Recent Duplication Research Articles

A first draft genome of holm oak (Quercus ilex subsp. ballota), the most representative species of the Mediterranean forest and the Spanish agrosylvopastoral ecosystem "dehesa".

The holm oak (Quercus ilex subsp. ballota) is the most representative species of the Mediterranean Basin and the agrosylvopastoral Spanish "dehesa" ecosystem. Being part of our life, culture, and subsistence since ancient times, it has significant environmental and economic importance. More recently, there has been a renewed interest in using the Q. ilex acorn as a functional food due to its nutritional and nutraceutical properties. However, the holm oak and its related ecosystems are threatened by different factors, with oak decline syndrome and climate change being the most worrying in the short and medium term. Breeding programs informed by the selection of elite genotypes seem to be the most plausible biotechnological solution to rescue populations under threat. To achieve this and other downstream analyses, we need a high-quality and well-annotated Q. ilex reference genome. Here, we introduce the first draft genome assembly of Q. ilex using long-read sequencing (PacBio). The assembled nuclear haploid genome had 530 contigs totaling 842.2Mbp (N50 = 3.3Mbp), of which 448.7Mb (53%) were repetitive sequences. We annotated 39,443 protein-coding genes of which 94.80% were complete and single-copy genes. Phylogenetic analyses showed no evidence of a recent whole-genome duplication, and high synteny of the 12 chromosomes between Q. ilex and Quercus lobata and between Q. ilex and Quercus robur. The chloroplast genome size was 142.3Kbp with 149 protein-coding genes successfully annotated. This first draft should allow for the validation of omics data as well as the identification and functional annotation of genes related to phenotypes of interest such as those associated with resilience against oak decline syndrome and climate change and higher acorn productivity and nutraceutical value.

Identification, Evolution and Expression Analysis of GRF Family Reveals Their Involvement in Shoot Growth and Abiotic Stress Response in Moso Bamboo

Growth-regulating factors (GRFs) play an important role in regulating plant organ development, acting primarily as positive regulators of cell proliferation. However, research on the evolutionary history and expression patterns of the moso bamboo GRF family has been limited. In this study, a total of 24 GRFs have been identified in the Moso bamboo genome, and they have been categorized into four subfamilies. Estimation of the divergence time of paralogous gene pairs provided evidence supporting the significant contribution of recent whole-genome duplication events in the expansion of the GRF gene family. Sliding window analysis revealed that coding regions of a few PheGRFs, including the WRC and QLQ domains, may have undergone positive selection, possibly due to the redundant functions of paralogous genes. Coexpression network analysis further revealed the regulatory role of miR396 and various lncRNAs in controlling PheGRF expression. Based on the analysis of tissue-specific expression patterns using transcriptome sequencing, qRT-PCR results, and in situ hybridization, it was observed that most GRFs, particularly PheGRF6a and PheGRF9b, exhibited high levels of accumulation in the moso bamboo shoot. This suggests that the involvement of most PheGRF genes may be crucial for the growth and development of the bamboo shoot. A yeast two-hybrid screening revealed interactions between PheGRF9b and several proteins associated with plant growth and development, including PH02Gene11097.t1 (GIF3), PH02Gene37618.t (Phytochrome B), and PH02Gene01921.t3 (WD40). Based on transcriptome expression analysis, it was observed that a substantial number of PheGRFs exhibited significant variations under cold or drought stress treatments, and most of these genes were found to be downregulated, suggesting their role as abiotic stress-responsive genes. Our findings offer new insights into the GRF family of moso bamboo and provide some experimental evidence to support further gene functional validation research of PheGRF.

Comparative genomics analysis provides insights into evolution and stress responses of Lhcb genes in Rosaceae fruit crops

BackgroundLight-harvesting chlorophyll a/b binding proteins (Lhcb) play crucial roles in plant growth, development, and the response to abiotic stress in higher plants. Previous studies have reported that Lhcb genes were involved in the phytochrome regulation and responded to different light and temperature conditions in Poaceae (such as maize). However, the evolution and functions of Lhcb genes remains poorly characterized in important Rosaceae species.ResultsIn this investigation, we conducted a genome-wide analysis and identified a total of 212 Lhcb genes across nine Rosaceae species. Specifically, we found 23 Lhcb genes in Fragaria vesca, 20 in Prunus armeniaca, 33 in Malus domestica ‘Gala’, 21 in Prunus persica, 33 in Rosa chinensis, 29 in Pyrus bretschneideri, 18 in Rubus occidentalis, 20 in Prunus mume, and 15 in Prunus salicina. Phylogenetic analysis revealed that the Lhcb gene family could be classified into seven major subfamilies, with members of each subfamily sharing similar conserved motifs. And, the functions of each subfamily was predicted based on the previous reports from other species. The Lhcb proteins were highly conserved within their respective subfamilies, suggesting similar functions. Interestingly, we observed similar peaks in Ks values (0.1–0.2) for Lhcb genes in apple and pear, indicating a recent whole genome duplication event (about 30 to 45 million years ago). Additionally, a few Lhcb genes underwent tandem duplication and were located across all chromosomes of nine species of Rosaceae. Furthermore, the analysis of the cis-acting elements in the 2000 bp promoter region upstream of the pear Lhcb gene revealed four main categories: light response correlation, stress response correlation, hormone response correlation, and plant growth. Quantitative expression analysis demonstrated that Lhcb genes exhibited tissue-specific expression patterns and responded differently to low-temperature stress in Rosaceae species.ConclusionsThese findings shed light on the evolution and phylogeny of Lhcb genes in Rosaceae and highlight the critical role of Lhcb in pear’s response to low temperatures. The results obtained provide valuable insights for further investigations into the functions of Lhcb genes in Rosaceae, and these functional genes will be used for further fruit tree breeding and improvement to cope with the current climate changes.

Genome-wide identification, expression analysis and gene duplication analysis of Dof transcription factors between quinoa and its ancestral diploid sub-genome species reveal key CDF homologs involved in photoperiodic flowering regulation

Dof (DNA binding with One Finger) proteins are plant-specific transcription factors characteristic of a highly conserved DNA binding domain. Dof family members have been shown to play important roles in growth, development, stress defense, and light and phytohormone responses. In this study, we identified 38 CqDof genes in quinoa (Chenopodium quinoa). Phylogenetic analysis of Dof genes from quinoa, Arabidopsis, rice, sugar beet, C. pallidicaule and C. suecicum indicated that those Dofs were clustered into 6 sub-groups. Gene structure and conserved motif analysis showed that motif composition varied between different sub-groups. Duplication analysis indicated CqDof family was expanded mainly by segmental duplication, and we found the duplication events CqDof31/CqDof36 and CqDof31/CqDof37 could be traced back to before the divergence of Chenopodium ancestor from sugar beet, and a recent duplication event CqDof33/CqDof34 was detected specific to quinoa. Analysis of cis-acting elements showed that CqDof genes may be involved in light, phytohormone and stress response. Expression pattern analysis showed that CqDof27, CqDof31/CqDof32, CqDof33/CqDof34 and CqDof35/CqDof36 in sub-group VI were affected by different photoperiods and they may act as important floral regulator. Based on the cis-element analysis and diurnal expression results, we speculated the recent duplication event CqDof33/CqDof34 may render quinoa some growth habits to adapt to different latitudes, and CqDof31/CqDof32 might be potential candidates for inflorescence branching and yield improvement. Together, the results obtained in this study will help understand the functions of Dof genes in quinoa.

Cloning and deorphanization of three inotocin (insect oxytocin/vasopressin-like) receptors and their ligand from the tick Ixodes scapularis

Many insects produce the cyclic neuropeptide inotocin (CLITNCPRGamide), which is the insect orthologue of the mammalian neuropeptides oxytocin and vasopressin. These insects also have one inotocin G protein-coupled receptor (GPCR), which is the orthologue of the mammalian oxytocin and vasopressin receptors. The tick Ixodes scapularis belongs to the subphylum Chelicerata, an arthropod taxon different from insects, to which also spiders, scorpions, and mites belong. I. scapularis is an ectoparasite and a health risk for humans, because it transfers pathogenic microorganisms to its human host during a blood meal, thereby causing serious neurological diseases, among them Lyme disease and tick-borne encephalitis (TBE). By annotating the genomic sequence of I. scapularis, we previously found one presumed tick inotocin preprohormone gene and, in contrast to insects, three genes coding for presumed inotocin GPCRs. We now find that these GPCR genes cluster on one genomic contig, suggesting that they originated by recent gene duplications. Closely located on the same contig are also four adipokinetic hormone/corazonin-related peptide (ACP) GPCR genes, and one crustacean cardioactive peptide (CCAP) GPCR gene, suggesting evolutionary relationships. These evolutionary relationships are confirmed by phylogenetic tree analyses of their gene products. We also cloned the tick inotocin preprohormone, which has a structural organization closely resembling mammalian oxytocin and vasopressin preprohormones, including the presence of a conserved neurophysin sequence, having seven cystine bridges. This neurophysin sequence has two cystine-knot domains, but in contrast to mammalian neurophysins, the tick neurophysin contains a canonical prohormone convertase cleavage signal and a peptide C-terminal amidation sequence (GKR), suggesting cleavage into two biologically active cystine-knot peptides. This cleavage/amidation sequence occurs in neurophysins from most hard tick species, but not in other chelicerates. Mature tick inotocin is different from insect inotocin and has the sequence CFITNCPPGamide. Finally, we cloned and stably expressed the three tick inotocin receptors in Chinese Hamster Ovary cells and found that each of them was activated by nanomolar concentrations of tick inotocin (EC50 for ITR1 = 1.6 × 10−8 M; EC50 for ITR2 = 5.8 × 10−9 M; EC50 for ITR3 = 9.3 × 10−9 M), thereby establishing that they are genuine tick inotocin receptors.

High-quality genome of a pioneer mangrove Laguncularia racemosa explains its advantages for intertidal zone reforestation.

Ecological restoration of mangrove ecosystems that became susceptible to recent habitat perturbations is crucial for tropical coast conservation. The white mangrove Laguncularia racemosa, a pioneer species inhabiting intertidal environments of the Atlantic East Pacific (AEP) region, has been used for reforestation in China for decades. However, the molecular mechanisms underlying its fast growth and high adaptive potential remain unknown. Using PacBio single-molecule real-time sequencing, we completed a high-quality L. racemosa genome assembly covering 1105 Mb with scaffold N50 of 3.46 Mb. Genomic phylogeny shows that L. racemosa invaded intertidal zones during a period of global warming. Multi-level genomic convergence analyses between L. racemosa and three native dominant mangrove clades show that they experienced convergent changes in genes involved in nutrient absorption and high salinity tolerance. This may explain successful L. racemosa adaptation to stressful intertidal environments after introduction. Without recent whole-genome duplications or activated transposable elements, L. racemosa has retained many tandem gene duplications. Some of them are involved in auxin biosynthesis, intense light stress and cold stress response pathways, associated with L. racemosa's ability to grow fast under high light or cold conditions when used for reforestation. In summary, our study identifies shared mechanisms of intertidal environmental adaptation and unique genetic changes underlying fast growth in mangrove-unfavourable conditions and sheds light on the molecular mechanisms of the white mangrove utility in ecological restoration.

Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone

Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.

A chromosome-level genome assembly of anesthetic drug–producing Anisodus acutangulus provides insights into its evolution and the biosynthesis of tropane alkaloids

Tropane alkaloids (TAs), which are anticholinergic agents, are an essential class of natural compounds, and there is a growing demand for TAs with anesthetic, analgesic, and spasmolytic effects. Anisodus acutangulus (Solanaceae) is a TA-producing plant that was used as an anesthetic in ancient China. In this study, we assembled a high-quality, chromosome-scale genome of A. acutangulus with a contig N50 of 7.4 Mb. A recent whole-genome duplication occurred in A. acutangulus after its divergence from other Solanaceae species, which resulted in the duplication of ADC1 and UGT genes involved in TA biosynthesis. The catalytic activities of H6H enzymes were determined for three Solanaceae plants. On the basis of evolution and co-expressed genes, AaWRKY11 was selected for further analyses, which revealed that its encoded transcription factor promotes TA biosynthesis by activating AaH6H1 expression. These findings provide useful insights into genome evolution related to TA biosynthesis and have potential implications for genetic manipulation of TA-producing plants.

Systematic evolution of bZIP transcription factors in Malvales and functional exploration of AsbZIP14 and AsbZIP41 in Aquilaria sinensis.

Agarwood, the dark-brown resin produced by Aquilaria trees, has been widely used as incense, spice, perfume or traditional medicine and 2-(2-phenethyl) chromones (PECs) are the key markers responsible for agarwood formation. But the biosynthesis and regulatory mechanism of PECs were still not illuminated. The transcription factor of basic leucine zipper (bZIP) presented the pivotal regulatory roles in various secondary metabolites biosynthesis in plants, which might also contribute to regulate PECs biosynthesis. However, molecular evolution and function of bZIP are rarely reported in Malvales plants, especially in Aquilaria trees. Here, 1,150 bZIPs were comprehensively identified from twelve Malvales and model species genomes and the evolutionary process were subsequently analyzed. Duplication types and collinearity indicated that bZIP is an ancient or conserved TF family and recent whole genome duplication drove its evolution. Interesting is that fewer bZIPs in A. sinensis than that species also experienced two genome duplication events in Malvales. 62 AsbZIPs were divided into 13 subfamilies and gene structures, conservative domains, motifs, cis-elements, and nearby genes of AsbZIPs were further characterized. Seven AsbZIPs in subfamily D were significantly regulated by ethylene and agarwood inducer. As the typical representation of subfamily D, AsbZIP14 and AsbZIP41 were localized in nuclear and potentially regulated PECs biosynthesis by activating or suppressing type III polyketide synthases (PKSs) genes expression via interaction with the AsPKS promoters. Our results provide a basis for molecular evolution of bZIP gene family in Malvales and facilitate the understanding the potential functions of AsbZIP in regulating 2-(2-phenethyl) chromone biosynthesis and agarwood formation.

A chromosome-scale Rhubarb (Rheum tanguticum) genome assembly provides insights into the evolution of anthraquinone biosynthesis

Rhubarb is the collective name for various perennial plants from the genus Rheum L. and the Polygonaceae family. They are one of the most ancient, commonly used, and important herbs in traditional Chinese medicine. Rhubarb is a major source of anthraquinones, but how they are synthesized remains largely unknown. Here, we generate a genome sequence assembly of one important medicinal rhubarb R. tanguticum at the chromosome level, with 2.76 Gb assembled into 11 chromosomes. The genome is shaped by two recent whole-genome duplication events and recent bursts of retrotransposons. Metabolic analyses show that the major anthraquinones are mainly synthesized in its roots. Transcriptomic analysis reveals a co-expression module with a high correlation to anthraquinone biosynthesis that includes key chalcone synthase genes. One CHS, four CYP450 and two BGL genes involved in secondary metabolism show significantly upregulated expression levels in roots compared with other tissues and clustered in the co-expression module, which implies that they may also act as candidate genes for anthraquinone biosynthesis. This study provides valuable insights into the genetic bases of anthraquinone biosynthesis that will facilitate improved breeding practices and agronomic properties for rhubarb in the future.

Genomic-wide identification and expression analysis of R2R3-MYB transcription factors related to flavonol biosynthesis in Morinda officinalis

BackgroundThe R2R3-MYB transcription factors are a crucial and extensive gene family in plants, which participate in diverse processes, including development, metabolism, defense, differentiation, and stress response. In the Lingnan region of China, Morinda officinalis is extensively grown and is renowned for its use as both a medicinal herb and food source. However, there are relatively few reports on the R2R3-MYB transcription factor family in M.officinalis.ResultsIn this study, we identified 97 R2R3-MYB genes in the genome of Morinda officinalis and classified them into 32 subgroups based on phylogenetic comparison with Arabidopsis thaliana. The lack of recent whole-genome duplication events in M.officinalis may be the reason for the relatively few members of the R2R3-MYB family. We also further analyzed the physical and chemical characteristics, conserved motifs, gene structure, and chromosomal location. Gene duplication events found 21 fragment duplication pairs and five tandem duplication event R2R3-MYB genes in M.officinalis may also affect gene family expansion. Based on phylogenetic analysis, cis-element analysis, co-expression analysis and RT-qPCR, we concluded that MoMYB33 might modulate flavonol levels by regulating the expression of 4-coumarate-CoA ligase Mo4CL2, chalcone isomerase MoCHI3, and flavonol synthase MoFLS4/11/12. MoMYB33 and AtMYB111 showed the highest similarity of 79% and may be involved in flavonol synthase networks by the STRING database. Moreover, we also identified MoMYB genes that respond to methyl Jasmonate (MeJA) and abscisic acid (ABA) stress by RT-qPCR.ConclusionsThis study offers a thorough comprehension of R2R3-MYB in M.officinalis, which lays the foundation for the regulation of flavonol synthesis and the response of MoMYB genes to phytohormones in M.officinalis.

Red palm weevil olfactory proteins annotated from the rostrum provide insights into the essential role in chemosensation and chemoreception

Red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is rapidly infesting palm trees (Arecaceae) in several countries, threatening coconut, date, and oil cultivations. The male-produced aggregation pheromone in palm weevils has been reported to be secreted through the mouth to the rostrum, a snout-like projection key for pheromone emission and dispersion. The olfactory mechanisms that underlie peripheral odorant detection in RPW have been addressed at the antennal level. However, the rostrum remains unexplored. Through RNA-seq, 27 odorant-binding proteins (OBPs), 6 chemosensory proteins (CSPs), 4 sensory neuron membrane proteins (SNMPs), 21 gustatory receptors (GRs), 25 odorant receptors (ORs) (including one odorant receptor coreceptor, Orco) and 10 ionotropic receptors (IRs), were identified. We reported 27 novel rostrum-specific olfactory proteins (4 IRs, 11 GRs, 2 CSPs, 3 OBPs, and 7 ORs) in R. ferrugineus (Rfer). The OBPs (RferSOBPs) [Rfer with “S” indicating “snout” (rostrum)] were the most abundant transcripts compared with the rest of the olfactory proteins. We identified several rostrum OBPs, which predominately emerged through gene duplication, and were found expressed in both rostrum and antennae. Noticeably, we found R. ferrugineus pheromone-binding protein (RferOBP1768) paralog in the rostrum (RferOBP14) and mapped it in the same scaffold at a different position on the RPW genome as a recent duplicate. We found that an OR (RferSOR1) was the most abundant for both field-collected and lab-reared RPWs, in the rostrum and antennae. Likewise, up-regulated olfactory-related proteins were established in field conditions compared with those from laboratory-reared. We found a rostrum-specific, highly expressing RferSIR1 in IR93a-clade related to hygrosensation. The role of these olfactory proteins as targets for identifying more specific and powerful semiochemicals is discussed in the context of pest management.

Impacts of Sex Ratio Meiotic Drive on Genome Structure and Function in a Stalk-Eyed Fly.

Stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio (SR) meiotic drive and impact the fitness of male and female carriers. Here, we assemble and describe a chromosome-level genome assembly of the stalk-eyed fly, Teleopsis dalmanni, to elucidate patterns of divergence associated with SR. The genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally and insertionally active TE families. By resequencing pools of SR and ST males using short and long reads, we find widespread differentiation and divergence between XSR and XST associated with multiple nested inversions involving most of the SR haplotype. Examination of genomic coverage and gene expression data revealed seven X-linked genes with elevated expression and coverage in SR males. The most extreme and likely drive candidate involves an XSR-specific expansion of an array of partial copies of JASPer, a gene necessary for maintenance of euchromatin and associated with regulation of TE expression. In addition, we find evidence for rapid protein evolution between XSR and XST for testis expressed and novel genes, that is, either recent duplicates or lacking a Dipteran ortholog, including an X-linked duplicate of maelstrom, which is also involved in TE silencing. Overall, the evidence suggests that this ancient XSR polymorphism has had a variety of impacts on repetitive DNA and its regulation in this species.

Integrated global analysis in spider flowers illuminates features underlying the evolution and maintenance of C4 photosynthesis.

The carbon concentrating mechanism-C4 photosynthesis-represents a classic example of convergent evolution, but how this important trait originated and evolved remains largely enigmatic. The spider flower Gynandropsis gynandra is a valuable leafy vegetable crop and medicinal plant that has also been recognized as a C4 model species. Here we present a high-quality chromosome-scale annotated genome assembly of G. gynandra through a combination of Oxford Nanopore Technology (ONT), HiFi and Hi-C technology. The 17 super-scaffolds cover 98.66% of the estimated genome (997.61Mb), with a contig N50 of 11.43Mb and a scaffold N50 of 51.02Mb. Repetitive elements occupy up to 71.91% of its genome, and over half are long terminal repeat retrotransposons (LTR-RTs) derived from recent bursts, contributing to genome size expansion. Strikingly, LTR-RT explosion also played a critical role in C4 evolution by altering expression features of photosynthesis-associated genes via preferential insertion in promoters. Integrated multiomics analyses of G. gynandra and the ornamental horticulture C3 relative Tarenaya hassleriana reveal that species-specific whole-genome duplication, gene family expansion, recent LTR-RT amplification, and more recent tandem duplication events have all facilitated the evolution of C4 photosynthesis, revealing uniqueness of C4 evolution in the Cleome genus. Moreover, high leaf vein density and heat stress resilience are associated with shifted gene expression patterns. The mode of C3-to-C4 transition found here yields new insights into evolutionary convergence of a complex plant trait. The availability of this reference-grade genomic resource makes G. gynandra an ideal model system facilitating efforts toward C4-aimed crop engineering.

The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes

Cluster bean (Cyamopsis tetragonoloba (L.) Taub 2n = 14, is commonly known as Guar. Apart from being a vegetable crop, it is an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan. Here, we are reporting a chromosome-scale reference genome assembly of a popular cluster bean cultivar RGC-936, by combining sequencing data from Illumina, 10X Genomics, Oxford Nanopore technologies. An initial assembly of 1580 scaffolds with an N50 value of 7.12 Mb was generated and these scaffolds were anchored to a high density SNP linkage map. Finally, a genome assembly of 550.31 Mb (94% of the estimated genome size of ~ 580 Mb (through flow cytometry) with 58 scaffolds was obtained, including 7 super scaffolds with a very high N50 value of 78.27 Mb. Phylogenetic analysis using single copy orthologs among 12 angiosperms showed that cluster bean shared a common ancestor with other legumes 80.6 MYA. No evidence of recent whole genome duplication event in cluster bean was found in our analysis. Further comparative transcriptomics analyses revealed pod-specific up-regulation of genes encoding enzymes involved in galactomannan biosynthesis. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted improvement of cluster bean.

Comparative Analysis of GRAS Genes in Six Cucurbitaceae Species Provides Insights into Their Evolution and Function

The Cucurbitaceae family comprises economically valuable vegetables such as cucumber, melon, and pumpkin. GRAS proteins, which are crucial transcription factors, play diverse roles in plant growth and development. However, comparative investigations of GRAS proteins across Cucurbitaceae species are limited. Here, we identified 241 GRAS family genes in six cucurbit crops. The number of GRAS genes in cucumber, melon, wax gourd, watermelon, and bottle gourd ranged from 36 to 37, while the pumpkin genome contained 57 GRAS genes, possibly due to a recent whole-genome duplication. We classified cucurbit GRAS genes into 16 subfamilies and identified species-specific motifs and specific-expression patterns in the SCLB and RAD1 subfamilies. Notably, we identified 38 tissue-specific expressed genes, particularly fruit-specific genes potentially involved in fruit development. Additionally, we predicted the role of GRAS genes in regulating hypocotyl elongation under weak or dark light conditions in cucurbit plants. These findings enhance our understanding of the characteristics, evolution, and potential functions of GRAS genes in six cucurbit crops, providing valuable resources for genetic research in the Cucurbitaceae family as well as important agronomic traits.

A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales.

Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract coloration and breeding. Here, we report a chromosome-level assembly of the giga-genome of Bougainvillea × buttiana 'Mrs Butt', a cultivar thought to be the origin of many other Bougainvillea cultivars. The assembled genome is ~5Gb with a scaffold N50 of 151 756 278bp and contains 86 572 genes which have undergone recent whole-genome duplication. We confirmed that multiple rounds of whole-genome multiplication have occurred in the evolutionary history of the Caryophyllales, reconstructed the relationship in the Caryophyllales at whole genome level, and found discordance between species and gene trees as the result of complex introgression events. We investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales species. To explore the potential formation mechanism of diverse bract colors in Bougainvillea, we analyzed the genes involved in betalain and anthocyanin biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars, which may limit anthocyanin biosynthesis. Our findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with bract color, and a higher expression level in the betalain biosynthetic pathway is required for colored bracts. This improved understanding of the correlation between gene expression and bract color allows plant breeding outcomes to be predicted with greater certainty.

Chromosome-level genome and multi-omics analyses provide insights into the geo-herbalism properties of Alpinia oxyphylla.

Alpinia oxyphylla Miquel (A. oxyphylla), one of the "Four Famous South Medicines" in China, is an essential understory cash crop that is planted widely in the Hainan, Guangdong, Guangxi, and Fujian provinces. Particularly, A. oxyphylla from Hainan province is highly valued as the best national product for geo-herbalism and is an important indicator of traditional Chinese medicine efficacy. However, the molecular mechanism underlying the formation of its quality remains unspecified. To this end, we employed a multi-omics approach to investigate the authentic quality formation of A. oxyphylla. In this study, we present a high-quality chromosome-level genome assembly of A. oxyphylla, with contig N50 of 76.96 Mb and a size of approximately 2.08Gb. A total of 38,178 genes were annotated, and the long terminal repeats were found to have a high frequency of 61.70%. Phylogenetic analysis demonstrated a recent whole-genome duplication event (WGD), which occurred before A. oxyphylla's divergence from W. villosa (~14 Mya) and is shared by other species from the Zingiberaceae family (Ks, ~0.3; 4DTv, ~0.125). Further, 17 regions from four provinces were comprehensively assessed for their metabolite content, and the quality of these four regions varied significantly. Finally, genomic, metabolic, and transcriptomic analyses undertaken on these regions revealed that the content of nootkatone in Hainan was significantly different from that in other provinces. Overall, our findings provide novel insights into germplasm conservation, geo-herbalism evaluation, and functional genomic research for the medicinal plant A. oxyphylla.

Dynamics of Gene Loss following Ancient Whole-Genome Duplication in the Cryptic Paramecium Complex.

Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages. The redundancy created by WGDs typically results in a phase of massive gene loss. However, some WGD-derived paralogs are maintained over long evolutionary periods, and the relative contributions of different selective pressures to their maintenance are still debated. Previous studies have revealed a history of three successive WGDs in the lineage of the ciliate Paramecium tetraurelia and two of its sister species from the Paramecium aurelia complex. Here, we report the genome sequence and analysis of 10 additional P. aurelia species and 1 additional out group, revealing aspects of post-WGD evolution in 13 species sharing a common ancestral WGD. Contrary to the morphological radiation of vertebrates that putatively followed two WGD events, members of the cryptic P. aurelia complex have remained morphologically indistinguishable after hundreds of millions of years. Biases in gene retention compatible with dosage constraints appear to play a major role opposing post-WGD gene loss across all 13 species. In addition, post-WGD gene loss has been slower in Paramecium than in other species having experienced genome duplication, suggesting that the selective pressures against post-WGD gene loss are especially strong in Paramecium. A near complete lack of recent single-gene duplications in Paramecium provides additional evidence for strong selective pressures against gene dosage changes. This exceptional data set of 13 species sharing an ancestral WGD and 2 closely related out group species will be a useful resource for future studies on Paramecium as a major model organism in the evolutionary cell biology.

Expansion and adaptive evolution of the WRKY transcription factor family in Avicennia mangrove trees

Mangroves are adapted to intertidal zones, which present extreme environmental conditions. WRKYs are among the most prominent transcription factors (TFs) in higher plants and act through various interconnected networks to regulate responses to multiple abiotic stressors. Here, based on omic data, we investigated the landscape and evolutionary patterns of WRKYs in the main mangrove genus Avicennia. We found that both the number and the proportion of TFs and WRKYs in Avicennia species exceeded their inland relatives, indicating a significant expansion of WRKYs in Avicennia. We identified 109 WRKY genes in the representative species Avicennia marina. Comparative genomic analysis showed that two recent whole-genome duplication (WGD) events played a critical role in the expansion of WRKYs, and 88% of Avicennia marina WRKYs (AmWRKYs) have been retained following these WGDs. Applying comparative transcriptomics on roots under experimental salt gradients, we inferred that there is high divergence in the expression of WGD-retained AmWRKYs. Moreover, we found that the expression of 16 AmWRKYs was stable between freshwater and moderately saline water but increased when the trees were exposed to high salinity. In particular, 14 duplicates were retained following the two recent WGD events, indicating potential neo- and sub-functionalization. We also found that WRKYs could interact with other upregulated genes involved in signalling pathways and natural antioxidant biosynthesis to enhance salt tolerance, contributing to the adaptation to intertidal zones. Our omic data of the WRKY family in A. marina broadens the understanding of how a TF family relates to the adaptive evolution of mangroves.