TWW) for irrigation, exacerbate these issues. Haloalkaliphilic bacteria, adapted to TWW conditions and exhibiting plant-growth promotion (PGP) and biocontrol traits, could offer solutions. In this study, 24 haloalkaliphilic bacterial strains were isolated from rhizosphere sample of olive tree irrigated with TWW for more than 20years. The bacterial identification using 16S rRNA gene sequencing showed that the haloalkaliphilic isolates, capable of thriving in high salinity and alkaline pH, were primarily affiliated to Bacillota (Oceanobacillus and Staphylococcus). Notably, these strains exhibited biofertilization and enzyme production under both normal and saline conditions. Traits such as phosphate solubilization, and the production of exopolysaccharide, siderophore, ammonia, and hydrogen cyanide were observed. The strains also demonstrated enzymatic activities, including protease, amylase, and esterase. Four selected haloalkaliphilic PGPR strains displayed antifungal activity against Alternaria terricola, with three showing tolerances to heavy metals and pesticides. The strain Oceanobacillus picturea M4W.A2 was selected for genome sequencing. Phylogenomic analyses indicated that the extreme environmental conditions probably influenced the development of specific adaptations in M4W.A2 strain, differentiating it from other Oceanobacillus picturae strains. The presence of the key genes associated with plant growth promotion, osmotic and oxidative stress tolerance, antibiotic and heavy metals resistance hinted the functional capabilities might help the strain M4W.A2 to thrive in TWW-irrigated soils. By demonstrating this connection, we aim to improve our understanding of genomic fitness to stressed environments. Moreover, the identification of gene duplication and horizontal gene transfer events through mobile genetic elements allow the comprehension of these adaptation dynamics. This study reveals that haloalkaliphilc bacteria from TWW-irrigated rhizosphere exhibit plant-growth promotion and biocontrol traits, with genomic adaptations enabling their survival in high salinity and alkaline conditions, offering potential solutions for soil salinization issues.

Improving heat tolerance in betel palm (Areca catechu) by characterisation and expression analyses of heat shock proteins under thermal stress

Context Heat shock proteins play a vital role in cellular homeostasis by protecting proteins against various environmental stresses, which facilitates the survival of plants under unfavourable conditions. Aims We aimed to provide the first comprehensive genomic and expression analysis of the HSP70 gene family in betel palm (Areca catechu) to elucidate its role in heat stress response. Methods Genomic analysis revealed 34 putative HSP70 genes distributed across 13 chromosomes. These were renamed AcatHSP70 and classified into five subfamilies (A–E) based on phylogenetic analysis. These genes are mostly localised in the chloroplast, cytoplasm, and nucleus. Gene ontology revealed that these genes are mostly involved in heat stress. The gene duplication events of HSP70 genes involved only segmental duplications. We subjected betel palm seedlings (2 years old) to heat stress under controlled conditions for 30 days at high, low, and room temperatures for expression analyses of HSP70 genes. Key results Expression analysis revealed eight putative candidate genes (AcatHSP70-3, AcatHSP70-13, AcatHSP70-22, AcatHSP70-19, AcatHSP70-21, AcatHSP70-24, AcatHSP70-25, and AcatHSP70-26) that showed significantly higher expression under high-temperature stress. AcatHSP70-5 showed higher expression under low-temperature treatment, and AcatHSP70-16 was responsive at room temperature treatment. Conclusion We conclude that the majority of AcatHSP70 genes play a crucial role under thermal stress conditions, and respond to high-temperature stress as shown by the quantitative reverse transcription polymerase chain reaction analysis. Implications This comprehensive characterisation of the HSP70 gene family provides novel insights into the thermal protection mechanisms of betel palms in changing climates.

Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid Genus Cypripedium L.

Cypripedium is the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny of Cypripedium and explore its evolutionary history using target capture data for the first time. We used the orchid-specific bait set Orchidaceae963 in combination with transcriptomic data to reconstruct the phylogeny of Cypripedium based on 913 nuclear loci, covering all 13 sections. Subsequently, we investigated discordance among nuclear and chloroplast trees, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies, and diversification rate shifts, and identified potential gene (genome) duplication and hybridization events. All sections were recovered as monophyletic, contrary to the two subsections within sect. Cypripedium. The two subclades within this section did not correspond to its subsections but matched the geographic distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect. Cypripedium, which can be attributed to hybridization events detected based on phylogenetic network analyses, and incomplete lineage sorting caused by rapid radiation. Our biogeographic analysis suggested a Neotropical origin of the genus during the Oligocene (~30 Ma), with a lineage of potentially hybrid origin spreading to the Old World in the Early Miocene (~22 Ma). The rapid radiation at the backbone likely occurred in Southeast Asia around the Middle Miocene Climatic Transition (~15-13 Ma), followed by several independent dispersals back to the New World. Moreover, the Pliocene-Quaternary glacial cycles may have contributed to further speciation and reticulate evolution within Cypripedium. Our study provided novel insights into the evolutionary history of Cypripedium based on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.

Genome-Wide Characterization and Expression Analysis of CsPALs in Cucumber (Cucumis sativus L.) Reveal Their Potential Roles in Abiotic Stress and Aphid Stress Tolerance.

Phenylalanine ammonia lyase (PAL) is a pivotal enzyme in the phenylalanine metabolic pathway in plants and has a crucial role in the plant's response to environmental stress. Although the PAL family has been widely studied in many plant species, limited is known about its particular role in cucumbers under stress. We investigated the physicochemical properties, gene structure, gene duplication events, conserved motifs, cis-acting elements, protein interaction networks, stress-related transcriptome data, and quantitatively validated key stress-related genes. The main results indicated that 15 PAL genes were grouped into four clades: I, II, and III when arranged in a phylogenetic tree of PAL genes in angiosperms. The analysis of the promoter sequence revealed the presence of multiple cis-acting elements related to hormones and stress responses in the cucumber PAL genes (CsPALs). The analysis of protein interaction networks suggested that CsPAL1 interacts with eight other members of the PAL family through CsELI5 and CsHISNA, and directly interacts with multiple proteins in the 4CL family. Further investigation into the expression patterns of CsPAL genes in different tissues and under various stress treatments (NaCl, Cu2+, Zn2+, PEG6000, aphids) demonstrated significant differential expression of CsPALs across cucumber tissues. In summary, our characterization of the CsPAL family offers valuable insights and provides important clues regarding the molecular mechanisms of CsPALs in managing abiotic and biotic stress interactions in cucumbers.