Recent Duplication Research Articles

Evolutionary analysis of CBFs/DREB1s in temperate and tropical woody bamboos and functional study of PeDREB1A3 under cold and drought stress.

Bamboo forests are vulnerable to extreme cold, as well as drought caused by declining rainfall or persistent hot, under global climate change. The C-repeat binding factors/dehydration-responsive element binding protein 1s (CBFs/DREB1s) are vital to acquiring tolerance to deal with the changing climate in plants. Herein, we investigated the evolution of CBFs/DREB1s in four temperate or tropical woody bamboos. In Phyllostachys edulis, Hsuehochloa calcarea, Dendrocalamus latiflorus, and Dendrocalamus brandisii, a total of 16, 12, 24, and 22 putative DREB1s were identified and were categorized into nine subclades, from DREB1A to DREB1I. DREB1s members increased with bamboo polyploidization, coinciding with the presence of at least two collinear DREB1s orthologs in different bamboos. It indicates the importance of polyploidization in driving the expansion of DREB1s. Except for the DREB1F, DREB1s of the other subclades showed direct collinearity with their orthologs in Poaceae. Tandemly linked loci of DREB1A, DREB1H, and DREB1B were of concern due to their conserved and inherited relationship in bamboo, and a recent duplication of DREB1A occurred during bamboo speciation. In P. edulis, PeDREB1A3/PeDREB1H1/PeDREB1B3 locus showed sensitivity to cold stimulation, especially for PeDREB1A3 rapidly induced after 0.5-h cold stimulation. PeDREB1A3 was proved as a nuclear-located transcription activator recognizing DRE cis-element. Moreover, overexpression of PeDREB1A3 improved both cold and drought tolerance of Arabidopsis thaliana. It suggested that the neoteric duplication of DREB1As might contribute to bamboo adaptability. DREB1A represents the potential locus for improving agronomic traits in the future. This research provides valuable information for excavating potential genes for bamboo adaptation and will facilitate the research on bamboo breeding for stress tolerance.

Genome assembly and multi-omics analyses of Isodon lophanthodies provide insights into the distribution of medicinal metabolites induced by exogenous methyl jasmonate

BackgroundIsodon lophanthodies is a perennial herb and the whole plant has medicinal value distributed in southern China and southeast Asia. The absence of a reference genome has hindered evolution and genomic breeding research of this species. Results: In this study, we present a high-quality, chromosome-level genome assembly of I. lophanthodies with integrating PacBio and Hi-C sequencing data. We assembled a genome of 412.78 Mb with a scaffold N50 of ~ 33.43 Mb, organized into 12 pseudochromosomes. This assembly includes 36,324 genes and 209.51 Mb of repetitive sequences. Phylogenetic analysis revealed that I. lophanthodies and its sister species Isodon rubescens diverged approximately 9.99 million years ago (MYA), and shared a recent whole-genome duplication (WGD) event. Combined with the gene expression profile and metabolite fluctuation in response to methyl jasmonate, two key enzymes involved in salicin synthesis pathway were further identified. Conclusions: This genome assembly provides an essential reference for future research on I. lophanthodies, and enhances our understanding of salicin synthesis and medicinal metabolite profiles in response to exogenous methyl jasmonate.

Asymmetrical evolution of promoter methylation of mammalian genes after duplication.

Even though gene duplication is a key source of new genes and evolutionary innovation, it is unclear how duplicates survive the period immediately following gene duplication, in which both copies are functionally redundant. In the absence of epigenetic silencing, the abundance of the gene product would double after gene duplication, which would often have deleterious effects. However, recent duplicates exhibit low expression levels, which could be at least partially explained by high levels of promoter methylation. What evolutionary paths lead to duplicate hypermethylation, and does it affect both duplicates, or only one? Here, we compare levels of promoter methylation in 10 human and 16 mouse tissues, between singletons and duplicates and among human-mouse orthologs of different kinds (one-to-one, one-to-many, many-to-one, and many-to-many). Our results indicate that: (1) on average, duplicates are more methylated than singletons in mouse, but less methylated than singletons in human, (2) recently duplicated genes tend to exhibit high levels of promoter methylation, (3) genes that undergo duplication tend to be highly methylated before duplication, (4) after gene duplication, one of the copies (the daughter copy, i.e. the one that relocates to a new genomic context) tends to undergo an additional increase in promoter methylation, whereas the other (the parental copy, which remains in the original genomic location) tends to retain pre-duplication methylation levels, and (5) daughter copies tend to be lowly expressed. These observations support a model in which daughter copies are repressed via promoter hypermethylation and can thus survive the filter of purifying selection until both copies diverge functionally.

Chromosome‐scale genomes of Toona fargesii provide insights into competency of root sprouting

AbstractToona fargesii A. Chev., a versatile tree in the Toona genus of the Meliaceae family, is renowned for its exquisite timber and medicinal properties, offering promising benefits. Due to natural regeneration obstacles and long‐term excessive exploitation, it has been threatened in China. Intriguingly, root sprouting, which may diminish the genetic diversity and hinder population development, dominates the reproductive pattern of T. fargesii in the wild. However, the lack of complete genome information has hampered basic studies on the regeneration, classification, evolution and conservation of this species. Here, we report the genome of T. fargesii, which was sequenced using the PacBio platform and assembled into a high‐quality genome with a total size of 535.24 Mb. Of this, 97.93% of the assembled contigs were anchored onto 28 pseudochromosomes, achieving a chromosome‐level genome. The long terminal repeat assembly index score was 21.34, and the consensus quality value was 39.90%, indicating the accuracy and completeness of the genome. Comparative genome analysis suggested that a recent whole genome duplication event occurred between 22.1 and 50.1 Mya in the Toona genus, with the divergence time between T. fargesii and its relative T. sinensis estimated at approximately ~16.7 Mya. Additionally, 13 TfARR genes, which play integral roles in root sprouting by mediating cytokinin signaling, underwent rapid gene expansion and showed significant enrichment in the plant hormone signal transduction pathway. Furthermore, transcriptomic analysis demonstrated that differentially expressed genes between root sprouts and nonroot sprouts were significantly enriched in the zeatin biosynthesis pathway, indicating that cytokinin regulation is involved in root sprouting development. Collectively, the findings provide valuable genomic resources for the Toona genus and genetic insights into the mechanisms of root sprouting in T. fargesii.

A multiomics investigation into the evolution and specialized metabolisms of three Toxicodendron cultivars.

Toxicodendron species are economically and medicinally important trees because of their rich sources of natural products. We present three chromosome-level genome assemblies of Toxicodendron vernicifluum 'Dali', Toxicodendron succedaneum 'Vietnam', and T. succedaneum 'Japan', which display diverse production capacities of specialized metabolites. Genome synteny and structural variation analyses revealed large genomic differences between the two species (T. vernicifluum and T. succedaneum) but fewer differences between the two cultivars within the species. Despite no occurrence of recent whole-genome duplications, Toxicodendron showed evidence of local duplications. The genomic modules with high expression of genes encoding metabolic flux regulators and chalcone synthase-like enzymes were identified via multiomics analyses, which may be responsible for the greater urushiol accumulation in T. vernicifluum 'Dali' than in other Toxicodendron species. In addition, our analyses revealed the regulatory patterns of lipid metabolism in T. succedaneum 'Japan', which differ from those of other Toxicodendron species and may contribute to its high lipid accumulation. Furthermore, we identified the key regulatory elements of lipid metabolism at each developmental stage, which could aid in molecular breeding to improve the production of urushiol and lipids in Toxicodendron species. In summary, this study provides new insights into the genomic underpinnings of the evolution and diversity of specialized metabolic pathways in three Toxicodendron cultivars through multiomics studies.

Comparative genomics of obligate predatory bacteria belonging to phylum Bdellovibrionota highlights distribution and predicted functions of lineage-specific protein families.

Comparative genomics of predatory bacteria is important to understand their ecology and evolution and explore their potential to treat drug-resistant infections. We compared chromosomes of 18 obligate predators from phylum Bdellovibrionota (16 intraperiplasmic, two epibiotic) and 15 non-predatory bacteria. Phylogenetics of conserved single-copy genes and analysis of genome-wide average amino acid identity provide evidence for at least five Bdellovibrio species and support recent reclassifications of predatory taxa. To define shared and differential genome content, we grouped predicted protein sequences into gene clusters based on sequence similarity. Few gene clusters are shared by all 33 bacteria or all 18 predatory bacteria; however, we identified gene clusters conserved within lineages, such as intraperiplasmic Bdellovibrio, and not found in other bacteria. Many of these are predicted to function in cell envelope biogenesis, signal transduction, and other roles important for predatory lifestyles. Among intraperiplasmic Bdellovibrio, we detected high abundance of gene clusters predicted to encode transglycosylases, endopeptidases, and lysozymes, and we identified six gene clusters (amidase, L,D-transpeptidase, four transglycosylases) with evidence of recent gene duplication and gene family expansion. Focusing on peptidoglycan metabolism, we defined a suite of gene clusters that include peptidoglycan-degrading and -modifying enzymes and occur only in predatory bacteria, suggesting these proteins may have evolved activities specific to predation. Our analyses highlight key genome content differences between obligate predatory bacteria and non-predatory relatives and identify gene clusters that may encode enzymes adapted to predatory lifestyles. These lineage-specific proteins are strong candidates for functional characterization to clarify their role in predation.IMPORTANCEEvolution of predation as a bacterial lifestyle involves selective pressure on and adaptation of enzymes that contribute to killing and digestion of prey bacteria, in some cases from within the prey itself. Such enzymes are a hallmark of obligate predatory bacteria belonging to phylum Bdellovibrionota, which includes the well-studied predator Bdellovibrio. By comparing protein sequences of obligate predatory bacteria and their non-predatory relatives, we define key genome content differences that distinguish bacterial predators and identify lineage-specific enzymes that may have evolved unique activities due to selective pressures related to a predatory lifestyle. In addition to providing insights into the ecology and evolution of predatory bacteria, comparative genomics studies, like this, can inform efforts to develop predatory bacteria and/or their enzymes as potential biocontrol agents to combat drug-resistant bacterial infections.

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

The establishment of reproductive barriers such as postzygotic hybrid incompatibility (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.

Somy evolution in the honey bee infecting trypanosomatid parasite Lotmaria passim.

Lotmaria passim is a ubiquitous trypanosomatid parasite of honey bees nestled within the medically important subfamily Leishmaniinae. Although this parasite is associated with honey bee colony losses, the original draft genome-which was completed before its differentiation from the closely related Crithidia mellificae-has remained the reference for this species despite lacking improvements from newer methodologies. Here, we report the updated sequencing, assembly, and annotation of the BRL-type (Bee Research Laboratory) strain (ATCC PRA-422) of Lotmaria passim. The nuclear genome assembly has been resolved into 31 complete chromosomes and is paired with an assembled kinetoplast genome consisting of a maxicircle and 30 minicircle sequences. The assembly spans 33.7 Mb and contains very little repetitive content, from which our annotation of both the nuclear assembly and kinetoplast predicted 10,288 protein-coding genes. Analyses of the assembly revealed evidence of a recent chromosomal duplication event within chromosomes 5 and 6 and provided evidence for a high level of aneuploidy in this species, mirroring the genomic flexibility employed by other trypanosomatids as a means of adaptation to different environments. This high-quality reference can therefore provide insights into adaptations of trypanosomatids to the thermally regulated, acidic, and phytochemically rich honey bee hindgut niche, which offers parallels to the challenges faced by other Leishmaniinae during the challenges they undergo within insect vectors, during infection of mammals, and exposure to antiparasitic drugs throughout their multi-host life cycles. This reference will also facilitate investigations of strain-specific genomic polymorphisms, their role in pathogenicity, and the development of treatments for pollinator infection.

OHDLF: A Method for Selecting Orthologous Genes for Phylogenetic Construction and Its Application in the Genus Camellia.

Accurate phylogenetic tree construction for species without reference genomes often relies on de novo transcriptome assembly to identify single-copy orthologous genes. However, challenges such as whole-genome duplication (WGD), heterozygosity, gene duplication, and loss can hinder the selection of these genes, leading to limited data for constructing reliable species trees. To address these issues, we developed a new analytical pipeline, OHDLF (Orthologous Haploid Duplication and Loss Filter), which filters orthologous genes from transcript data and adapts parameter settings based on genomic characteristics for further phylogenetic tree construction. In this study, we applied OHDLF to the genus Camellia and evaluated its effectiveness in constructing phylogenetic trees. The results highlighted the pipeline's ability to handle challenges like high heterozygosity and recent gene duplications by selectively retaining genes with a missing rate and merging duplicates with high similarity. This approach ensured the preservation of informative sites and produced a highly supported consensus tree for Camellia. Additionally, we evaluate the accuracy of the OHDLF phylogenetic trees for different species, demonstrating that the OHDLF pipeline provides a flexible and effective method for selecting orthologous genes and constructing accurate phylogenetic trees, adapting to the genomic characteristics of various plant groups.

Functional diversification within the heme-binding split-barrel family

Due to neofunctionalization, a single fold can be identified in multiple proteins that have distinct molecular functions. Depending on the time that has passed since gene duplication and the number of mutations, the sequence similarity between functionally divergent proteins can be relatively high, eroding the value of sequence similarity as the sole tool for accurately annotating the function of uncharacterized homologs. Here, we combine bioinformatic approaches with targeted experimentation to reveal a large multi-functional family of putative enzymatic and non-enzymatic proteins involved in heme metabolism. This family (homolog of HugZ (HOZ)) is embedded in the “FMN-binding split barrel” superfamily and contains separate groups of proteins from prokaryotes, plants, and algae, which bind heme and either catalyze its degradation or function as non-enzymatic heme sensors. In prokaryotes these proteins are often involved in iron assimilation, whereas several plant and algal homologs are predicted to degrade heme in the plastid or regulate heme biosynthesis. In the plant Arabidopsis thaliana, which contains two HOZ subfamilies that can degrade heme in vitro (HOZ1 and HOZ2), disruption of AtHOZ1 (AT3G03890) or AtHOZ2A (AT1G51560) causes developmental delays, pointing to important biological roles in the plastid. In the tree Populus trichocarpa, a recent duplication event of a HOZ1 ancestor has resulted in localization of a paralog to the cytosol. Structural characterization of this cytosolic paralog and comparison to published homologous structures suggests conservation of heme-binding sites. This study unifies our understanding of the sequence-structure-function relationships within this multi-lineage family of heme-binding proteins and presents new molecular players in plant and bacterial heme metabolism.

Telomere-to-telomere, gap-free assembly of the Rosa rugosa reference genome

Rosa, a genus esteemed worldwide for its ornamental plants, has encountered barriers in functional genomic studies and further genetic enhancement due to incomplete sequences and floating regions in previously sequenced genomes. Our groundbreaking study introduced a meticulously assembled, continuous, and fully bridged reference genome for Rosa rugosa, constructed through a sophisticated combination of PacBio High-Fidelity, ONT ultra-long reads, and Hi-C data. This robust assembly spanned 444.55 Mb and encompassed 34 109 protein-coding genes. We have uniquely assembled each chromosome into single, gap-free structures, successfully identifying all 14 telomeres and seven centromeres, a feat not achieved previously. The centromeric regions were distinguished by tandem repeats, primarily composed of centromere-specific 159-bp monomers, and a significant enrichment of ATHILA/Gypsy long terminal repeat retrotransposons in proximal regions. Our research highlighted recent tandem duplications as instrumental in bolstering R. rugosa's stress tolerance, environmental adaptability, and enhanced anthocyanin synthesis. Furthermore, our study ventured into uncharted territory by predicting transcription factors potentially regulating anthocyanin biosynthesis through the employment of gene co-expression networks, providing new avenues for research. This comprehensive reference genome not only serves as a cornerstone for in-depth exploration of genomic architecture and functionalities in R. rugosa but also acts as a catalyst for innovative breeding strategies and genetic refinement within the genus.

Olfactory receptor coexpression and co-option in the dengue mosquito.

The olfactory sensory neurons of vinegar flies and mice tend to express a single ligand-specific receptor. While this 'one neuron-one receptor' motif has long been expected to apply broadly across insects, recent evidence suggests it may not extend to mosquitoes. We sequenced and analyzed the transcriptomes of 46,000 neurons from antennae of the dengue mosquito Aedes aegypti to resolve all olfactory, thermosensory, and hygrosensory neuron subtypes and identify the receptors expressed therein. We find that half of all olfactory subtypes coexpress multiple receptors. However, coexpression occurs almost exclusively among genes from the same family-among odorant receptors (ORs) or among ionotropic receptors (IRs). Coexpression of ORs with IRs is exceedingly rare. Many coexpressed receptors are recent duplicates. In other cases, the recruitment or co-option of single receptors by multiple neuron subtypes has placed these genes together in the same cells with distant paralogs. Close examination of data from Drosophila reveal rare cases of both phenomena, indicating that the olfactory systems of these two species are not fundamentally different, but instead fall at different locations along a continuum likely to encompass diverse insects.

Identification and Analysis of WRKY Transcription Factors in Response to Cowpea Fusarium Wilt in Cowpea.

In plants, WRKY transcription factors play a crucial role in plant growth, development, and response to abiotic and biotic stress. Cowpea (Vigna unguiculata) is an important legume crop. However, cowpea Fusarium wilt (CFW), caused by Fusarium oxysporum f. sp. tracheiphilum (Fot), poses a serious threat to its production. In this study, we systematically identified members of the cowpea WRKY (VuWRKY) gene family and analyzed their expression patterns under CFW stress. A total of 91 WRKY transcription factors were identified in the cowpea genome. Phylogenetic and synteny analyses indicated that the expansion of VuWRKY genes in cowpea is primarily due to recent duplication events. Transcriptome analysis of cowpea inoculated with Fo revealed 31 differentially expressed VuWRKY genes, underscoring their role in the response to CFW infection. Four differentially expressed WRKY genes were selected for validation. Subcellular localization and Western blot assays showed their nuclear localization and normal expression in N. benthamiana. Additionally, yeast one-hybrid assays demonstrated that VuWRKY2 can bind to the promoter region of the Catalase (CAT) gene, indicating its potential role in transcriptional regulation. This study establishes a foundation for further exploration of the role and regulatory mechanisms of VuWRKY genes in response to CFW stress.

Receptor-like cytoplasmic kinase 58 reduces tolerance of maize seedlings to low magnesium via promoting H2O2 over-accumulation.

ZmRLCK58, a negative growth regulator, reduces tolerance of maize seedlings to low Mg via enhancing H2O2 accumulation in the shoot. Magnesium (Mg) deficiency is one of critical limiting factors for crop production in widespread acidic soils worldwide. However, the molecular mechanism of crop response to Mg deficiency is still largely unclear. Here, we found higher concentrations of H2O2, soluble sugars, and starch (1.5-, 1.9-, and 1.4-fold, respectively) in the shoot of low-Mg-treated maize seedlings, compared with Mg sufficient plants under hydroponic culture. Consistent with over-accumulation of H2O2, transcriptome profiling revealed significant enrichment of 175 differentially expressed genes (DEGs) in "response to oxygen-containing compound" out of 641 DEGs in the shoot under low Mg. Among 175 DEGs, a down-regulated receptor-like cytoplasmic kinase ZmRLCK58 underwent a recent duplication event before Poaceae divergence and was highly expressed in the maize shoot. ZmRLCK58 overexpression enhanced H2O2 accumulation in shoots by 21.3% and 29.8% under control and low-Mg conditions, respectively, while reducing biomass accumulation compared with wild-type plants. Low Mg further led to 39.7% less starch accumulation in the ZmRLCK58 overexpression shoot and lower Mg utilization efficiency. Compared with wild-type plants, overall down-regulated expression of genes related to response to carbohydrate, photosynthesis, H2O2 metabolic, oxidation-reduction, and ROS metabolic processes in ZmRLCK58 overexpression lines preconditioned aforementioned physiological alterations. Together, ZmRLCK58, as a negative growth regulator, reduces tolerance of maize seedlings to low Mg via enhancing H2O2 accumulation.

Following the Evolutionary Paths of Dscam1 Proteins toward Highly Specific Homophilic Interactions.

Many adhesion proteins, evolutionarily related through gene duplication, exhibit distinct and precise interaction preferences and affinities crucial for cell patterning. Yet, the evolutionary paths by which these proteins acquire new specificities and prevent cross-interactions within their family members remain unknown. To bridge this gap, this study focuses on Drosophila Down syndrome cell adhesion molecule-1 (Dscam1) proteins, which are cell adhesion proteins that have undergone extensive gene duplication. Dscam1 evolved under strong selective pressure to achieve strict homophilic recognition, essential for neuronal self-avoidance and patterning. Through a combination of phylogenetic analyses, ancestral sequence reconstruction, and cell aggregation assays, we studied the evolutionary trajectory of Dscam1 exon 4 across various insect lineages. We demonstrated that recent Dscam1 duplications in the mosquito lineage bind with strict homophilic specificities without any cross-interactions. We found that ancestral and intermediate Dscam1 isoforms maintained their homophilic binding capabilities, with some intermediate isoforms also engaging in promiscuous interactions with other paralogs. Our results highlight the robust selective pressure for homophilic specificity integral to the Dscam1 function within the process of neuronal self-avoidance. Importantly, our study suggests that the path to achieving such selective specificity does not introduce disruptive mutations that prevent self-binding but includes evolutionary intermediates that demonstrate promiscuous heterophilic interactions. Overall, these results offer insights into evolutionary strategies that underlie adhesion protein interaction specificities.

Systematic characterization of immunoglobulin loci and deep sequencing of the expressed repertoire in the Atlantic cod (Gadus morhua)

BackgroundThe Atlantic cod is a prolific species in the Atlantic, despite its inconsistent specific antibody response. It presents a peculiar case within vertebrate immunology due to its distinct immune system, characterized by the absence of MHCII antigen presentation pathway, required for T cell-dependent antibody responses. Thorough characterisation of immunoglobulin loci and analysis of the antibody repertoire is necessary to further our understanding of the Atlantic cod’s immune response on a molecular level.ResultsA comprehensive search of the cod genome (gadmor3.0) identified the complete set of IgH genes organized into three sequential translocons on chromosome 2, while IgL genes were located on chromosomes 2 and 5. The Atlantic cod displayed a moderate germline V gene diversity, comprising four V gene families for both IgH and IgL, each with distinct chromosomal locations and organizational structures. 5’RACE sequencing revealed a diverse range of heavy chain CDR3 sequences and relatively limited CDR3 diversity in light chains. The analysis highlighted a differential impact of V-gene germline CDR3 length on receptor CDR3 length between heavy and light chains, underlining different recombination processes.ConclusionsThis study reveals that the Atlantic cod, despite its inconsistent antibody response, maintains a level of immunoglobulin diversity comparable to other fish species. The findings suggest that the extensive recent duplications of kappa light chain genes do not result in increased repertoire diversity. This research provides a comprehensive view of the Atlantic cod's immunoglobulin gene organization and repertoire, necessary for future studies of antibody responses at the molecular level.

HpFBH3 transactivates HpCO7 via binding to the E-boxes in the promoter and may accelerate flower formation in pitaya1

Hylocereus polyrhizus, also known as pitaya or dragon fruit, is a climbing cactus grown worldwide because of its excellent performance under drought stress and appealing red-purple fruits. In practice, accelerating flower formation and inducing more flowers usually result in higher yield. However, the genes for this purpose have not been well characterized in pitaya. Previously, FLOWERING BHLHs (FBHs) have been identified as positive regulators of flower formation. In the present work, a total of eight FBHs were identified in pitaya. This is a greater number than in beet and spinach, possibly because of the recent whole-genome duplication that occurred in the pitaya genome. The phylogenetic tree indicated that the FBHs could be divided into three groups. In TYPE II, the genes of Caryophyllales encode atypical FBHs and are generated by dispersed duplication. The Ka/Ks ratios indicated that HpFBHs are under purifying selection. Promoter and expression analysis of HpFBHs revealed that they are spatiotemporally activated in flower-related tissues and responsive to multiple abiotic stresses. These results indicated that HpFBHs are involved in the flower formation of pitaya. Therefore, typical HpFBH1/3 from TYPE III and an atypical HpFBH8 from TYPE II were selected for functional verification. HpFBH3 was found to heterodimerize with HpFBH1 in the nucleus using subcellular localization, yeast two-hybrid and luciferase complementation assays. With bioinformatic analysis, all HpFBHs were predicted to transactivate downstream genes via binding to the E-boxes, which were frequently detected in the promoters of HpCOs, HpFTs and HpSOC1s. RNA-Seq datasets showed that these flowering accelerators were expressed in coordination with HpFBH3. Yeast one-hybrid and dual-luciferase reporter assays further verified that HpFBH3 transactivated HpCO7 by selectively binding to the E-boxes in the promoter. Moreover, ectopic overexpression of HpFBH3 accelerated flower formation in Arabidopsis. In summary, this study systematically characterized the typical HpFBHs, especially HpFBH3, as positive regulators of flower formation, which could be target genes for the genetic improvement of pitaya.

Chromosome-Scale Genome Assembly for Soft-Stem Bulrush (Schoenoplectus tabernaemontani) Confirms a Clade-Specific Whole-Genome Duplication in Cyperaceae.

Schoenoplectus tabernaemontani (C. C. Gmelin) Palla is a typical macrophyte in diverse wetland ecosystems. This species holds great potential in decontamination applications and carbon sequestration. Previous studies have shown that this species may have experienced recent polyploidization. This would make S. tabernaemontani a unique model to study the processes and consequences of whole-genome duplications in the context of the well-documented holocentric chromosomes and dysploidy events in Cyperaceae. However, the inference was not completely solid because it lacked homology information that is essential to ascertain polyploidy. We present here the first chromosome-level genome assembly for S. tabernaemontani. By combining Oxford Nanopore Technologies (ONT) long reads and Illumina short reads, plus chromatin conformation via the Hi-C method, we assembled a genome spanning 507.96 Mb, with 99.43% of Hi-C data accurately mapped to the assembly. The assembly contig N50 value was 3.62 Mb. The overall BUSCO score was 94.40%. About 68.94% of the genome was comprised of repetitive elements. A total of 36,994 protein-coding genes were predicted and annotated. Long terminal repeat retrotransposons accounted for ∼26.99% of the genome, surpassing the content observed in most sequenced Cyperid genomes. Our well-supported haploid assembly comprised 21 pseudochromosomes, each harboring putative holocentric centromeres. Our findings corroborated a karyotype of 2n = 2X = 42. We also confirmed a recent whole-genome duplication occurring after the divergence between Schoenoplecteae and Bolboschoeneae. Our genome assembly expands the scope of sequenced genomes within the Cyperaceae family, encompassing the fifth genus. It also provides research resources on Cyperid evolution and wetland conservation.

Human lncRNAs harbor conserved modules embedded in different sequence contexts

We analyzed the structure of human long non-coding RNA (lncRNAs) genes to investigate whether the non-coding transcriptome is organized in modular domains, as is the case for protein-coding genes. To this aim, we compared all known human lncRNA exons and identified 340 pairs of exons with high sequence and/or secondary structure similarity but embedded in a dissimilar sequence context. We grouped these pairs in 106 clusters based on their reciprocal similarities. These shared modules are highly conserved between humans and the four great ape species, display evidence of purifying selection and likely arose as a result of recent segmental duplications. Our analysis contributes to the understanding of the mechanisms driving the evolution of the non-coding genome and suggests additional strategies towards deciphering the functional complexity of this class of molecules.

Genomic and transcriptomic analyses highlight evolutionary and functional characteristics of WRKY genes in Asterids

WRKY transcription factors regulate development, dormancy, germination, senescence, and reactions to abiotic and biotic stress. Asterids, a major group of eudicots, are commercially and pharmacologically important. However, large-scale WRKY gene family analyses in Asterids are lacking. We performed genome-wide re-annotation and downstream analyses of WRKY genes in nine Asterid species in addition to Arabidopsis thaliana and Beta vulgaris. We identified a total of 1,013 WRKY genes, 91 of which were newly annotated in our analysis. These were divided into six subgroups based on domain structure, phylogeny, and motif composition. Duplication analysis revealed increased copy numbers of WRKY genes belonging to specific subgroups in Helianthus annuus (sunflower), Actinidia chinensis (kiwifruit), and Olea europaea var. sylvestris (wild olive). Both H. annuus and A. chinensis displayed recent duplications of the WRKY gene after their divergence, whereas O. europaea var. sylvestris showed ancient duplication of WRKY genes. Transcriptome analyses suggested the potential function of WRKY genes in responses to abiotic and biotic stresses in H. annuus and A. chinensis, respectively. Our data shed light on the evolutionary and functional characteristics of WRKY genes, especially among Asterid plant species.