Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

Beyond the trinity: unraveling a fourth clade in the PEBP gene family in plants

KEY MESSAGE

Proposal for a new fourth PEBP gene group (SFT-like) in a genomic context different from 21 the other three. FT/TFL groups evolved from MFT, but then became sub-, neo-functionalized. The phosphatidylethanolamine-binding protein (PEBP) gene family plays crucial roles in plant development, principally involved in flowering time regulation and seed development. Traditionally, PEBP genes are classified into three clades: MOTHER OF FT AND TFL1 (MFT), FLOWERING LOCUS T (FT), and TERMINAL FLOWER 1 (TFL). We used phylogenomic and microsynteny network analyses to explore the PEBP family across 275 plant genomes from different lineages. The phylogenetic tree of the identified 3707 PEBP proteins allows us to visualize a fourth clade within the PEBP family. This new clade, named SFT (Sibling of FT/TFL), is closely related to the MFT clade but sister to the branch point of FT/TFL subfamilies, suggesting a long-standing evolutionary divergence. In addition, the SFT subfamily is in a different genomic context, whereas FT and TFL share a common origin with MFT. Motif analyzes show differences between this new clade and those already reported, suggesting functions other than flowering or seed development. The Ka/Ks analysis also suggests that SFT clade had fewer duplication events, so these genes could have an important function for the plant that had not yet been elucidated. These findings offer new insights into the evolutionary history and functional diversification of PEBP genes in plants. This study provides an update on the classification of the PEBP family. By understanding the syntenic relationships and evolutionary dynamics within the PEBP family, this research sets the stage for future functional studies on PEBP genes in plant biology, particularly the recently identified SFT clade.

Novel repetitive elements in plant-specific tails of Gγ proteins as the functional unit in G-protein signaling in crops

Heterotrimeric G-proteins act as molecular switches in signal transduction in response to stimuli in all eukaryotes. However, what specifies G-protein signaling in plants and how the mechanism evolved and diverged remain unsolved. Here, we found that the recently evolved tails of three Gγ subunits, Dense and erect panicle 1 (DEP1), G-protein gamma subunit 2 of type C (GGC2), and Grain size 3 (GS3), determine their distinct functions and specify grain size in rice (Oryza sativa L.). These Gγ subunits originated and expanded by an ancestral σ duplication ∼130 million years ago (mya) and a pancereal ρ duplication ∼70 mya in monocots, increasing genome complexity and inspiring functional innovations. In particular, through the comprehensive creation of artificial chimeric Gγ proteins, we found that this signaling selectivity is driven by repetitive elements and a link region hidden in plant-specific Gγ tails, allowing crops to switch from positive regulation to negative control. Unlike the tails, the conserved Gγ heads did not bias the signaling specificity; however, the change in the interaction between the mutated Gβ and Gγ affected the subsequent downstream signal transduction and grain size. Manipulating G-protein signaling also affects organ size in maize (Zea mays) and is expected to constitute a general mechanism for crop improvement. Collectively, these findings reveal that plant-specific Gγ tails drive signaling selectivity and serve as valuable targets for optimizing crop traits through G-protein manipulation.

The MYB-related transcription factor family in rubber dandelion (Taraxacum kok-saghyz): An insight into a latex-predominant member, TkMYBR090

MYB-related (MYBR) proteins play diverse roles in plant growth and development. However, the MYBR genes in Taraxacum kok-saghyz, a promising alternative source of natural rubber, a valuable biopolymer, remain scarcely investigated. Here, a total of 122 MYBR genes, namely TkMYBRs, were identified and classified into the groups of GARP-like, CCA1-like/R-R, and a heterogenous one in T. kok-saghyz. Collinearity analysis revealed a high similarity in MYBRs across two Taraxacum species with contrasting rubber yield. TkMYBR090 showed predominant expression in latex, the cytoplasm of rubber-producing laticifers. Transient overexpression of TkMYBR090 in tobacco and T. kok-saghyz demonstrated its localizations in nucleus and cytoplasm. Yeast two-hybrid assay revealed that the C-terminus of TkMYBR090 possessed transcriptional activation activity. DAP-seq analysis identified 18,232 TkMYBR090-targeted candidate genes, and four significantly enriched TkMYBR090 DNA-binding promoter motifs that were validated by yeast one-hybrid assay. The binding of TkMYBR090 on the promoter of an ascorbate oxidase gene was verified by yeast one-hybrid and dual luciferase activity assays, suggesting a role in ROS metabolism. Such assumption was supported by heterologous expression assays of TkMYBR090 in tobacco and yeast. This study is beneficial to further functional dissection of MYBRs in T. kok-saghyz, especially the roles in development and function of rubber-producing laticifers.

A chromosome-level genome assembly of the varied leaved jewelflower, Streptanthus diversifolius, reveals a recent whole genome duplication

The Streptanthoid complex, a clade of primarily Streptanthus and Caulanthus species in the Thelypodieae (Brassicaceae) is an emerging model system for ecological and evolutionary studies. This complex spans the full range of the California Floristic Province including desert, foothill, and mountain environments. The ability of these related species to radiate into dramatically different environments makes them a desirable study subject for exploring how plant species expand their ranges and adapt to new environments over time. Ecological and evolutionary studies for this complex have revealed fascinating variation in serpentine soil adaptation, defense compounds, germination, flowering, and life history strategies. Until now a lack of publicly available genome assemblies has hindered the ability to relate these phenotypic observations to their underlying genetic and molecular mechanisms. To help remedy this situation, we present here a chromosome-level genome assembly and annotation of Streptanthus diversifolius, a member of the Streptanthoid Complex, developed using Illumina, Hi-C, and HiFi sequencing technologies. Construction of this assembly also provides further evidence to support the previously reported recent whole genome duplication unique to the Thelypodieae. This whole genome duplication may have provided individuals in the Streptanthoid Complex the genetic arsenal to rapidly radiate throughout the California Floristic Province and to occupy commonly inhospitable environments including serpentine soils.

Allelic variation and duplication of the dmrt1 were associated with sex chromosome turnover in three representative Scatophagidae fish species

Fish species of the family Scatophagidae possessing known candidate sex-determining genes (male-specific dmrt1Ys), offer suitable models for studying sex chromosome evolution. Here, we analyzed sex chromosome turnover events in three representative fish species of the family Scatophagidae, belonging to the genera Scatophagus and Selenotoca, which diverged 12.8 million years ago (Mya). Prior to the divergence of Sc. argus and Sc. tetracanthus 7.2 Mya, their dmrt1Y was differentiated from its locus, the truncated dmrt1ΔX, through allelic variation. The Y chromosome (Chr1) of Sc. tetracanthus is the result of the fusion of the original Y chromosome (Chr4) with an autosome (Chr13). The Se. multifasciata dmrt1Y arose from a duplication of dmrt1 on Chr4 and then translocated to the new Y chromosome (Chr18). The divergent evolutionary trajectories of the dmrt1Ys were accompanied by sex chromosome turnover in these three species. The sex chromosomes of the Scatophagidae family have evolved rapidly, albeit not randomly.

Identification and Characterization of Histone Modification Gene Families and Their Expression Patterns During Pod and Seed Development in Peanut

Histone methylation and acetylation play potential roles in plant growth and development through various histone modification (HM) genes. However, studies of HM genes are still limited in peanut (Arachis hypogaea L.), a globally important oilseed crop. Here, comprehensive identification and investigation of HM genes were performed using the whole genome of peanut, and a total of 207 AhHMs encoding 108 histone methyltransferases, 51 histone demethylases, 16 histone acetylases, and 32 histone deacetylases were identified. Detailed analysis of these AhHMs, including chromosome locations, gene structures, protein motifs, and protein-protein interactions, was performed. Tandem, segmental, transposed, dispersed, and whole-genome duplications were involved in the evolution and expansion of the HM gene families in peanut. Ka/Ks analysis indicated that the AhHMs underwent purifying selection. The expression profiles of the 207 AhHMs were investigated during the pod and seed development stages on the basis of the transcriptome sequencing results. Quantitative real-time PCR confirmed that eight AhHMs were differentially expressed during pod and seed development. These results provide data support for further studying the epigenetic mechanism of peanut histones, deepen the understanding of seed development, and provide a new direction for the cultivation of more high-yield and high-quality peanut varieties.

Lineage-Specific Class-A GPCR Dynamics Reflect Diverse Chemosensory Adaptations in Lophotrochozoa

Sensing external chemosensory cues via Class-A G protein-coupled receptors (GPCRs) is crucial for a multitude of behavioral and biological functions, influencing animal evolution and ecological adaptations. While extensively studied in vertebrates and echinoderms, the role of GPCR-mediated chemoreception in major protostome clades like Lophotrochozoa remains obscure despite their remarkable ecological adaptations across diverse aquatic and terrestrial environments. Utilizing 238 lophotrochozoan genomes across eight phyla, we conducted a large-scale comparative genomics analysis to identify lineage-specific expansions of Class-A GPCR subsets that are likely adapted for chemoreception. Using phylogeny and orthology-inference-based clustering, we distinguished these expansions from conserved orthogroups of prospective endogenous ligand-binding Class-A GPCR subsets. Across phyla, lineage-specific expansions correlated with adaptations to various habitats, ecological niches, and lifestyles, while the influence of whole-genome duplications in driving these lineage-specific expansions appeared to be less significant. Species adapted to various coastal, freshwater, and terrestrial habitats across several classes of Mollusca, Annelida, and other analyzed phyla exhibit large and diverse lineage-specific expansions, while adaptations to extreme deep-sea environments, parasitic lifestyles, sessile behaviors, or alternative chemosensory mechanisms consistently exhibit reductions. Sequence heterogeneity, signatures of positive selection, and conformational flexibility in ligand-binding pockets further highlighted adaptations to environmental signals. In summary, the evolutionary dynamics of Class-A GPCRs in lophotrochozoans reveal a widespread pattern of lineage-specific expansions driven by adaptations for chemoreception across diverse environmental niches, mirroring the trends and prominent roles seen in deuterostome lineages. The comprehensive datasets spanning numerous genomes offer a valuable foundation for advancing GPCR-mediated chemoreception studies in Lophotrochozoa.

Genomic investigation of plant secondary metabolism: insights from synteny network analysis of oxidosqualene cyclase flanking genes

The clustered distribution of genes involved in metabolic pathways within the plant genome has garnered significant attention from researchers. By comparing and analyzing changes in the flanking regions of metabolic genes across a diverse array of species, we can enhance our understanding of the formation and distribution of biosynthetic gene clusters (BGCs). In this study, we have designed a workflow that uncovers and assesses conserved positional relationships between genes in various species by using synteny neighborhood networks (SNN). This workflow is then applied to the analysis of flanking genes associated with oxidosqualene cyclases (OSCs). The method allows for the recognition and comparison of homologous blocks with unique flanking genes accompanying different subfamilies of OSCs. The examination of the flanking genes of OSCs in 122 plant species revealed multiple genes with conserved positional relationships with OSCs in angiosperms. Specifically, the earliest adjacency of OSC genes and CYP716 genes first appeared in basal eudicots, and the nonrandom occurrence of CYP716 genes in the flanking region of OSC persists across different lineages of eudicots. Our study showed the substitution of genes in the flanking region of the OSC varies across different plant lineages, and our approach facilitates the investigation of flanking gene rearrangements in the formation of OSC-related BGCs.

Comparative analysis using a chromosome-scale genome assembly for Funaria hygrometrica suggests greater collinearity in mosses than in seed plants

Mosses, the largest lineage of seed-free plants, have smaller and less variable genome sizes than flowering plants. Nevertheless, whether this difference results from divergent genome dynamics is poorly known. Here, we use newly generated chromosome-scale genome assemblies for Funaria hygrometrica and comparative analysis with other moss and seed plant genomes to investigate moss genome dynamics. Although some aspects of moss genome dynamics are seed plant-like, such as the mechanism of genome size change and de novo gain/loss of genes, moss genomes retain higher synteny, and collinearity over evolutionary time than seed plant genomes. Furthermore, transposable elements and genes are more evenly distributed along chromosomes in mosses than in seed plants, a feature shared with other sequenced seed-free plant genomes. Overall, our findings support the hypothesis that large-scale genome structure and dynamics of mosses and seed plants differ. In particular, our data suggest a lower rate of gene order reshuffling along chromosomes in mosses compared to seed plants. We speculate that such lower rate of structural genomic variation and unique chromosome structure in mosses may contribute to their relatively smaller and less variable genome sizes.

Genome-wide identification, characterization and expression analysis of tubulin gene family in Populus deltoides

BACKGROUND

Tubulin proteins, the main components of microtubules in all eukaryotes, are involved in numerous aspects of plant morphogenesis and adaptation to the environment. In woody plants, microtubules are closely associated with the orientation of cellulose microfibril deposition in the secondary xylem cells and thereby exert an influence on the strength and flexibility of wood. Three major types of tubulin proteins-α-, β- and γ-tubulin-are ubiquitously present in all flowering plants, with α- and β- tubulin serving as basic subunits of microtubules and γ-tubulin directing microtubule nucleation. Compared with herbaceous plants, information on tubulin gene family has been limited in forest trees. This study aimed to characterize the tubulin gene family in the model forest tree Populus deltoides.

RESULT

Based on the whole genome sequence of P. deltoides, 25 PdTubulin genes were identified, including 6 PdTUAs, 17 PdTUBs, and 2 PdTUBGs were identified, with an uneven distribution across 14 chromosomes. Unlike Arabidopsis, which has only three pairs of tubulin paralogs, nearly all PdTubulin were paralogous duplicates, primarily generated by p-whole genome duplication (WGD), γ-WGD, or segmental duplication, indicating multiple rounds of gene family expansion. After the duplication events, the number of TUA genes in Populus was more strictly constrained compared to TUB genes. All paralogous and orthologous tubulin pairs have been under strong purifying selection. Expression analysis revealed that each PdTubulin gene was preferentially expressed in one of three organs: root, leaf, or stem. 5 PdTUB paralogs exhibited similar expression patterns, suggesting potential redundancy. Additionally, expression analysis in male and female floral buds across developmental stages indicated that different members might be involved in sex-specific processes.

Harnessing the spatial and transcriptional regulation of monoterpenoid indole alkaloid metabolism in Alstonia scholaris leads to the identification of broad geissoschizine cyclase activities

Monoterpene indole alkaloids (MIAs) are valuable metabolites produced in numerous medicinal plants from the Apocynaceae family such as Alstonia scholaris, which synthesizes strictamine, a MIA displaying neuropharmacological properties of a potential importance. To get insights into the MIA metabolism in A. scholaris, we studied here both the spatial and transcriptional regulations of MIA genes by performing a robust transcriptomics analysis of the main plant organs, leaf epidermis but also by sequencing RNA from leaves transiently overexpressing the master transcriptional regulator MYC2. These transcriptomic studies notably demonstrated that the first steps of the MIA pathway are successively distributed in the internal phloem associated parenchyma and epidermis, and that MYC2 exerts a remarkable transcriptional effect by modulating the expression of around 1000 genes. By combining these distinct datasets, we initiated the search for MIA-related genes encoding CYP71, based on the similarity of expression compared to already known MIA genes. Transient expression of these candidates in Nicotiana benthamiana leaves and yeast notably led to the identification of a related isoform of rhazimal synthase (RHS) capable of converting the MIA precursor geissoschizine into akuammicine, strictamine and 16-epi-pleiocarpamine. Investigating its catalytic mechanism revealed that strictamine results from rhazimal deformylation and that a similar mechanism may also explain 16-epi-pleiocarpamine synthesis. This prompted us to rename these enzymes geissoschizine cyclase due to their capacity of cyclizing geissoschizine into three different MIA scaffolds and to form both C-C and C-N bonds. This identification thus illustrates the potential of integrating spatial and transcriptional regulation analysis for MIA gene identification.

Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region

Amaranthus palmeri (Palmer amaranth), Amaranthus retroflexus (redroot pigweed), and Amaranthus hybridus (smooth pigweed) are troublesome weeds that are economically damaging to several cropping systems. Collectively referred to as "pigweeds," these species are incredibly adaptive and have become successful competitors in diverse agricultural settings. The development of genomic resources for these species promises to facilitate the elucidation of the genetic basis of traits such as biotic and abiotic stress tolerance (e.g., herbicide resistance) and sex determination. Here, we sequenced and assembled chromosome-level genomes of these three pigweeds. By combining the haplotype-resolved assembly of A. palmeri with existing restriction site-associated DNA sequencing data, we identified an approximately 2.84 Mb region on chromosome 3 of Hap1 that is male-specific and contains 37 genes. Transcriptomic analysis revealed that two genes, RESTORER OF FERTILITY 1 (RF1) and TLC DOMAIN-CONTAINING PROTEIN (TLC), within the male-specific region were upregulated in male individuals across the shoot apical meristem, the floral meristem, and mature flowers, indicating their potential involvement in sex determination in A. palmeri. In addition, we rigorously classified cytochrome P450 genes in all three pigweeds due to their involvement in non-target-site herbicide resistance. Finally, we identified contiguous extrachromosomal circular DNA (eccDNA) in A. palmeri, a critical component of glyphosate resistance in this species. The findings of this study advance our understanding of sex determination in A. palmeri and provide genomic resources for elucidating the genetic basis and evolutionary origins of adaptive traits within the genus.

Chromosome-level reference genome for the Jonah crab, Cancer borealis

The Jonah crab, Cancer borealis, is integral to marine ecosystems and supports a rapidly growing commercial fishery in the northwest Atlantic Ocean. This species also has a long history as a model for neuroscience that has expanded our understanding of central pattern generators, neuromodulation, synaptic plasticity, and the connectivity of neural circuits. Here, we present a highly contiguous reference genome for the Jonah crab that will provide an essential resource to advance fisheries, conservation, and biomedical research. Using a combination of PacBio long-read sequencing and Omni-C scaffolding, we generated a final genome assembly spanning 691 Mb covering 51 chromosome-length scaffolds and 106 additional contigs. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis indicated a high-quality assembly with a completeness score of 90.8%. Repeat annotation identified 1,649 repeat families making up 48.27% of the Jonah crab genome. Gene model predictions annotated 24,830 protein coding genes with a 92.3% BUSCO score. Gene family evolution analysis revealed the expansion of gene families associated with nervous system function, and targeted analysis revealed an extensive repertoire of neural genes. The Jonah crab genome will not only provide a resource for neuroscience research but will also serve as a foundation to investigate adaptation to stress and population structure to support sustainable fisheries management during this time of rapidly changing environmental conditions in the northwest Atlantic Ocean.

Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories

Balanced mating type polymorphisms offer a distinct window into the forces shaping sexual reproduction strategies. Multiple hermaphroditic genera in Juglandaceae, including walnuts (Juglans) and hickories (Carya), show a 1:1 genetic dimorphism for male versus female flowering order (heterodichogamy). We map two distinct Mendelian inheritance mechanisms to ancient (>37 million years old) genus-wide structural DNA polymorphisms. The dominant haplotype for female-first flowering in Juglans contains tandem repeats of the 3' untranslated region of a gene putatively involved in trehalose-6-phosphate metabolism and is associated with increased cis gene expression in developing male flowers, possibly mediated by small RNAs. The Carya locus contains ~20 syntenic genes and shows molecular signatures of sex chromosome-like evolution. Inheritance mechanisms for heterodichogamy are deeply conserved, yet may occasionally turn over, as in sex determination.

Genome-based discovery of pachysiphine synthases in Tabernaemontana elegans

Plant-specialized metabolism represents an inexhaustible source of active molecules, some of which have been used in human health for decades. Among these, monoterpene indole alkaloids (MIAs) include a wide range of valuable compounds with anticancer, antihypertensive, or neuroactive properties. This is particularly the case for the pachysiphine derivatives which show interesting antitumor and anti-Alzheimer activities but accumulate at very low levels in several Tabernaemontana species. Unfortunately, genome data in Tabernaemontanaceae are lacking and knowledge on the biogenesis of pachysiphine-related MIAs in planta remains scarce, limiting the prospects for the biotechnological supply of many pachysiphine-derived biopharmaceuticals. Here, we report a raw version of the toad tree (Tabernaemontana elegans) genome sequence. These new genomic resources led to the identification and characterization of a couple of genes encoding cytochrome P450 with pachysiphine synthase activity. Our phylogenomic and docking analyses highlight the different evolutionary processes that have been recruited to epoxidize the pachysiphine precursor tabersonine at a specific position and in a dedicated orientation, thus enriching our understanding of the diversification and speciation of the MIA metabolism in plants. These gene discoveries also allowed us to engineer the synthesis of MIAs in yeast through the combinatorial association of metabolic enzymes resulting in the tailor-made synthesis of non-natural MIAs. Overall, this work represents a step forward for the future supply of pachysiphine-derived drugs by microbial cell factories.

The genome of Lupinus mutabilis: Evolution and genetics of an emerging bio-based crop

Lupinus mutabilis is an under-domesticated legume species from the Andean region of South America. It belongs to the New World lupins clade, which groups several lupin species displaying large genetic variation and adaptability to highly different environments. L. mutabilis is attracting interest as a potential multipurpose crop to diversify the European supply of plant proteins, increase agricultural biodiversity, and fulfill bio-based applications. This study reports the first high-quality L. mutabilis genome assembly, which is also the first sequenced assembly of a New World lupin species. Through comparative genomics and phylogenetics, the evolution of L. mutabilis within legumes and lupins is described, highlighting both genomic similarities and patterns specific to L. mutabilis, potentially linked to environmental adaptations. Furthermore, the assembly was used to study the genetics underlying important traits for the establishment of L. mutabilis as a novel crop, including protein and quinolizidine alkaloids contents in seeds, genomic patterns of classic resistance genes, and genomic properties of L. mutabilis mycorrhiza-related genes. These analyses pointed out copy number variation, differential genomic gene contexts, and gene family expansion through tandem duplications as likely important drivers of the genomic diversity observed for these traits between L. mutabilis and other lupins and legumes. Overall, the L. mutabilis genome assembly will be a valuable resource to conduct genetic research and enable genomic-based breeding approaches to turn L. mutabilis into a multipurpose legume crop.

Genome-wide and functional analysis of late embryogenesis abundant (LEA) genes during dormancy and sprouting periods of kernel consumption apricots (P. armeniaca L. × P. sibirica L.)

Late embryogenesis abundant (LEA) proteins play a crucial role in protecting cells from stress, making them potential contributors to abiotic stress tolerance. This study focuses on apricot (P. armeniaca L. × P. sibirica L.), where a comprehensive genome-wide analysis identified 54 LEA genes, categorized into eight subgroups based on phylogenetic relationships. Synteny analysis revealed 14 collinear blocks containing LEA genes between P. armeniaca × P. sibirica and Arabidopsis thaliana, with an additional 9 collinear blocks identified between P. armeniaca × P. sibirica and poplar. Examination of gene structure and conserved motifs indicated that these subgroups exhibit consistent exon-intron patterns and shared motifs. The expansion and duplication of LEA genes in P. armeniaca × P. sibirica were driven by whole-genome duplication (WGD), segmental duplication, and tandem duplication events. Expression analysis, utilizing RNA-seq data and quantitative real-time RT-PCR (qRT-PCR), indicated induction of PasLEA2-20, PasLEA3-2, PasLEA6-1, Pasdehydrin-3, and Pasdehydrin-5 in flower buds during dormancy and sprouting phases. Coexpression network analysis linked LEA genes with 15 cold-resistance genes. Remarkably, during the four developmental stages of flower buds in P. armeniaca × P. sibirica - physiological dormancy, ecological dormancy, sprouting period, and germination stage - the expression patterns of all PasLEAs coexpressed with cold stress-related genes remained consistent. Protein-protein interaction networks, established using Arabidopsis orthologs, emphasized connections between PasLEA proteins and cold resistance pathways. Overexpression of certain LEA genes in yeast and Arabidopsis conferred advantages under cold stress, including increased pod length, reduced bolting time and flowering time, improved survival and seed setting rates, elevated proline accumulation, and enhanced antioxidative enzymatic activities. Furthermore, these overexpressed plants exhibited upregulation of genes related to flower development and cold resistance. The Y1H assay confirmed that PasGBF4 and PasDOF3.5 act as upstream regulatory factors by binding to the promoter region of PasLEA3-2. PasDOF2.4, PasDnaJ2, and PasAP2 were also found to bind to the promoter of Pasdehydrin-3, regulating the expression levels of downstream genes. This comprehensive study explores the evolutionary relationships among PasLEA genes, protein interactions, and functional analyses during various stages of dormancy and sprouting in P. armeniaca × P. sibirica. It offers potential targets for enhancing cold resistance and manipulating flower bud dormancy in this apricot hybrid.

Expression and functional divergence of a type-A response regulator paralog pair formed by dispersed duplication during Populus deltoides evolution

Gene duplication and divergence are essential to plant evolution. The Arabidopsis type-A response regulator (ARR) family, negative regulators in cytokinin signaling, exemplifies gene expansion and differential retention. Despite extensive research, the understanding of type-A RR homologs in woody plants remains limited. In this study, the evolution history of type-A RR gene families across four rosids and one monocot has been comprehensively investigated. Focusing on Populus deltoides, a unique pair of dispersed duplicates, PdRR8 and PdFERR, is identified, and their duplication is estimated to have occurred in the common ancestor of the four rosids. The duplication remnants corresponding to PdRR8 have been retained in all rosids but the counterpart of PdFERR has been lost. In poplar, PdRR8 shows the highest expression levels in leaves, while PdFERR is specifically expressed in female floral buds. Among various external stimuli, cold strongly represses PdRR8 promoter activity, whereas 6-BA markedly inhibits that of PdFERR. Overexpression of PdRR8 in the Arabidopsis arr16arr17 double-mutant fully complements the reduced hydrotropic response. In contrast, PdFERR fails to rescue the hydrotropic defects of the mutant. Results of evolutionary, expression and functional analyses indicate that PdRR8, rather than PdFERR, is the true ortholog of the ARR16-ARR17 paralogs. Though PdRR8 and PdFERR originate from a common ancestral gene and evolve under strong negative selection, these two dispersed duplicates have exhibited differential expression and some degree of functional divergence.

Telomerase reverse transcriptase, a telomere length maintenance protein in alfalfa (Medicago sativa), confers Arabidopsis thaliana seeds aging tolerance via modulation of telomere length

Numerous studies have investigated seed aging, with a particular emphasis on the involvement of reactive oxygen species. Reactive oxygen species diffuse into the nucleus and damage telomeres, resulting in loss of genetic integrity. Telomerase reverse transcriptase (TERT) plays an essential role in maintaining plant genomic stability. Genome-wide analyses of TERT genes in alfalfa (Medicago sativa) have not yet been conducted, leaving a gap in our understanding of the mechanisms underlying seed aging associated with TERT genes. In this study, four MsTERT genes were identified in the alfalfa genome. The expression profiles of the four MsTERT genes during seed germination indicated that MS. gene79077 was significantly upregulated by seed aging. Transgenic seeds overexpressing MS. gene79077 in Arabidopsis exhibited enhanced tolerance to seed aging by reducing the levels of H2O2 and increasing telomere length and telomerase activity. Furthermore, transcript profiling of aging-treated Arabidopsis wild-type and overexpressing seeds showed an aging response in genes related to glutathione-dependent detoxification and antioxidant defense pathways. These results revealed that MS. gene79077 conferred Arabidopsis seed-aging tolerance via modulation of antioxidant defense and telomere homeostasis. This study provides a new way to understand stress-responsive MsTERT genes for the potential genetic improvement of seed vigor.

Genome-wide identification and expression analyses of SWEET gene family reveal potential roles in plant development, fruit ripening and abiotic stress responses in cranberry (Vaccinium macrocarpon Ait)

The sugars will eventually be exported transporter (SWEET) family is a novel class of sugar transporters that play a crucial role in plant growth, development, and responses to stress. Cranberry (Vaccinium macrocarpon Ait.) is a nutritious berry with economic importance, but little is known about SWEET gene family functions in this small fruit. In this research, 13 VmSWEET genes belonging to four clades were identified in the cranberry genome for the first time. In the conserved domains, we observed seven phosphorylation sites and four amino acid residues that might be crucial for the binding function. The majority of VmSWEET genes in each clade shared similar gene structures and conserved motifs, showing that the VmSWEET genes were highly conserved during evolution. Chromosomal localization and duplication analyses showed that VmSWEET genes were unevenly distributed in eight chromosomes and two pairs of them displayed synteny. A total of 79 cis-acting elements were predicted in the promoter regions of VmSWEETs including elements responsive to plant hormones, light, growth and development and stress responses. qRT-PCR analysis showed that VmSWEET10.1 was highly expressed in flowers, VmSWEET16 was highly expressed in upright and runner stems, and VmSWEET3 was highly expressed in the leaves of both types of stems. In fruit, the expression of VmSWEET14 and VmSWEET16 was highest of all members during the young fruit stage and were downregulated as fruit matured. The expression of VmSWEET4 was higher during later developmental stages than earlier developmental stages. Furthermore, qRT-PCR results revealed a significant up-regulation of VmSWEET10.2, under osmotic, saline, salt-alkali, and aluminum stress conditions, suggesting it has a crucial role in mediating plant responses to various environmental stresses. Overall, these results provide new insights into the characteristics and evolution of VmSWEET genes. Moreover, the candidate VmSWEET genes involved in the growth, development and abiotic stress responses can be used for molecular breeding to improve cranberry fruit quality and abiotic stress resistance.

Annelid Comparative Genomics and the Evolution of Massive Lineage-Specific Genome Rearrangement in Bilaterians

The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here, we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while many annelid lineages have maintained the conserved bilaterian genome structure, the Clitellata, a group containing leeches and earthworms, possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show that, compared to the last common ancestor of bilaterians, leeches and earthworms have among the most highly rearranged genomes of any currently sampled species. We further show that bilaterian genomes can be classified into two distinct categories-high and low rearrangement-largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion, or rapid, all-encompassing changes over short evolutionary timescales.

Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes

Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here, we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii. We show that weeping willow arose from crosses between a female ancestor from the Salix-clade, which has XY sex chromosomes on chromosome 7, and a male ancestor from the Vetrix-clade, which has ancestral XY sex chromosomes on chromosome 15. We find that weeping willow has one pair of sex chromosomes, ZW on chromosome 15, that derived from the ancestral XY sex chromosomes in the male ancestor of the Vetrix-clade. Moreover, the ancestral 7X chromosomes from the female ancestor of the Salix-clade have reverted to autosomal inheritance. Duplicated intact ARR17-like genes on the four homologous chromosomes 19 likely have contributed to the maintenance of dioecy during polyploidization and sex chromosome turnover. Taken together, our results suggest the rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow.

Hordedane diterpenoid phytoalexins restrict Fusarium graminearum infection but enhance Bipolaris sorokiniana colonization of barley roots

Plant immunity is a multilayered process that includes recognition of patterns or effectors from pathogens to elicit defense responses. These include the induction of a cocktail of defense metabolites that typically restrict pathogen virulence. Here, we investigate the interaction between barley roots and the fungal pathogens Bipolaris sorokiniana (Bs) and Fusarium graminearum (Fg) at the metabolite level. We identify hordedanes, a previously undescribed set of labdane-related diterpenoids with antimicrobial properties, as critical players in these interactions. Infection of barley roots by Bs and Fg elicits hordedane synthesis from a 600-kb gene cluster. Heterologous reconstruction of the biosynthesis pathway in yeast and Nicotiana benthamiana produced several hordedanes, including one of the most functionally decorated products 19-β-hydroxy-hordetrienoic acid (19-OH-HTA). Barley mutants in the diterpene synthase genes of this cluster are unable to produce hordedanes but, unexpectedly, show reduced Bs colonization. By contrast, colonization by Fusarium graminearum, another fungal pathogen of barley and wheat, is 4-fold higher in the mutants completely lacking hordedanes. Accordingly, 19-OH-HTA enhances both germination and growth of Bs, whereas it inhibits other pathogenic fungi, including Fg. Analysis of microscopy and transcriptomics data suggest that hordedanes delay the necrotrophic phase of Bs. Taken together, these results show that adapted pathogens such as Bs can subvert plant metabolic defenses to facilitate root colonization.

Genomic Anatomy of Homozygous XX Females and YY Males Reveals Early Evolutionary Trajectory of Sex-determining Gene and Sex Chromosomes in Silurus Fishes

Sex chromosomes display remarkable diversity and variability among vertebrates. Compared with research on the X/Y and Z/W chromosomes, which have long evolutionary histories in mammals and birds, studies on the sex chromosomes at early evolutionary stages are limited. Here, we precisely assembled the genomes of homozygous XX female and YY male Lanzhou catfish (Silurus lanzhouensis) derived from an artificial gynogenetic family and a self-fertilized family, respectively. Chromosome 24 (Chr24) was identified as the sex chromosome based on resequencing data. Comparative analysis of the X and Y chromosomes showed an approximate 320 kb Y-specific region with a Y-specific duplicate of anti-Mullerian hormone type II receptor (amhr2y), which is consistent with findings in 2 other Silurus species but on different chromosomes (Chr24 of Silurus meridionalis and Chr5 of Silurus asotus). Deficiency of amhr2y resulted in male-to-female sex reversal, indicating that amhr2y plays a male-determining role in S. lanzhouensis. Phylogenetic analysis and comparative genomics revealed that the common sex-determining gene amhr2y was initially translocated to Chr24 of the Silurus ancestor along with the expansion of transposable elements. Chr24 was maintained as the sex chromosome in S. meridionalis and S. lanzhouensis, whereas a sex-determining region transition triggered sex chromosome turnover from Chr24 to Chr5 in S. asotus. Additionally, gene duplication, translocation, and degeneration were observed in the Y-specific regions of Silurus species. These findings present a clear case for the early evolutionary trajectory of sex chromosomes, including sex-determining gene origin, repeat sequence expansion, gene gathering and degeneration in sex-determining region, and sex chromosome turnover.

Species-tree topology impacts the inference of ancient whole-genome duplications across the angiosperm phylogeny

PREMISE

The history of angiosperms is marked by repeated rounds of ancient whole-genome duplications (WGDs). Here we used state-of-the-art methods to provide an up-to-date view of the distribution of WGDs in the history of angiosperms that considers both uncertainty introduced by different WGD inference methods and different underlying species-tree hypotheses.

METHODS

We used the distribution synonymous divergences (Ks) of paralogs and orthologs from transcriptomic and genomic data to infer and place WGDs across two hypothesized angiosperm phylogenies. We further tested these WGD hypotheses with syntenic inferences and Bayesian models of duplicate gene gain and loss.

RESULTS

The predicted number of WGDs in the history of angiosperms (~170) based on the current taxon sampling is largely similar across different inference methods, but varies in the precise placement of WGDs on the phylogeny. Ks-based methods often yield alternative hypothesized WGD placements due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation. However, errors in species-tree inference can still produce spurious WGD hypotheses, regardless of method used.

CONCLUSIONS

Here we showed that different WGD inference methods largely agree on an average of 3.5 WGD in the history of individual angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the WGD inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods.

Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes

Scaffolding is crucial for constructing most chromosome-level genomes. The high-throughput chromatin conformation capture (Hi-C) technology has become the primary scaffolding strategy due to its convenience and cost-effectiveness. As sequencing technologies and assembly algorithms advance, constructing haplotype-resolved genomes is increasingly preferred because haplotypes can provide additional genetic information on allelic and non-allelic variations. ALLHiC is a widely used allele-aware scaffolding tool designed for this purpose. However, its dependence on chromosome-level reference genomes and a higher chromosome misassignment rate still impede the unravelling of haplotype-resolved genomes. Here we present HapHiC, a reference-independent allele-aware scaffolding tool with superior performance on chromosome assignment as well as contig ordering and orientation. In addition, we provide new insights into the challenges in allele-aware scaffolding by conducting comprehensive analyses on various adverse factors. Finally, with the help of HapHiC, we constructed the haplotype-resolved allotriploid genome for Miscanthus × giganteus, an important lignocellulosic bioenergy crop.

Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation

Pollinator-driven evolution of floral traits is thought to be a major driver of angiosperm speciation and diversification. Ophrys orchids mimic female insects to lure male pollinators into pseudocopulation. This strategy, called sexual deception, is species-specific, thereby providing strong premating reproductive isolation. Identifying the genomic architecture underlying pollinator adaptation and speciation may shed light on the mechanisms of angiosperm diversification. Here, we report the 5.2 Gb chromosome-scale genome sequence of Ophrys sphegodes. We find evidence for transposable element expansion that preceded the radiation of the O. sphegodes group, and for gene duplication having contributed to the evolution of chemical mimicry. We report a highly differentiated genomic candidate region for pollinator-mediated evolution on chromosome 2. The Ophrys genome will prove useful for investigations into the repeated evolution of sexual deception, pollinator adaptation and the genomic architectures that facilitate evolutionary radiations.

Genetic factors acting prior to dormancy in sour cherry influence bloom time the following spring

Understanding the process of Prunus species floral development is crucial for developing strategies to manipulate bloom time and prevent crop loss due to climate change. Here, we present a detailed examination of flower development from initiation until bloom for early- and late-blooming sour cherries (Prunus cerasus) from a population segregating for a major bloom time QTL on chromosome 4. Using a new staging system, we show floral buds from early-blooming trees were persistently more advanced than those from late-blooming siblings. A genomic DNA coverage analysis revealed the late-blooming haplotype of this QTL, k, is located on a subgenome originating from the late-blooming P. fruticosa progenitor. Transcriptome analyses identified many genes within this QTL as differentially expressed between early- and late-blooming trees during the vegetative-to-floral transition. From these, we identified candidate genes for the late bloom phenotype, including multiple transcription factors homologous to Reproductive Meristem B3 domain-containing proteins. Additionally, we determined that the basis of k in sour cherry is likely separate from candidate genes found in sweet cherry-suggesting several major regulators of bloom time are located on Prunus chromosome 4.

Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX

As different taxa evolve, gene order often changes slowly enough that chromosomal 'blocks' with conserved gene orders (synteny) are discernible. The MCScanX toolkit ( https://github.com/wyp1125/MCScanX ) was published in 2012 as freely available software for the detection of such 'colinear blocks' and subsequent synteny and evolutionary analyses based on genome-wide gene location and protein sequence information. Owing to its simplicity and high efficiency for colinear block detection, MCScanX provides a powerful tool for conducting diverse synteny and evolutionary analyses. Moreover, the detection of colinear blocks has been embraced as an integral step for pangenome graph construction. Here, new application trends of MCScanX are explored, striving to better connect this increasingly used tool to other tools and accelerate insight generation from exponentially growing sequence data. We provide a detailed protocol that covers how to install MCScanX on diverse platforms, tune parameters, prepare input files from data from the National Center for Biotechnology Information, run MCScanX and its visualization and evolutionary analysis tools, and connect MCScanX with external tools, including MCScanX-transposed, Circos and SynVisio. This protocol is easily implemented by users with minimal computational background and is adaptable to new data of interest to them. The data and utility programs for this protocol can be obtained from http://bdx-consulting.com/mcscanx-protocol .

A chromosome-scale assembly of Brassica carinata (BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions into B. juncea (AABB)

Brassica carinata (BBCC) commonly referred to as Ethiopian mustard is a natural allotetraploid containing the genomes of Brassica nigra (BB) and Brassica oleracea (CC). It is an oilseed crop endemic to the northeastern regions of Africa. Although it is under limited cultivation, B. carinata is valuable as it is resistant/highly tolerant to most of the pathogens affecting widely cultivated Brassica species of the U's triangle. We report a chromosome-scale genome assembly of B. carinata accession HC20 using long-read Oxford Nanopore sequencing and Bionano optical maps. The assembly has a scaffold N50 of ~39.8 Mb and covers ~1.11 Gb of the genome. We compared the long-read genome assemblies of the U's triangle species and found extensive gene collinearity between the diploids and allopolyploids with no evidence of major gene losses. Therefore, B. juncea (AABB), B. napus (AACC), and B. carinata can be regarded as strict allopolyploids. We cataloged the nucleotide-binding and leucine-rich repeat immune receptor (NLR) repertoire of B. carinata and, identified 465 NLRs, and compared these with the NLRs in the other Brassica species. We investigated the extent and nature of early-generation genomic interactions between the constituent genomes of B. carinata and B. juncea in interspecific crosses between the two species. Besides the expected recombination between the constituent B genomes, extensive homoeologous exchanges were observed between the A and C genomes. Interspecific crosses, therefore, can be used for transferring disease resistance from B. carinata to B. juncea and broadening the genetic base of the two allotetraploid species.

Genomic signatures of exceptional longevity and negligible aging in the long-lived red sea urchin

The red sea urchin (Mesocentrotus franciscanus) is one of the Earth's longest-living animals, reported to live more than 100 years with indeterminate growth, life-long reproduction, and no increase in mortality rate with age. To understand the genetic underpinnings of longevity and negligible aging, we constructed a chromosome-level assembly of the red sea urchin genome and compared it to that of short-lived sea urchin species. Genome-wide syntenic alignments identified chromosome rearrangements that distinguish short- and long-lived species. Expanded gene families in long-lived species play a role in innate immunity, sensory nervous system, and genome stability. An integrated network of genes under positive selection in the red sea urchin was involved in genomic regulation, mRNA fidelity, protein homeostasis, and mitochondrial function. Our results implicated known longevity genes in sea urchin longevity but also revealed distinct molecular signatures that may promote long-term maintenance of tissue homeostasis, disease resistance, and negligible aging.

Automated recognition of chromosome fusion using an alignment-free natural vector method

Chromosomal fusion is a significant form of structural variation, but research into algorithms for its identification has been limited. Most existing methods rely on synteny analysis, which necessitates manual annotations and always involves inefficient sequence alignments. In this paper, we present a novel alignment-free algorithm for chromosomal fusion recognition. Our method transforms the problem into a series of assignment problems using natural vectors and efficiently solves them with the Kuhn-Munkres algorithm. When applied to the human/gorilla and swamp buffalo/river buffalo datasets, our algorithm successfully and efficiently identifies chromosomal fusion events. Notably, our approach offers several advantages, including higher processing speeds by eliminating time-consuming alignments and removing the need for manual annotations. By an alignment-free perspective, our algorithm initially considers entire chromosomes instead of fragments to identify chromosomal structural variations, offering substantial potential to advance research in this field.

Genomic and transcriptomic studies on flavonoid biosynthesis in Lagerstroemia indica

BACKGROUND

Lagerstroemia indica is a widely cultivated ornamental woody shrub/tree of the family Lythraceae that is used as a traditional medicinal plant in East Asia and Egypt. However, unlike other ornamental woody plants, its genome is not well-investigated, which hindered the discovery of the key genes that regulate important traits and the synthesis of bioactive compounds.

RESULTS

In this study, the genomic sequences of L. indica were determined using several next-generation sequencing technologies. Altogether, 324.01 Mb sequences were assembled and 98.21% (318.21 Mb) of them were placed in 24 pseudo-chromosomes. The heterozygosity, repeated sequences, and GC residues occupied 1.65%, 29.17%, and 38.64% of the genome, respectively. In addition, 28,811 protein-coding gene models, 327 miRNAs, 552 tRNAs, 214 rRNAs, and 607 snRNAs were identified. The intra- and interspecies synteny and Ks analysis revealed that L. indica exhibits a hexaploidy. The co-expression profiles of the genes involved in the phenylpropanoid (PA) and flavonoid/anthocyanin (ABGs) pathways with the R2R3 MYB genes (137 members) showed that ten R2R3 MYB genes positively regulate flavonoid/anthocyanin biosynthesis. The colors of flowers with white, purple (PB), and deep purplish pink (DPB) petals were found to be determined by the levels of delphinidin-based (Dp) derivatives. However, the substrate specificities of LiDFR and LiOMT probably resulted in the different compositions of flavonoid/anthocyanin. In L. indica, two LiTTG1s (LiTTG1-1 and LiTTG1-2) were found to be the homologs of AtTTG1 (WD40). LiTTG1-1 was found to repress anthocyanin biosynthesis using the tobacco transient transfection assay.

CONCLUSIONS

This study showed that the ancestor L. indica experienced genome triplication approximately 38.5 million years ago and that LiTTG1-1 represses anthocyanin biosynthesis. Furthermore, several genes such as LiDFR, LiOMTs, and R2R3 LiMYBs are related to anthocyanin biosynthesis. Further studies are required to clarify the mechanisms and alleles responsible for flower color development.

Genome-Wide Analysis of the Liriodendron chinense Hsf Gene Family under Abiotic Stress and Characterization of the LcHsfA2a Gene

Heat shock factors (Hsfs) play a crucial role in plant defense processes. However, the distribution and functional characteristics of Hsf genes in the relict plant Liriodendron chinense are still unclear. In this study, a total of 19 LcHsfs were identified and divided into three separate subgroups, comprising 10 LcHsfA, 7 LcHsfB, and 2 LcHsfC genes, respectively, based on their phylogenetic tree and the presence/absence of conserved protein domains. Whole-genome duplication and segmental duplication led to an expansion of the LhHsf gene family. The promoters of LcHsf genes are enriched for different types of cis-acting elements, including hormone responsive and abiotic-stress-responsive elements. The expression of LcHsfA3, LcHsfA4b, LcHsfA5, LcHsfB1b, and LcHsfB2b increased significantly as a result of both cold and drought treatments. LcHsfA2a, LcHsfA2b, and LcHsfA7 act as important genes whose expression levels correlate strongly with the expression of the LcHsp70, LcHsp110, and LcAPX genes under heat stress. In addition, we found that transiently transformed 35S:LcHsfA2a seedlings showed significantly lower levels of hydrogen peroxide (H2O2) after heat stress and showed a stronger thermotolerance. This study sheds light on the possible functions of LcHsf genes under abiotic stress and identifies potentially useful genes to target for molecular breeding, in order to develop more stress-resistant varieties.

Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories

The maintenance of stable mating type polymorphisms is a classic example of balancing selection, underlying the nearly ubiquitous 50/50 sex ratio in species with separate sexes. One lesser known but intriguing example of a balanced mating polymorphism in angiosperms is heterodichogamy - polymorphism for opposing directions of dichogamy (temporal separation of male and female function in hermaphrodites) within a flowering season. This mating system is common throughout Juglandaceae, the family that includes globally important and iconic nut and timber crops - walnuts (Juglans), as well as pecan and other hickories (Carya). In both genera, heterodichogamy is controlled by a single dominant allele. We fine-map the locus in each genus, and find two ancient (>50 Mya) structural variants involving different genes that both segregate as genus-wide trans-species polymorphisms. The Juglans locus maps to a ca. 20 kb structural variant adjacent to a probable trehalose phosphate phosphatase (TPPD-1), homologs of which regulate floral development in model systems. TPPD-1 is differentially expressed between morphs in developing male flowers, with increased allele-specific expression of the dominant haplotype copy. Across species, the dominant haplotype contains a tandem array of duplicated sequence motifs, part of which is an inverted copy of the TPPD-1 3' UTR. These repeats generate various distinct small RNAs matching sequences within the 3' UTR and further downstream. In contrast to the single-gene Juglans locus, the Carya heterodichogamy locus maps to a ca. 200-450 kb cluster of tightly linked polymorphisms across 20 genes, some of which have known roles in flowering and are differentially expressed between morphs in developing flowers. The dominant haplotype in pecan, which is nearly always heterozygous and appears to rarely recombine, shows markedly reduced genetic diversity and is over twice as long as its recessive counterpart due to accumulation of various types of transposable elements. We did not detect either genetic system in other heterodichogamous genera within Juglandaceae, suggesting that additional genetic systems for heterodichogamy may yet remain undiscovered.

Phylogenomic curation of Ovate Family Proteins (OFPs) in the U's Triangle of Brassica L. indicates stress-induced growth modulation

The Ovate Family Proteins (OFPs) gene family houses a class of proteins that are involved in regulating plant growth and development. To date, there is no report of the simultaneous functional characterization of this gene family in all members of U's Triangle of Brassica. Here, we retrieved a combined total of 256 OFP protein sequences and analyzed their chromosomal localization, gene structure, conserved protein motif domains, and the pattern of cis-acting regulatory elements. The abundance of light-responsive elements like G-box, MRE, and GT1 motif suggests that OFPs are sensitive to the stimuli of light. The protein-protein interaction network analysis revealed that OFP05 and its orthologous genes were involved in regulating the process of transcriptional repression through their interaction with homeodomain transcription factors like KNAT and BLH. The presence of domains like DNA binding 2 and its superfamily speculated the involvement of OFPs in regulating gene expression. The biotic and abiotic stress, and the tissue-specific expression analysis of the RNA-seq datasets revealed that some of the genes such as BjuOFP30, and BnaOFP27, BolOFP11, and BolOFP10 were highly upregulated in seed coat at the mature stage and roots under various chemical stress conditions respectively which suggests their crucial role in plant growth and development processes. Experimental validation of prominent BnaOFPs such as BnaOFP27 confirmed their involvement in regulating gene expression under salinity, heavy metal, drought, heat, and cold stress. The GO and KEGG pathway enrichment analysis also sheds light on the involvement of OFPs in regulating plant growth and development. These findings have the potential to serve as a forerunner for future studies in terms of functionally diverse analysis of the OFP gene family in Brassica and other plant species.

A Multi-Omics Analysis Revealed the Diversity of the MYB Transcription Factor Family's Evolution and Drought Resistance Pathways

The MYB transcription factor family can regulate biological processes such as ABA signal transduction to cope with drought stress, but its evolutionary mechanism and the diverse pathways of response to drought stress in different species are rarely reported. In this study, a total of 4791 MYB family members were identified in 908,757 amino acid sequences from 12 model plants or crops using bioinformatics methods. It was observed that the number of MYB family members had a linear relationship with the chromosome ploidy of species. A phylogenetic analysis showed that the MYB family members evolved in subfamily clusters. In response to drought stress, the pathways of MYB transcription factor families exhibited species-specific diversity, with closely related species demonstrating a higher resemblance. This study provides abundant references for drought resistance research and the breeding of wheat, soybean, and other plants.

Genome-wide analysis of AP2/ERF gene and functional analysis of CqERF24 gene in drought stress in quinoa

Quinoa is a crop with high nutritional value and strong stress resistance. AP2/ERF transcription factors play a key role in plant growth and development. In this study, 148 AP2/ERF genes were identified in quinoa, which were divided into 5 subfamilies, including ERF, AP2, DREB, RAV and Soloist. The results showed that the number of introns ranged from 0 to 11, and the Motif 1-Motif 4 was highly conserved in most CqAP2/ERF proteins. The 148 CqAP2/ERF genes were distributed on 19 chromosomes. There were 93 pairs of duplicating genes in this family, and gene duplication played a critical role in the expansion of this family. Protein-protein interaction indicated that the proteins in CqAP2/ERF subfamily exhibited complex interactions, and GO enrichment analysis indicated that 148 CqAP2/ERF proteins were involved in transcription factor activity. In addition, CqAP2/ERF gene contains a large number of elements related to hormones in promoter region (IAA, GA, SA, ABA and MeJA) and stresses (salt, drought, low temperature and anaerobic induction). Transcriptome analysis under drought stress indicated that most of the CqAP2/ERF genes were responsive to drought stress, and subcellular localization indicated that CqERF24 was location in the nucleus, qRT-PCR results also showed that most of the genes such as CqERF15, CqERF24, CqDREB03, CqDREB14, CqDREB37 and CqDREB43 also responded to drought stress in roots and leaves. Overexpression of CqERF24 in Arabidopsis thaliana enhanced drought resistance by increasing antioxidant enzyme activity and activation-related stress genes, and the gene is sensitive to ABA, while silencing CqERF24 in quinoa decreased drought tolerance. In addition, overexpression of CqERF24 in quinoa calli enhanced resistance to mannitol. These results lay a solid foundation for further study on the role of AP2/ERF family genes in quinoa under drought stress.

The chromosome-level genome assembly of Fraxinus americana provides insights into the evolution of Oleaceae plants

White ash (Fraxinus americana linn.) originates from the southeastern United States. It is a tall and fast-growing tree species with strong salt-alkali resistance and cold tolerance, making it an important reforestation species and widely planted worldwide. Here, we completed the chromosome-level reference genome assembly of F. americana based on Illumina, PacBio, and Hi-C reads, with a genome size of 878.98 Mb, an N50 of 3.27 Mb, and a heterozygosity rate of 0.3 %. Based on de novo prediction, transcriptome prediction, and homology-based protein prediction, we obtained 39,538 genes. Approximately 843.21 Mb of the assembly genome was composed of 37,928 annotated protein-coding genes, with a gene function annotation rate of 95.93 %. 99.94 % of the overlap clusters (877.44 Mb) were anchored to 23 chromosomes. Synteny analysis of F. americana and other Oleaceae plants showed that F. americana underwent frequent chromosome rearrangements. The amplification of the Ale transposons effectively promoted the genome size of F. americana. Compared with other Oleaceae plants, the Glutathione S-transferase (GST) gene family in the F. americana genome has undergone significant expansion, which may help F. americana cope with adverse natural environments. Furthermore, we found that key enzyme-coding gene families related to lignin biosynthesis were expanded and highly expressed in F. americana leaves. These key genes drive lignin synthesis and benefit F. americana in fast-growing, as well as resisting biotic and abiotic stress. Overall, the F. americana genome assembly provides insights into the evolution of Oleaceae plants and provides abundant resources for breeding and germplasm conservation of white ash.

Divergent Retention of Sucrose Metabolism Genes after Whole Genome Triplication in the Tomato (Solanum lycopersicum)

Sucrose, the primary carbon transport mode and vital carbohydrate for higher plants, significantly impacts plant growth, development, yield, and quality formation. Its metabolism involves three key steps: synthesis, transport, and degradation. Two genome triplication events have occurred in Solanaceae, which have resulted in massive gene loss. In this study, a total of 48 and 65 genes from seven sucrose metabolism gene families in Vitis vinifera and Solanum lycopersicum were identified, respectively. The number of members comprising the different gene families varied widely. And there were significant variations in the pattern of gene duplication and loss in the tomato following two WGD events. Tandem duplication is a major factor in the expansion of the SWEET and Acid INV gene families. All the genes are irregularly distributed on the chromosomes, with the majority of the genes showing collinearity with the grape, particularly the CIN family. And the seven gene families were subjected to a purifying selection. The expression patterns of the different gene families exhibited notable variations. This study presents basic information about the sucrose metabolism genes in the tomato and grape, and paves the way for further investigations into the impact of SCT events on the phylogeny, gene retention duplication, and function of sucrose metabolism gene families in the tomato or Solanaceae, and the adaptive evolution of the tomato.

A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus

The Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have been hampered by the lack of genomic resources. Here, we present a high‐quality, haplotype‐resolved, chromosome‐scale genome assembly and annotation for M. fusca. The genome was assembled using high‐fidelity long‐reads and scaffolded using genetic maps and high‐throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co‐linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference‐quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA‐informed introgression breeding.

Chromosome-level genome assembly of the largefin longbarbel catfish (Hemibagrus macropterus)

The largefin longbarbel catfish, Hemibagrus macropterus, is an economically important fish species in southwestern China, with males growing faster than females. This study presents a high-quality chromosome-level genome assembly of the largefin longbarbel catfish, generated by integrating Illumina short reads, PacBio HiFi long reads, and Hi-C data. The assembled genome size was 858.5 Mb, with a contig and scaffold N50 of 5.8 Mb and 28.4 Mb, respectively. A total of 656 contigs were successfully anchored to 30 pseudochromosomes with a BUSCO score of 97.7%, consistent with the number of chromosomes analyzed by karyotype. The genome contained 29.5% repeat sequences, and a predicted total of 26,613 protein-coding genes, of which 25,769 (96.8%) were functionally annotated in different databases. Evolutionary analysis showed that H. macropterus was most closely related to H. wyckioides, with a divergence time of approximately 16.3 million years. Chromosomal syntenic relationships among H. macropterus, H. wyckioides, and Pelteobagrus fulvidraco revealed a one-to-one relationship for most chromosomes, except for break, fission, and inversion of some chromosomes. The first high-quality reference genome will not only provide a valuable genetic resource for the study of sex determination mechanisms and genetic breeding of largefin longbarbel catfish, but also contribute to comparative analyses of genome and chromosome evolution within Siluriformes.

Symmetric expression of ohnologs encoding conserved antiviral responses in tetraploid common carp suggest absence of subgenome dominance after whole genome duplication

Allopolyploids often experience subgenome dominance, with one subgenome showing higher levels of gene expression and greater gene retention. Here, we address the functionality of both subgenomes of allotetraploid common carp (Cyprinus carpio) by analysing a functional network of interferon-stimulated genes (ISGs) crucial in anti-viral immune defence. As an indicator of subgenome dominance we investigated retainment of a core set of ohnologous ISGs. To facilitate our functional genomic analysis a high quality genome was assembled (WagV4.0). Transcriptome data from an in vitro experiment mimicking a viral infection was used to infer ISG expression. Transcriptome analysis confirmed induction of 88 ISG ohnologs on both subgenomes. In both control and infected states, average expression of ISG ohnologs was comparable between the two subgenomes. Also, the highest expressing and most inducible gene copies of an ohnolog pair could be derived from either subgenome. We found no strong evidence of subgenome dominance for common carp.

Discovery of isoflavone phytoalexins in wheat reveals an alternative route to isoflavonoid biosynthesis

Isoflavones are a group of phenolic compounds mostly restricted to plants of the legume family, where they mediate important interactions with plant-associated microbes, including in defense from pathogens and in nodulation. Their well-studied health promoting attributes have made them a prime target for metabolic engineering, both for bioproduction of isoflavones as high-value molecules, and in biofortification of food crops. A key gene in their biosynthesis, isoflavone synthase, was identified in legumes over two decades ago, but little is known about formation of isoflavones outside of this family. Here we identify a specialized wheat-specific isoflavone synthase, TaCYP71F53, which catalyzes a different reaction from the leguminous isoflavone synthases, thus revealing an alternative path to isoflavonoid biosynthesis and providing a non-transgenic route for engineering isoflavone production in wheat. TaCYP71F53 forms part of a biosynthetic gene cluster that produces a naringenin-derived O-methylated isoflavone, 5-hydroxy-2',4',7-trimethoxyisoflavone, triticein. Pathogen-induced production and in vitro antimicrobial activity of triticein suggest a defense-related role for this molecule in wheat. Genomic and metabolic analyses of wheat ancestral grasses further show that the triticein gene cluster was introduced into domesticated emmer wheat through natural hybridization ~9000 years ago, and encodes a pathogen-responsive metabolic pathway that is conserved in modern bread wheat varieties.

Characterization and the comprehensive expression analysis of tobacco valine-glutamine genes in response to trichomes development and stress tolerance

Valine-glutamine genes (VQ) acted as transcription regulators and played the important roles in plant growth and development, and stress tolerance through interacting with transcription factors and other co-regulators. In this study, sixty-one VQ genes containing the FxxxVQxxTG motif were identified and updated in the Nicotiana tobacum genome. Phylogenetic analysis indicated that NtVQ genes were divided into seven groups and genes of each group had highly conserved exon-intron structure. Expression patterns analysis firstly showed that NtVQ genes expressed individually in different tobacco tissues including mixed-trichome (mT), glandular-trichome (gT), and nonglandular-trichome (nT), and the expression levels were also distinguishing in response to methyl jasmonate (MeJA), salicylic acid (SA), gibberellic acid (GA), ethylene (ETH), high salinity and PEG stresses. Besides, only NtVQ17 of its gene family was verified to have acquired autoactivating activity. This work will not only lead a foundation on revealing the functions of NtVQ genes in tobacco trichomes but also provided references to VQ genes related stress tolerance research in more crops.

A chromosome-level genome assembly for Erianthus fulvus provides insights into its biofuel potential and facilitates breeding for improvement of sugarcane

Erianthus produces substantial biomass, exhibits a good Brix value, and shows wide environmental adaptability, making it a potential biofuel plant. In contrast to closely related sorghum and sugarcane, Erianthus can grow in degraded soils, thus releasing pressure on agricultural lands used for biofuel production. However, the lack of genomic resources for Erianthus hinders its genetic improvement, thus limiting its potential for biofuel production. In the present study, we generated a chromosome-scale reference genome for Erianthus fulvus Nees. The genome size estimated by flow cytometry was 937 Mb, and the assembled genome size was 902 Mb, covering 96.26% of the estimated genome size. A total of 35 065 protein-coding genes were predicted, and 67.89% of the genome was found to be repetitive. A recent whole-genome duplication occurred approximately 74.10 million years ago in the E. fulvus genome. Phylogenetic analysis showed that E. fulvus is evolutionarily closer to S. spontaneum and diverged after S. bicolor. Three of the 10 chromosomes of E. fulvus formed through rearrangements of ancestral chromosomes. Phylogenetic reconstruction of the Saccharum complex revealed a polyphyletic origin of the complex and a sister relationship of E. fulvus with Saccharum sp., excluding S. arundinaceum. On the basis of the four amino acid residues that provide substrate specificity, the E. fulvus SWEET proteins were classified as mono- and disaccharide sugar transporters. Ortho-QTL genes identified for 10 biofuel-related traits may aid in the rapid screening of E. fulvus populations to enhance breeding programs for improved biofuel production. The results of this study provide valuable insights for breeding programs aimed at improving biofuel production in E. fulvus and enhancing sugarcane introgression programs.

Global dissection of R2R3-MYB in Pogostemon cablin uncovers a species-specific R2R3-MYB clade

MYB family is one of the largest transcription factor families in plants and plays a crucial role in regulating plant biochemical and physiological processes. However, R2R3-MYBs in patchouli have not been systematically investigated. Here, based on the gene annotation of patchouli genome sequence, 484 R2R3-MYB transcripts were detected. Further in-depth analysis of the gene structure and expression of R2R3-MYBs supported the tetraploid hybrid origin of patchouli. When combined with R2R3-MYBs from Arabidopsis, a phylogenetic tree of patchouli R2R3-MYBs was constructed and divided into 31 clades. Interestingly, a patchouli-specific R2R3-MYB clade was found and confirmed by homologous from other Lamiaceae species. The syntenic analysis demonstrated that tandem duplication contributed to its evolution. This study systematically analysed the R2R3-MYB family in patchouli, providing information on its gene characterization, functional prediction, and species evolution.

Genome of tetraploid sour cherry (Prunus cerasus L.) 'Montmorency' identifies three distinct ancestral Prunus genomes

Sour cherry (Prunus cerasus L.) is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors closely related to extant Prunus fruticosa (ground cherry) and Prunus avium (sweet cherry). Here we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency, the predominant cultivar grown in the USA. We also generated a draft assembly of P. fruticosa to use alongside a published P. avium sequence for syntelog-based subgenome assignments for 'Montmorency' and provide compelling evidence P. fruticosa is also an allotetraploid. Using hierarchal k-mer clustering and phylogenomics, we show 'Montmorency' is trigenomic, containing two distinct subgenomes inherited from a P. fruticosa-like ancestor (A and A') and two copies of the same subgenome inherited from a P. avium-like ancestor (BB). The genome composition of 'Montmorency' is AA'BB and little-to-no recombination has occurred between progenitor subgenomes (A/A' and B). In Prunus, two known classes of genes are important to breeding strategies: the self-incompatibility loci (S-alleles), which determine compatible crosses, successful fertilization, and fruit set, and the Dormancy Associated MADS-box genes (DAMs), which strongly affect dormancy transitions and flowering time. The S-alleles and DAMs in 'Montmorency' and P. fruticosa were manually annotated and support subgenome assignments. Lastly, the hybridization event 'Montmorency' is descended from was estimated to have occurred less than 1.61 million years ago, making sour cherry a relatively recent allotetraploid. The 'Montmorency' genome highlights the evolutionary complexity of the genus Prunus and will inform future breeding strategies for sour cherry, comparative genomics in the Rosaceae, and questions regarding neopolyploidy.

Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages

BACKGROUND

In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages.

RESULTS

Our research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations.

CONCLUSIONS

This study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication.

The heavy metal-associated isoprenylated plant protein (HIPP) gene family plays a crucial role in cadmium resistance and accumulation in the tea plant (Camellia sinensis L.)

Heavy metal-associated isoprenylated plant proteins (HIPPs) are only distributed in vascular plants, and are essential for the detoxification and vascular transport of heavy metals in plants. However, the HIPP gene family has not been thoroughly explored in the tea plant (Camellia sinensis). In this study, we systematically identified 56C. sinensis CsHIPP genes from five groups and characterized their phylogeny, structures, and the features of the encoded proteins. The expression patterns of CsHIPP genes in various tissues of C. sinensis were investigated based on a previous RNA-seq data analysis. The expression patterns of CsHIPP genes were explored in cadmium (Cd)-treated C. sinensis roots using our RNA-seq data. Three CsHIPP genes (CsHIPP22, CsHIPP24, and CsHIPP36) with high expression levels in Cd-treated C. sinensis roots were selected as candidate genes associated with Cd tolerance. Overexpression of CsHIPP22, CsHIPP24, and CsHIPP36 in a yeast mutant (ycf1) rescued Cd-sensitive ycf1 yeast and increased the yeast resistance to Cd stress, implying that these three CsHIPPs might be involved in Cd tolerance. These findings will enable the roles of HIPPs in Cd absorption and detoxification to be better understood as well as improving our understanding of the Cd-resistance and Cd-accumulation mechanisms in tea plant.