A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

Carbon metabolism and partitioning in citrus leaves is determined by hybrid, cultivar and leaf type

The partitioning and metabolism of carbohydrates and lignin in leaves are essential for numerous physiological functions, growth and development of plants. This study was aimed to characterize these processes in four leaf types (i.e., autumn-, summer-, spring- and current-year spring shoots) of two citrus hybrids (loose-skin mandarin cultivars OP (i.e., cultivars 'Orah' (OR) Citrus reticulata Blanco and 'Ponkan' (PO) Citrus reticulata Blanco and the sweet orange cultivars NT 'Newhall navel orange' (NO) Citrus sinensis (L.) Osbeck and 'Tarocco' (TA) Citrus sinensis (L.) Osbeck) differing in fruit maturation under field conditions. For this purpose, we analyzed the levels of foliar structural, non-structural carbohydrates and lignin and the expression of related genes. Our results showed that the contents of structural, non-structural carbohydrates and lignin measured in the two hybrids and its partitioning were mostly determined by differences in gene expression recorded in hybrids, cultivars and leaf type. Particularly, differences between leaf types were largely attributed to up- and down-regulation of the expression of genes of cellulose synthesis, lignin precursor synthesis, the Calvin cycle, glycolysis, the tricarbonic acid and starch synthesis and degradation pathways. These differences between leaf types required more complex transcriptional regulation than differences between hybrids and cultivars. The present results indicated that the two citrus hybrids studied differed in the expression of structural, non-structural carbohydrates and lignin-related genes. Future studies have to show if the differences observed in foliar partitioning and metabolism of carbohydrates and lignin are translated into partitioning and metabolism of carbohydrates and lignin in the roots.

Comparative Transcriptome Analysis Reveals the Molecular Response of Sesame Capsules to Infection by Alternaria alternata

The genus Alternaria (Nees) is a major phytopathogen responsible for diseases. In Sesame, Alternaria alternata infects capsules during the rainy season (August-September) in Northeast China, inducing lesion expansion and compromising seed yield and quality. To investigate the molecular response of Sesame to Alternaria alternata infection, transcriptome analyses of "Liaozhi No. 9" were conducted on the pericarp and seeds of sesame capsules before and after A. alternata infection. For the data quality control, the GC content and the proportion of Q30 bases indicated that the sequencing quality was good. The correlation analysis and principal component analysis (PCA) among sample groups demonstrated that the biological replicates had high similarity and there were obvious differences between groups. Differential gene expression analysis was performed using DESeq2. There were 5892 and 9120 differentially expressed genes in the pericarp and seeds, respectively, and among them, 2788 were the same differential genes. GO functional annotation was carried out on the differentially expressed genes, and the results showed that the differential genes were mainly enriched in biological processes (cellular processes, metabolic processes), molecular functions (catalytic activity and binding), and cellular components (cellular anatomical entities and intracellular components). KEGG metabolic pathway analysis revealed that metabolic pathways such as plant hormone signal transduction and plant-pathogen interaction were enriched after the infection of A. alternata. The genes in the jasmonic acid pathway (MYC2) and in the salicylic acid pathway (NPR1 and TGA) of the plant hormone signal transduction pathway were induced after A. alternata infection. Meanwhile, the genes in plant-pathogen interaction pathway, such as CML, CDPK and CNCGs were also induced after the infection. This study indicates that sesame capsules respond to the infection of Alternaria alternata through the genes in the plant hormone signal transduction pathway and the plant-pathogen interaction metabolic pathway, providing a theoretical basis for the subsequent research on sesame disease-resistant breeding and its molecular mechanism.

Transcriptome analysis reveals candidate genes involved in quercetin biosynthesis in Euphorbia maculata

An investigation was conducted through transcriptome sequencing in various tissues at different stages to explore the quercetin biosynthesis pathway in Euphorbia maculata. A total of 83,028 unigenes was assembled utilizing Trinity software, with an N50 length of 1721 bp and a mean length of 1004 bp. Among these unigenes, 51,822 were annotated in six public databases. The transcriptome analysis revealed 45,727 CDS sequences and 56 TF families. Candidate genes involved in quercetin biosynthesis were also revealed, including phenylalanine ammonia-lyase (17 unigenes), cinnamate 4-hydroxylase (3 unigenes), 4-coumarate-CoA ligase (16 unigenes), chalcone synthase (5 unigenes), chalcone isomerase (4 unigenes), flavanone 3-hydroxylase (1 unigene), flavonoid 3'-hydroxylase (4 unigenes), and flavonol synthase (9 unigenes). Additionally, 42 key differentially expressed genes (DEGs) related to quercetin biosynthesis were identified in the same tissues at different stages, with 35 DEGs exhibiting down-regulated expression and 7 DEGs displaying up-regulated expression. These findings not only enhance the genetic knowledge of E. maculata, but also establish a basis for further investigating the mechanism of quercetin biosynthesis, and improving the quality of E. maculata.

Alternaria alternata botybirnavirus 1 (AaBRV1) Infection Affects the Biological Characteristics of Its Host Fungus Alternaria alternata

A botybirnavirus, Alternaria alternata botybirnavirus 1 (AaBRV1), had been identified from Alternaria alternata strain SD-BZF-19 isolated from diseased watermelon leaves in our previous study. In the current study, AaBRV1 was eliminated from its host fungus strain SD-BZF-19 using single hyphal tip culture method combined with high-temperature treatment to obtain the AaBRV1-free strain, which was named SD-BZF-19-G14. Compared with strain SD-BZF-19-G14, following AaBRV1 infection, colony color of strain SD-BZF-19 changed, and colony growth rate, dry weight of mycelial biomass, and sensitivity to difenoconazole, fludioxonil, and tebuconazole of strain SD-BZF-19 all decreased. However, the virulence of strain SD-BZF-19 was not significantly different from strain SD-BZF-19-G14, with disease index of watermelon leaves inoculated with SD-BZF-19 and SD-BZF-19-G14 being 90.83 and 81.67, respectively. A total of 1244 differentially expressed genes (DEGs) were identified in a comparative transcriptome analysis between the two strains, SD-BZF-19 and SD-BZF-19-G14. Relative to strain SD-BZF-19, the number of upregulated and downregulated DEGs in strain SD-BZF-19-G14 was 660 and 584, respectively. Notably, Pfam database annotated that the number of DEGs related to Major Facilitator Superfamily (MFS) and Cytochrome P450 (CYP450) was 36 and 28, respectively. To our knowledge, this is the first documentation of biological characteristics induced by AaBRV1 infection in A. alternata.

Transcriptome Analysis and Identification of Chemosensory Membrane Proteins in the Head of Euplatypus parallelus

Euplatypus parallelus is a polyphagous pest capable of harming multiple plant species. Adult beetles invade tree trunks by boring holes, which negatively impacts the trees' growth and may result in tree death. E. parallelus depends on plant volatiles to identify and locate appropriate hosts for feeding or reproduction, with its olfactory system playing a vital role in volatile detection. In this work, we applied transcriptomics, phylogenetic analysis, and expression analysis to investigate four chemosensory membrane protein gene families that play a role in olfaction in E. parallelus. Based on the annotation analysis, 41 odorant receptors (ORs), 12 gustatory receptors (GRs), 14 ionotropic receptors (IRs), and 4 sensory neuron membrane proteins (SNMPs) were identified in the head. We used differential gene expression (DGE) and fragments per kilobase per million (FPKM) values to compare the transcription levels of chemosensory membrane protein gene families between males and females. The data indicate that the chemosensory membrane protein gene families in E. parallelus exhibit different expression levels in male and female heads, with some genes showing significant differences and displaying sex-biased expression. These results offer a basis for future exploration of the functions of chemosensory membrane protein gene families in E. parallelus and offer a theoretical framework for designing innovative eco-friendly control technologies.

Transcriptomic analysis of wrinkled leaf development of Tai-cai (Brassica rapa var. tai-tsai) and its synthetic allotetraploid via RNA and miRNA sequencing

The allotetraploid (AACC) was synthesized through wide hybridization between 'Mottle-leaf Tai-cai' (Brassica rapa var. tai-tsai Hort. AA) and 'Big Yellow Flower Chinese Kale' (B. oleracea var. alboglabra Bailey. CC) in earlier study, which owns a stronger wrinkled leaf and wave margin than Tai-cai. To analyze the structure and developmental mechanism of wrinkled leaf and wave edge, four leaf development stages were chosen for RNA-seq and their key stages for anatomical observation. As a result, the number of cell layers and compactness of AA and AACC were significantly increased in folded parts, and the enlargement of epidermal cells causes the leaf edge to curve inward. The gene expression bias of AACC showed no difference in the cotyledon stage, favored the A genome in the first leaf stage, however, favored the C genome in the third leaf and fifth leaf stages, showing an expression level advantage over the C genome parent. During the leaf development, the plant hormone signaling pathway were significantly enriched, PIN1 (BraC07g037600), AUX1 (BraC05g007870), AUX/IAA (BraC03g037630), and GH3 (BraC10g026970), which maintained high expression during the euphylla leaf stage of AA and AACC. And these genes performed different patterns in CC. In addition, the expression levels of miR319 and miR156 of AA were significantly higher than those of CC, and the expression levels of their target genes TCP and SPL were lower. These genes were jointly involved in the development of AA and AACC leaves and may be closely related to the formation of leaf folds and waves.

NHR-85 modulates mitochondrial and lipid homeostasis to protect against α-synuclein aggregation in C. elegans

Peroxisome proliferator-activated receptors (PPARs), such as PPARδ, are transcription factors that play a pivotal role in energy and fat metabolism. PPARδ activates genes involved in lipid and glucose metabolism and is expressed in various human tissues, including all brain regions and especially neurons, where it regulates lipid homeostasis and contributes to neuroprotection. However, the precise molecular mechanisms underlying these protective effects remain poorly understood. Here, we identify the Caenorhabditis elegans nuclear hormone receptor NHR-85 as a putative orthologue of human PPARδ. Furthermore, we show that NHR-85 functions as an essential regulator of fat and energy metabolism, with significant impact on mitochondrial homeostasis, at least in part through modulation of mitophagy. Finally, we find that NHR-85 prevents α-synuclein aggregation in a nematode model of Parkinson's disease, suggesting that it might play a protective role in neurodegenerative diseases. Our results indicate that NHR-85 is a functional orthologue of PPARδ and support the use of C. elegans as a powerful in vivo model for dissecting PPARδ-related metabolic and neurodegenerative processes.

MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data

Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets.

Telomere-to-telomere genome and multi-omics analysis of Prunus avium cv. Tieton provides insights into its genomic evolution and flavonoid biosynthesis

The European sweet cherry (Prunus avium) is highly valued for its superior quality, delectable taste, and robust stress resistance, leading to its extensive cultivation in the world. However, the previous incomplete genome assemblies have impeded its evolution and genetic regulation studies. In this study, we generated a Telomere-to-Telomere gap-free genome assembly of P. avium cv. Tieton, using advanced sequencing technologies. The assembled genome comprises eight pseudochromosomes with a genome size of 342.23 Mb and a contig N50 of 40.66 Mb. Comparative genomic analysis identified several unique stress resistance-related genes, possibly associated with the species' environmental adaptation. The integrative analyses of genomics, transcriptomes and metabolomes identified some key structural genes and metabolites crucial to flavonoid biosynthesis of sweet cherry. Our analyses revealed that 85 flavonoid metabolites, which are highly differentially accumulated among five tissues (flesh, stem, leaf, bud, and seed) of cherry. Interestingly, eight abundant flavonoids (Narcissoside, Typhaneoside, Myricetin 3-0-galactoside, Diosmin, Neohesperidin, Liquiritin apioside, 5,6,7-Trimethoxyflavone and Oroxin B) were highly accumulated in cherry flesh tissues. The gene-metabolite correlation analysis revealed that seven genes (HTC8, HTC6, CYP75B1_9, CYP75B1_10, 4CL1, DFR1, and FLS1) significantly regulated flavonoid accumulation in cherry flesh. Additionally, some structural genes (4CL6, PAL3, CYP75A2, F3H1, CYP75B1_8, and CYP75B1_10) were identified in the flavonoid biosynthetic pathway and were highly expressed, aligning with high flavonoid metabolite content in cherry flesh. These identified genes and metabolites are likely pivotal in conferring sweet cherry's stress resistance and high-quality traits. These findings offer deep insights into the mechanisms of genomic evolution and flavonoid biosynthesis, which also lay a solid foundation for further function genomics studies and breeding improvement in cherry.

Physiological Responses and Transcriptome Analysis of Camellia reticulata Under Low-Temperature Stress

Background:Camellia species are highly ornamental but sensitive to habitat temperature, making cross-border domestication challenging. Methods: In this study, physiological indicators and transcriptome data of Camellia reticulata 'shizhitou' were analyzed to identify key factors involved in the response to cold. Results: The findings provide a scientific basis for the conservation of Camellia germplasm resources and breeding of cold-tolerant varieties. Under prolonged low-temperature stress, significant changes were observed in the physiological indices of C. reticulata 'shizhitou'. Among soluble substances, soluble protein content continuously increased, while soluble sugar content exhibited a fluctuation pattern of increase-decrease-increase. Under prolonged low-temperature stress, significant changes were observed in the physiological indexes of C. reticulata 'shizhitou', while soluble sugar content exhibited a fluctuation pattern of increase-decrease-increase. Overall, soluble sugar and soluble protein contents were significantly positively correlated. Chlorophyll content initially decreased and then increased, whereas peroxidase (POD) and catalase (CAT) activities fluctuated and were negatively correlated with chlorophyll content. Malondialdehyde (MDA) content showed an irregular fluctuation trend. A total of 56,424 unigenes were obtained by transcriptome sequencing, of which 39,278 were annotated, while 10,816 differentially expressed genes (DEGs) were identified, including 5748 up-regulated and 5068 down-regulated genes, with 143 DEGs commonly shared across conditions. Congclusions: Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that low-temperature stress significantly influenced glucose metabolism, lipid metabolism, and amino acid metabolism, and the core pathways of cold stress included zeatin synthesis, hormone signaling, and galactose metabolism. Both physiological responses and transcriptome-based enrichment of DEGs indicate that the redox system and metabolic pathways play crucial regulatory roles in C. reticulata under cold stress.

Genomic signatures associated with the evolutionary loss of egg yolk in parasitoid wasps

Trait regression and loss have occurred repeatedly in numerous lineages in response to environmental changes. In parasitoid wasps, a megadiverse group of hymenopteran insects, yolk protein reduction or loss has been observed in many species, likely linked to the transition from ectoparasitism to endoparasitism. However, the genetic basis of this trait and the impact of its loss on genome evolution remain poorly understood. Here, we performed a comparative genomic analysis of 64 hymenopteran insects. The conserved insect yolk protein gene vitellogenin (Vg) underwent five independent loss events in four families, involving 23 of the analyzed endoparasitoid species. Whole-genome alignment suggested that Vg loss occurred during genome rearrangement events. Analysis of Vg receptor gene (VgR) loss, selection, and structural variation in lineages lacking Vg demonstrated functional biases in the patterns of gene loss. The ectoparasitism to endoparasitism transition did not appear to be the primary driver of Vg loss or the subsequent VgR evolution. Together, these findings reveal the genomic changes underlying a unique trait loss in parasitoid wasps. More broadly, this study enhances our understanding of yolk protein loss evolution outside the class Mammalia, highlighting a potential evolutionary trend arising from the availability of an alternative nutrient source for embryonic development.

Chromosome-level genome assembly of an important ethnic medicinal plant Callicarpa nudiflora

Callicarpa nudiflora is one of high medicinal and economic value plants in China, which was recorded in Chinese pharmacopoeia (2020 edition) and widely used to treat tropical bacterial infections, acute infectious hepatitis, and internal and external bleeding. In this study, we assembled the C. nudiflora genome with a size of approximately 597.82 Mb and a contig N50 length of 34.14 Mb. A total of 98.61% of the assembled sequences were anchored to 17 pseudo-chromosomes by using PacBio long reads and Hi-C sequencing data. We totally predicted 31,266 protein-coding genes, of which 92.45% could be annotated in databases such as NR, GO, KOG, and KEGG. In addition, we identified 2,303 rRNAs, 884 MicroRNAs and 531 tRNAs from the genome. The chromosome-scale genome represents a crucial resource for investigating the molecular mechanisms underlying the biosynthesis of medicinal components and facilitates the exploration and conservation of C. nudiflora.

Genomic insights and the conservation potential of captive breeding: The case of Chinese alligator

Despite 40 years of conservation of the critically endangered Chinese alligator (Alligator sinensis), the genomic underpinnings of its status remained uncharted. Genome sequencing data of 244 individuals uncovered relatively low overall genomic diversity/heterozygosity and long runs of homozygosity, with captive populations exhibiting higher heterozygosity and smaller inbreeding coefficients compared to wild individuals. The decreased level of inbreeding in the captive population demonstrates the contribution of the large captive breeding population. The estimated recent effective population size was around a few dozen. To combat challenges of inbreeding depression and reduced adaptability, we used genome-wide SNP-based kinship analysis on captive populations to enable a genome-informed breeding program that minimizes inbreeding. Long-term field monitoring revealed that the Chinese government greatly advanced the conservation of A. sinensis through conservation measures and reintroduction programs. Our research enriches the understanding of the Chinese alligator's genetic landscape, offering invaluable genomic resources for breeding and conservation strategies.

Chromosome-scale genome assembly of Zoysia japonica uncovers cold tolerance candidate genes

Zoysiagrass stands out as a crucial native turfgrass due to its exceptional abiotic stress tolerance, extensive adaptability, and high ornamental value. In this study, we generated a high-quality chromosome-level genome assembly of Compadre (COM) zoysiagrass, leveraging PacBio SMRT sequencing and Hi-C scaffolding technologies. The resulting genome assembly (312.42 Mb) is anchored on 20 chromosomes, with a Scaffold N50 of 18.72 Mb. In total, 49,074 genes and 306,768 repeat sequences were annotated in the assembled genome. The first chromosome-scale genome of Zoysia japonica 'Compadre' provides a critical genetic resource for cold-tolerant turfgrass breeding through identifying stress-responsive candidate genes. Additionally, we have successfully established a cell nucleus extraction and library construction protocol tailored for zoysiagrass ATAC-seq technology, and a total of 80 low temperature tolerance candidate genes were preliminarily identified via ATAC-seq and RNA-seq profiling, thereby initiating the exploration of turfgrass epigenomics.

Exosomal miR-92b-5p regulates N4BP1 to enhance PTEN mono-ubiquitination in doxorubicin-resistant AML

Aim: Doxorubicin, pivotal for acute myeloid leukemia (AML) treatment, often succumbs to resistance, impeding therapeutic success. Although exosomal transfer is linked to chemoresistance, the detailed role of exosomal miRNAs in doxorubicin resistance remains incompletely understood. Methods: We employed miRNA sequencing to delineate the profile of exosomal miRNAs in doxorubicin-resistant K562/DOX cells and AML patients. Subsequently, qPCR was utilized to scrutinize the expression of exosomal miR-92b-5p in these resistant cells and AML patients. A dual-luciferase reporter assay was conducted to elucidate the direct binding of miR-92b-5p to NEDD4 binding protein 1 (N4BP1). Furthermore, interactions between N4BP1 and NEDD4, as well as between NEDD4 and PTEN, were investigated by co-immunoprecipitation (Co-IP). Meanwhile, the ubiquitination of PTEN was also examined by Co-IP. Western blot analysis was applied to assess the expression levels of N4BP1, NEDD4, PTEN, RAD51, and proteins associated with the PI3K-AKT-mTOR pathway. Gain- and loss-of-function studies were conducted to ascertain the functional role of miR-92b-5p in doxorubicin resistance by using miR-92b-5p-mimic and miR-92b-5p-inhibitor transfections. Results: Our study found exosomal miR-92b-5p was upregulated both in doxorubicin-resistant cells and AML patients. Moreover, miR-92b-5p targets N4BP1, promoting NEDD4-mediated mono-ubiquitination of PTEN. This alters PTEN's subcellular localization, promoting nuclear PTEN and reducing cytoplasmic PTEN, which in turn leads to increased RAD51 for DNA repair and activation of the PI3K-AKT-mTOR pathway for cell proliferation, contributing to doxorubicin resistance. Conclusion: Our study reveals a novel mechanism of doxorubicin resistance mediated by exosomal miR-92b-5p and provides potential therapeutic targets for overcoming drug resistance in AML.

Ecotype-specific phenolic acid accumulation and root softness in Salvia miltiorrhiza are driven by environmental and genetic factors

Salvia miltiorrhiza Bunge, a renowned medicinal herb in traditional Chinese medicine, displays distinctive root texture and high phenolic acid content, traits influenced by genetic and environmental factors. However, the underlying regulatory networks remain unclear. Here, we performed multi-omics analyses on ecotypes from four major Chinese regions, focusing on environmental impacts on root structure, phenolic acid accumulation and lignin composition. Lower temperatures and increased UV-B radiation were associated with elevated rosmarinic acid (RA) and salvianolic acid B (SAB) levels, particularly in the Sichuan ecotype. Structural models indicated that the radial arrangement of xylem conduits contributes to greater root hardness. Genomic assembly and comparative analysis of the Sichuan ecotype revealed a unique phenolic acid metabolism gene cluster, including SmWRKY40, a WRKY transcription factor essential for RA and SAB biosynthesis. Overexpression of SmWRKY40 enhanced phenolic acid levels and lignin content, whereas its knockout reduced root hardness. Integrating high-throughput (DNA affinity purification sequencing) and point-to-point (Yeast One-Hybrid, Dual-Luciferase and Electrophoretic Mobility Shift Assay) protein-DNA interaction detection platform further identified SmWRKY40 binding sites across ecotypes, revealing specific regulatory networks. Our findings provide insights into the molecular basis of root texture and bioactive compound accumulation, advancing breeding strategies for quality improvement in S. miltiorrhiza.

Genome mining the black-yeast Aureobasidium pullulans NRRL 62031 for biotechnological traits

Aureobasidium pullulans is a yeast-like fungus known for its commercial biomanufacturing of pullulan. This study explores the genome of A. pullulans NRRL 62031, highlighting its biosynthetic potential, metabolic pathways, and physiological traits. Additionally, it demonstrates actual product formation and links molecular features to biotechnological applications. Phylogenetic analysis suggested it might be closely related to Aureobasidium melanogenum. While the functional annotation revealed a wide carbohydrate catabolism, growth evaluation demonstrated that the microbe can utilize not only saccharides but also polyols and organic acids. The extracellular cellulolytic, xylanolytic, and pectinolytic activities were indicated by the formation of visible halos on agar plates. The antiSMASH pipeline, NCBI Blastp alignment, and product qualification confirmed that A. pullulans NRRL 62031 can produce melanin, pullulan, polymalate, and polyol lipids. Moreover, yanuthone D, burnettramic acid A, choline, fructooligosaccharides, gluconic acid, and β-glucan might be synthesized by A. pullulans NRRL 62031. The results clearly show the extraordinary potential of A. pullulans NRRL 62031 as a microbial chassis for valorizing biomass residues into value-added bioproducts. The strong catabolic and anabolic capacities indicate significant promise for biotechnological applications. The results are discussed in the context of metabolic engineering of Aureobasidium.

Whole transcriptomic analysis reveals the lncRNA-miRNA-mRNA regulatory mechanism underlying the heat-hardening formation in Mytilus coruscus

Heat-hardening is a critical adaptation mechanism that enables the mussel Mytilus coruscus to endure high-temperature events caused by low tides and adverse weather condition. However, the molecular regulatory mechanism underlying heat-hardening remains unclear. Herein, we analyzed the whole transcriptome of heat-hardening M. coruscus to explore formation mechanism of heat-hardening. M. coruscus were treated with 27 °C for 5 days, 3 h per day, to promote heat-hardening formation, and sampled at 6, 8, 10, 12, 14, and 16 days. We identified 203 differentially expressed lncRNAs (DE-lncRNAs), 11 differentially expressed miRNAs (DE-miRNAs) and 207 differentially expressed mRNAs (DE-mRNAs). GO and KEGG enrichment analysis revealed that the DE-mRNAs were mainly enriched in arachidonic acid metabolism pathway, apoptosis pathway, NOD-like receptor signaling pathway and the platelet-activated pathway, WGCNA results suggested that arachidonic acid metabolism and cytochrome P450 were significantly correlated with heat-hardening during formation. PLA2 was identified as an essential gene in heat-hardening, with high node degrees, enriched in the arachidonic acid metabolism pathway and regulated by a lncRNA (MSTRG.113849.1) and a miRNA (novel_miR_425). MSTRG.113849.1-novel_miR_425-PLA2 relationship pairs were identified for heat-hardening in M. coruscus. Our finding suggests that miRNAs and lncRNAs play pivotal roles in heat-hardening by targeting PLA2, providing a mechanism for M. coruscus to adapt to heat stress, which also offers a mechanism to adapt to stressors arising from a rapidly changing oceanic environment.

A Preliminary Exploration of Transcriptome and Proteomic Changes During the Young and Harvest Periods in Morchella sextelata

Based on transcriptome and proteome sequencing technologies, this study aims to preliminarily reveal the molecular mechanisms of growth and development and related metabolic regulation in Morchella sextelat. A total of 42.31 GB of Clean Data was acquired from the transcriptome sequencing (RNA-seq) of six samples in two development phases (n = 3) of M. sextelata. In the young phase (YP) and harvest phase (HP), there were 2887 differentially expressed genes (DEGs), including 1910 up-regulated genes and 977 down-regulated genes. In YP and HP, there were 987 differentially expressed proteins (DEPs), including 417 up-regulated ones and 570 down-regulated ones. Based on GO and KEGG analysis, significant differences in the transcriptomes and proteins in metabolic pathways are disclosed. Glycometabolism, especially starch, saccharose, and polysaccharide metabolism, plays a crucial role in the growth of M. sextelata. In addition, expression changes in the genes related to selenium metabolism are here recognized. These research results not only offer strong support for further exploration of the biological significance and functional differences of M. sextelata, but are also conducive to discovering key genes and understanding their regulation network during growth.

Screening CYP450 genes from Gleditsia japonica Miq. and identifying CYP710A157 and CYP71D752 functions in the catalysis of echinocystic acid and betulin

The triterpenes and saponin compounds of Gleditsia japonica Miq. play a key role in the suppression of various human tumor cell lines. Cytochrome P450 monooxygenases (CYP450s) are critical for the triterpene skeleton diversification and functional modification. This study systematically analyzed 104 full-length GjCYP450 genes in G. japonica from northeast China, classifying them into nine clans using bioinformatics. Co-expression modules and response patterns of GjCYP450s with triterpene pathway genes were constructed. Four genes - CYP710A157, CYP714E97, CYP716A377, and CYP71D752 - were selected for functional studies based on their high expression in different tissues of G. japonica and their homology with triterpenoid-related CYP450s in Arabidopsis thaliana. Co-expression of the CYP710A157 gene with the BpY gene (encoding β-amyrin synthase), and CYP71D752 with the BpW gene (encoding lupeol synthase) in tobacco significantly enhanced the catalytic efficiency of echinocystic acid (EA) and betulin (BT) compared to the control, by achieving 10.22-fold and 3.73-fold increases, respectively. Overexpression of CYP710A157 and CYP71D752 in Saccharomyces cerevisiae JWy602 yielded EA and BT at 3.25 mg l-1 and 13.84 mg l-1, respectively, whereas no product accumulation was detected in the control. Additionally, CYP710A157 and CYP714E97 enhanced yeast alkaline tolerance (500 mmol l-1 Na2CO3), while CYP716A377 and CYP71D752 improved their salt tolerance (10% NaCl). We reported the catalytic activity of CYP450 genes responsible for EA and BT synthesis within the CYP710A and CYP71D subfamilies in G. japonica for the first time here. These findings provide valuable genetic resources for plants' triterpene biosynthesis, including ginsenosides, and betulinic acid, and insights into regulating the triterpene metabolic network in G. japonica.

The chromosome-scale genome of black wolfberry (Lycium ruthenicum) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance

The black wolfberry (L ycium ruthenicum; 2n = 2x = 24) is an important medicinal plant with ecological and economic value. Its fruits have numerous beneficial pharmacological activities, especially those of anthocyanins, polysaccharides, and alkaloids, and have high nutritional value. However, the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms. In this study, we developed the telomere-to-telomere (T2T) nearly gapless genome of L. ruthenicum (2.26 Gb) by integrating PacBio HiFi, Nanopore Ultra-Long, and Hi-C technologies. The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated. Approximately 80% of the repetitive sequences were identified, of which long terminal repeats (LTRs) were the most abundant, accounting for 73.01%. The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species. The species-specific genes of L. ruthenicum were related to defense mechanisms, salt tolerance, drought resistance, and oxidative stress, further demonstrating their superior adaptability to arid environments. Based on the assembled genome and fruit transcriptome data, we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L. ruthenicum, most of which were highly expressed at a later stage in fruit development. Furthermore, 154 potential disease resistance-related nucleotide-binding genes have been identified in the L. ruthenicum genome. The whole-genome and proximal, dispersed, and tandem duplication genes in the L. ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways. These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.

Full-Length Transcriptome Sequencing and Comparative Transcriptomics Reveal the Molecular Mechanisms Underlying Gonadal Development in Sleepy Cod (Oxyeleotris lineolata)

Sleepy cod (Oxyeleotris lineolata) is native to Australia and is now an economically valuable fish cultured in China and Southern Asian countries. Its growth rate exhibits as sexually dimorphic, with males generally growing more rapidly and attaining a larger body size compared to females. Thus, the effective development of sex control breeding can significantly contribute to increased yields and output value. Nevertheless, due to the lack of genomic and transcriptomic data, the molecular mechanisms underlying sex determination and gonadal differentiation in sleepy cod remain poorly understood. In this study, long-read PacBio isoform sequencing (Iso-Seq) was performed to obtain a full-length transcriptome from a pooled sample of eight tissues (kidney, brain, liver, muscle, heart, spleen, ovary and testis). A total of 30.41 G subread bases were generated and 49,113 non-redundant full-length transcripts with an average length of 2948 bp were produced. Using the full-length transcriptome as a reference, short-read Illumina sequencing was performed to investigate the differences in gene expression at the transcriptome level between ovaries and testes from 12-month-old individuals. A total of 19,102 differentially expressed transcripts (DETs) were identified, of which 8510 (44.55%) were up-regulated in the ovary and 10,592 (55.45%) were up-regulated in the testis. The DETs were mainly clustered into 241 KEGG pathways, in which oocyte meiosis and arachidonic acid metabolism were the most relevant pathways involved in gonadal differentiation. To verify the validity of the transcriptomic data, 20 DETs were selected to investigate the gonad expression profiles based on qPCR. The expression levels of all 20 screened genes were consistent with the transcriptome sequencing results. The present study provides new genetic resources-including full-length transcriptome sequences and annotation information-as a coding genomic-level reference for sleepy cod-yielding valuable insights into the genetic mechanisms of sex determination and gonadal differentiation in this economically important species.

Molecular Mechanisms of Gene Expression Regulation in Response to Heat Stress in Hemerocallis fulva

Hemerocallis fulva is one of the three major flowers in the world; its flower type and color are very rich, with high ornamental value and economic value. Heat stress severely limits the cultivation and geographical distribution of H. fulva. Genetic resources and their underlying molecular mechanisms constitute the cornerstone of contemporary breeding technologies. However, research on the response of H. fulva to heat stress remains relatively scant. In this study, we used the heat-resistant 'Dan Yang' variety and heat-sensitive 'Nuo Mi Lu' variety with phenotypic expression as experimental materials to determine the changes in substance and gene expression levels, and used bioinformatics technology to study the molecular mechanisms and gene resource mining of H. fulva in response to heat stress. We identified several thousand differentially expressed genes (DEGs) in different comparison groups. At the same time, 1850 shared DEGs were identified in two H. fulva genotypes responding to heat stress. The dynamic cutting algorithm was used to cluster the genes, and 23 gene co-expression modules were obtained. The MEorangered, MElightpink, and MEmagenta modules were significantly correlated with physiological and biochemical traits. We identified ten key genes closely related to the response of H. fulva to heat stress, including plant-pathogen interactions, plant hormone signal transduction, oxidative transduction phosphorylation, and the plant hormone signal transduction pathway. This study not only analyzes the molecular mechanism of H. fulva response to heat stress, but also provides genetic resources for breeding H. fulva heat tolerance.

The Rise of Algae promoted eukaryote predation in the Neoproterozoic benthos

The proliferation of marine algae in the Neoproterozoic Era is thought to have stimulated the ecology of predatory microbial eukaryotes. To test this proposal, we introduced algal particulate matter (APM) to marine sediments underlying a modern marine oxygen minimum zone with bottom-water oxygen concentrations approximating those of the late Neoproterozoic water column. We found that under anoxia, APM significantly stimulated microbial eukaryote gene expression, particularly genes involved in anaerobic energy metabolism and phagocytosis, and increased the relative abundance of 18S rRNA from known predatory clades. We additionally confirmed that APM promoted the reproduction of benthic foraminifera under anoxia with higher-than-expected net growth efficiencies. Overall, our findings suggest that algal biomass exported to the Neoproterozoic benthos stimulated the ecology of benthic predatory protists under anoxia, thereby creating more modern food webs by enhancing the transfer of fixed carbon and energy to eukaryotes occupying higher trophic levels, including the earliest benthic metazoans.

N-acetylglucosamine sensing in the filamentous soil fungus Trichoderma reesei

N-acetylglucosamine (GlcNAc) is involved in diverse signaling pathways in dimorphic yeasts and bacteria and is related to morphogenetic switching, mating, stress, virulence, and cell death. Recently, GlcNAc has been shown to promote plant growth by shaping the bacterial soil community. However, the role of GlcNAc sensing in filamentous soil fungi has not been investigated. By using Trichoderma reesei as a model organism, we show here that GlcNAc impacts the expression of around 2100 genes. Carbohydrate metabolism, amino acid metabolism, and secondary metabolism were the three most strongly affected classes of eukaryotic orthologous groups (KOG classes). Two key regulators of GlcNAc catabolism, the NDT80 domain-containing transcriptional regulator RON1, and a GlcNAc sensor, NGS1, are needed for differential regulation of two-thirds of these genes. In silico structural modeling of NGS1 identified a domain with homology to the GCN5-related histone acetyltransferase from Candida albicans, which serves as a GlcNAc catabolism regulator and GlcNAc sensor. Finally, we characterized the third regulator of GlcNAc sensing in T. reesei, which is the highly specific GlcNAc transporter N-acetylglucosamine transporter (NGT1). Using a deletion mutant of ngt1, we demonstrate that GlcNAc has to enter the cell to activate the GlcNAc catabolic gene expression. Interestingly, in contrast to dimorphic yeasts, the pathways for defense and pathogenicity seem to be induced in T. reesei by external GlcNAc. Given the ancestral role of Trichoderma spp. in the fungal kingdom and the highly conserved GlcNAc catabolism cluster that includes their regulators in many species of fungi, we propose a regulatory network for GlcNAc sensing in soil fungi.

Analysis of Gene Regulatory Network and Transcription Factors in Different Tissues of the Stropharia rugosoannulata Fruiting Body

Stropharia rugosoannulata is a mushroom that is rich in nutrients and has a pleasant flavor. Its cultivation area is expanding rapidly due to its simplicity and diversity. However, the developmental mechanism of the fruiting body, which constitutes the edible portion of S. rugosoannulata, remains to be elucidated. To address this knowledge gap, we conducted a comprehensive study. Our approach entailed the observation of sections through the fruiting body of S. rugosoannulata and the sequencing of the transcriptomes of various fruiting body tissues. The results demonstrated significant variations in the structure of the pileipellis, pileus, gill, veil, stipe, and trama of S. rugosoannulata. The predominant metabolic pathways included the amino acid metabolism of the pileus, sugar metabolism of the stipe, tryptophan metabolism, and wax production of the pileipellis, the DNA pathway of the gill, amino sugar metabolism of the veil, and the nitrogen metabolism of the trama. The promoter cis-element analysis revealed the roles of light response, methyl jasmonate, oxygen, and temperature on the differentiation of the veil, trama, and pileipellis, respectively. In summary, the present findings offer a molecular mechanism for the development of the fruiting body and provide directions for the enhancement of cultivation techniques of S. rugosoannulata.

Separation of life stages within anaerobic fungi (Neocallimastigomycota) highlights differences in global transcription and metabolism

Anaerobic gut fungi of the phylum Neocallimastigomycota are microbes proficient in valorizing low-cost but difficult-to-breakdown lignocellulosic plant biomass. Characterization of different fungal life stages and how they contribute to biomass breakdown are critical for biotechnological applications, yet we lack foundational knowledge about the transcriptional, metabolic, and enzyme secretion behavior of different life stages of anaerobic gut fungi: zoospores, germlings, immature thalli, and mature zoosporangia. A Miracloth-based technique was developed to enrich cell pellets with zoospores - the free-swimming, flagellated, young life stage of anaerobic gut fungi. By contrast, fungal mats contained relatively more vegetative, encysted, mature sporangia that form films. Global gene expression profiles were compared from two sample types (zoospore-enriched cell pellets vs. mature mats) harvested from the anaerobic gut fungal strain Neocallimastix californiae G1. Despite cultures being grown on glucose, the fungal zoospore-enriched samples were transcriptionally primed to encounter plant matter substrate, as evidenced by upregulation of catabolic carbohydrate-active enzymes and putative carbohydrate transporters. Furthermore, we report significant differential gene expression for gene annotation groups, including putative secondary metabolites and transcription factors. Understanding global gene expression differences between the fungal zoospore-enriched cells and mature fungi aid in characterizing fungal development, unmasking gene function, and guiding cultivation conditions and engineering targets to promote enzyme secretion.

Genome-Wide Analysis of bZIP Transcription Factors and Expression Patterns in Response to Salt and Drought Stress in Vaccinium corymbosum

The basic leucine zipper (bZIP) transcription factors play essential roles in multiple stress responses and have been identified and functionally characterized in many plant species. However, the bZIP family members in blueberry are unclear. In this study, we identified 102 VcbZIP genes in Vaccinium corymbosum. VcbZIPs were divided into 10 groups based on phylogenetic analysis, and each group shared similar motifs, domains, and gene structures. Predictions of cis-regulatory elements in the upstream sequences of VcbZIP genes indicated that VcbZIP proteins are likely involved in phytohormone signaling pathways and abiotic stress responses. Analyses of RNA deep sequencing data showed that 18, 13, and 7 VcbZIP genes were differentially expressed in response to salt, drought, and ABA stress, respectively, for the blueberry cultivar Northland. Ten VcbZIP genes responded to both salt and drought stress, indicating that salt and drought have unique and overlapping signals. Of these genes, VcbZIP1-3 are responsive to salt, drought, and abscisic acid treatments, and their encoded proteins may integrate salt, drought, and ABA signaling. Furthermore, VcbZIP1-3 from group A and VcbZIP83-84 and VcbZIP75 from group S exhibited high or low expression under salt or drought stress and might be important regulators for improving drought or salt tolerance. Pearson correlation analyses revealed that VcbZIP transcription factors may regulate stress-responsive genes to improve drought or salt tolerance in a functionally redundant manner. Our study provides a useful reference for functional analyses of VcbZIP genes and for improving salt and drought stress tolerance in blueberry.

Integrated Metabolome, Transcriptome, and Physiological Analysis of the Flavonoid and Phenylethanol Glycosides Accumulation in Wild Phlomoides rotata Roots from Different Habitats

Phlomoides rotata, a traditional medicinal plant, is commonly found on the Tibetan Plateau at altitudes of 3100-5200 m. Its primary active medicinal compounds, flavonoids and phenylethanol glycosides (PhGs), exhibit various pharmacological effects, including hemostatic, anti-inflammatory, antitumor, immunomodulatory, and antioxidant activities. This study analyzed flavonoid and PhG metabolites in the roots of P. rotata collected from Henan County (HN), Guoluo County (GL), Yushu County (YS), and Chengduo County (CD) in Qinghai Province. A total of differentially abundant metabolites (DAMs) including 38 flavonoids and 21 PhGs were identified. Six genes (UFGT1, CHS1, COMT2, C4H3, C4H8, and C4H5) and four enzymes (4CL, C4H, PPO, and ALDH) were found to play key roles in regulating flavonoid and PhG biosynthesis in P. rotata roots. With increasing altitude, the relative content of 15 metabolites, the expression of seven genes, and the activity of four enzymes associated with flavonoid and PhG metabolism increased. These findings enhance our understanding of the regulatory mechanisms of flavonoid and PhG metabolism in P. rotata and provide insights into the potential pharmaceutical applications of its bioactive compounds.

PiERF1 regulates cold tolerance in Plumbago indica L. through ethylene signalling

Ethylene is a signalling factor that plays a key role in the response of plants to abiotic stresses, such as cold stress. Recent studies have shown that the exogenous application of 1-aminocyclopropane-1-carboxylate (ACC), an ethylene promoter, affects plant cold tolerance. The cold-responsive specific gene DREB plays a crucial role in enhancing cold tolerance in plants by activating several cold-responsive (COR) genes. However, how the ethylene biosynthesis pathway regulates this gene in the cold response of thermophilic plants has yet to be fully elucidated. In this study, the thermophilic plant Plumbago indica L. was used as an example. Physiological experiments and transcriptomic analyses revealed that cold stress treatment induced the synthesis of endogenous ACC and regulated the ethylene signalling activator PiERF1, and cold signalling also activated PiDREB1A. Spray experiments also revealed that ACC-induced upregulation of the PiERF1 gene reduced the cold tolerance of P. indica and decreased the expression level of the PiDREB1A gene. These results indicate that ethylene signalling directly regulates the downstream gene PiERF1 and initiates the DREB‒COR cold-responsive signalling pathway to regulate cold tolerance, resulting in the negative regulation of cold tolerance in thermophilic plants.

The telomere-to-telomere genome of flowering cherry (Prunus campanulata) reveals genomic evolution of the subgenus Cerasus

BACKGROUND

Prunus campanulata, a species of ornamental cherry, holds significant genetic and horticultural value. Despite the availability of various cherry genomes, a fully resolved telomere-to-telomere (T2T) assembly for this species has been lacking. Recent advancements in long-read sequencing technologies have made it possible to generate gap-free genome assemblies, providing comprehensive insights into genomic structures that were previously inaccessible.

FINDINGS

We present the first T2T genome assembly for P. campanulata "Lianmeiren" (v2.0), achieved through the integration of PacBio HiFi, ultra-long Oxford Nanopore Technologies, Illumina, and Hi-C sequencing. The assembly resulted in a highly contiguous genome with a total size of 266.23 Mb and a contig N50 of 31.6 Mb. The genome exhibits remarkable completeness (98.9% BUSCO) and high accuracy (quality value of 48.75). Additionally, 13 telomeres and putative centromere regions were successfully identified across the 8 pseudochromosomes. Comparative analysis with the previous v1.0 assembly revealed 336,943 single nucleotide polymorphisms, 107,521 indels, and 1,413 structural variations, along with the annotation of 1,402 new genes.

CONCLUSIONS

This T2T genome assembly of P. campanulata "Lianmeiren" provides a critical reference for understanding the genetic architecture of the species. It enhances our ability to study structural variations, gene function, and evolutionary biology within the Prunus genus.

Analysis of full length transcriptome and resistance characteristics of Atraphaxis bracteata under drought

Drought is one of the main environmental factors affecting plant survival and growth. Atraphaxis bracteata is a common desert plant mainly utilized in afforestation and desertification control. This study analyzed the morphological, physiological and molecular regulatory characteristics of different organs of A. bracteata under drought stress. The results showed that with the intensification of drought stress, the height, root length and leaf area of A. bracteata seedlings decreased, while the content of osmotic substances and antioxidant enzyme activity increased. Furthermore, a total of 63 907 non-redundant transcript sequences, of which 55 574 transcripts were annotated, 248 178 FLNC sequences, 107 112 high-quality consistent sequences and 291 314 CCSs were obtained from Iso-Seq. Meanwhile, a total of 2 039 AS events, 22 919 SSR, 40 404 CDS and 5 902 lncRNA were also obtained. The RNA-Seq analysis results revealed that a total of 2 821, 3 907 and 5 532 DETs were identified from roots, stems and leaves, respectively, and which had significantly enrichment in "circadian rhythm-plant" and "starch and sucrose metabolism" pathway. These results would be great significance for further research on the stress resistance of A. bracteata and these DETs function.

Full-length transcriptome annotation of a pyrosome, Pyrosoma atlanticum (Chordata, Thaliacea)

Pyrosomes represent a group of marine holozooplankton. They do not exist as individual entities but as intricate colonies comprising numerous zooids, well-known for their bioluminescent properties. Pyrosomes inhabit most oceanic waters spanning tropical to temperate regions. They serve as significant consumers of phytoplankton, playing a crucial role in transport of organic carbon and sedimentation of organic matter debris. Nonetheless, the knowledge about this group remains limited, particularly concerning genomic and gene aspects. To further investigate the pyrosome at the molecular level, we used Pyrosoma atlanticum, which is the best known of pyrosome, for investigation in this study. We performed PacBio Iso-Seq and Illumina RNA-seq to generate high-quality and full-length transcript data from P. atlanticum. The systematic gene functional annotation was performed by integrated data. The full-length transcriptome produced in this study represents the inaugural dataset of transcriptome within the class Thaliacea, serving as a reference for future investigations. Additionally, as a stem group for chordates, the information of pyrosomes can provide a valuable research foundation for the evolution of vertebrates.

The role of sugar transporter BrSWEET11 in promoting plant early flowering and preliminary exploration of its molecular mechanism

KEY MESSAGE

BrSWEET11 accelerated Arabidopsis thaliana flowering, while silencing Brsweet11 in Brassica rapa delayed flowering relative to controls. BrSWEET11 is involved in sucrose transport after being induced by long-day conditions. SWEETs (Sugars Will Eventually Be Exported Transporters) are sugar outflow transporters that may participate in the regulation of plant flowering. In this study, the open reading frame of Brassica rapa ssp. pekinensis SWEET11 (BrSWEET11) was cloned and found to be 858 bp in length and encode 285 amino acids, which is typical of SWEET family proteins. The BrSWEET11 gene was strongly expressed in reproductive growth organs, particularly flowers, according to tissue expression analyses and GUS histochemical staining. BrSWEET11 promotes early flowering in Arabidopsis thaliana by 3-4 days, whereas Brsweet11 silencing in Brassica rapa delays flowering by 8-12 days relative to controls. BrSWEET11 promoted early flowering in A. thaliana, and compared with that in control plants, flowering was delayed in Brsweet11-silenced Brassica rapa. Transcriptome analysis of BrSWEET11-overexpressing A. thaliana and wild-type (WT) plants was performed and the results showed that eight key flowering genes jointly regulated flowering time, which was also validated in the Brsweet11-silenced plants. In addition, through photoperiod treatments and sugar content measurements, it was found that the expression of BrSWEET11 is induced by long-day conditions and is involved in sucrose transport. Further investigation using yeast library screening, yeast two-hybrid, and bimolecular fluorescence complementation assay techniques revealed that the BrSWEET11 protein interacts with the sugar transporter 4a (BrSUT4a) protein. Therefore, BrSWEET11 was induced by long-day conditions, and may promote early flowering in Brassica rapa through sucrose transport. This study provides a theoretical basis for elucidating the molecular mechanism through which SWEET genes are involved in flowering time regulation in Brassica rapa.

Nanopore-Based Sequencing of the Full-Length Transcriptome of Male and Female Cleavage-Stage Embryos of the Chinese Mitten Crab (Eriocheir sinensis)

The cleavage stage plays a crucial role in embryo development, characterized by a swift surge in cell proliferation alongside the accurate genetic material transmission to offspring. To delve into the characteristics of sex development during the cleavage stage of embryos, we generated the full-length transcriptome of Eriocheir sinensis male and female cleavage-stage embryos using Oxford Nanopore Technologies (ONT). Notably, this investigation represents the first sequencing effort distinguishing between genders in E. sinensis embryos. In the transcriptome structure analysis, male and female cleavage-stage embryos, while not clustered, exhibited a comparable frequency of alternative splicing (AS) occurrences. We also successfully identified 2875 transcription factors (TFs). The quantitative analysis showed the top 150 genes, in which the highly expressed genes in male embryos predominantly related to protein synthesis and metabolism. Further investigation unveiled 500 differentially expressed genes (DEGs), of which 7 male-biased ribosomal protein genes (RPGs) were particularly noteworthy and further confirmed. These analyses suggest that there may be a more active protein synthesis process in male E. sinensis cleavage-stage embryos. Furthermore, among the 2875 identified TFs, we predicted that 18 TFs could regulate the differentially expressed RPGs, with most TFs belonging to the zf-C2H2 and Homeobox families, which are crucial for embryonic development. During the cleavage stage of E. sinensis, the differential RPGs between genders were intricately linked to energy metabolism. We proposed that these RPGs exert regulatory effects on gene expression in E. sinensis, thereby regulating the difference of development between male and females. Our research sheds light on the developmental mechanisms of E. sinensis during the embryo stage and establishes a groundwork for a deeper understanding of sex development in E. sinensis. The results also provide comprehensive full-length transcriptome data for future gene expression and genetic studies in E. sinensis.

'140R' Rootstock Regulates Resveratrol Content in 'Cabernet Sauvignon' Grapevine Leaves Through miRNA

Grafting is important for increasing the resistance of grapevines to environmental stress, improving fruit quality, and shortening the reproductive period. In this study, 'Cabernet Sauvignon' (CS) grafted on the resistant rootstock 140R (CS/140R), self-grafted grapevines of the resistant rootstock 140R (140R/140R), and self-grafted grapevines of CS (CS/CS) were subjected to high-throughput sequencing; small RNA (sRNA) libraries were constructed, and miRNAs responsive to the grafting process were identified. A total of 177 known miRNAs and 267 novel miRNAs were identified. Many miRNAs responsive to the grafting process were significantly down-regulated in CS/140R leaves relative to CS/CS leaves, such as vvi-miR171c, vvi-miR171e, et al., suggesting that the expression of these miRNAs might be affected by grafting. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the differentially expressed miRNAs regulated the expression of genes in the phenylpropanoid synthesis pathway. Grapevine leaves transiently overexpressing vvi-miR171c were assayed, and the expression of the target gene, VvMYB154, and the resveratrol content were decreased, indicating that vvi-miR171c negatively regulates the expression of VvMYB154. In sum, 140R increased the resveratrol content of the scion by grafting, down-regulating the expression of vvi-miR171c. These results provide new information that will aid future analyses of the effects of grafting on the content of secondary metabolites.

Comparative Transcriptomic Analysis Reveals Domestication and Improvement Patterns of Broomcorn Millet (Panicum miliaceum L.)

Broomcorn millet (Panicum miliaceum L.) is one of the earliest crops, domesticated nearly 8000 years ago in northern China. It gradually spread across the entire Eurasian continent, as well as to America and Africa, with recent improvement in various reproductive and vegetative traits. To identify the genes that were selected during the domestication and improvement processes, we performed a comparative transcriptome analysis based on wild types, landraces, and improved cultivars of broomcorn millet at both seeding and filling stages. The variations in gene expression patterns between wild types and landraces and between landraces and improved cultivars were further evaluated to explore the molecular mechanisms underlying the domestication and improvement of broomcorn millet. A total of 2155 and 3033 candidate genes involved in domestication and a total of 84 and 180 candidate genes related to improvement were identified at seedling and filling stages of broomcorn millet, respectively. The annotation results suggested that the genes related to metabolites, stress resistance, and plant hormones were widely selected during both domestication and improvement processes, while some genes were exclusively selected in either domestication or improvement stages, with higher selection pressure detected in the domestication process. Furthermore, some domestication- and improvement-related genes involved in stress resistance either lost their functions or reduced their expression levels due to the trade-offs between stress resistance and productivity. This study provided novel genetic materials for further molecular breeding of broomcorn millet varieties with improved agronomic traits.

Gonadal Development and Differentiation of Hybrid F1 Line of Ctenopharyngodon idella (♀) × Squaliobarbus curriculus (♂)

The hybrid F1 offspring of Ctenopharyngodon idella (♂) and Squaliobarbus curriculus (♀) exhibit heterosis in disease resistance and also show abnormal sex differentiation. To understand the mechanism behind gonadal differentiation in the hybrid F1, we analyzed the transcriptomes of C. idella, S. curriculus, and the hybrid F1; screened for genes related to gonad development in these samples; and measured their expression levels. Our results revealed that compared to either C. idella or S. curriculus, the gene expressions in most sub-pathways of the SNARE interactions in the vesicular transport pathway in the hypothalamus, pituitary, and gonadal tissues of their hybrid F1 offspring were significantly up-regulated. Furthermore, insufficient transcription of genes involved in oocyte meiosis may be the main reason for the insufficient reproductive ability of the hybrid F1 offspring. Through transcriptome screening, we identified key molecules involved in gonad development, including HSD3B7, HSD17B1, HSD17B3, HSD20B2, CYP17A2, CYP1B1, CYP2AA12, UGT2A1, UGT1A1, and FSHR, which showed significant differences in expression levels in the hypothalamus, pituitary, and gonads of these fish. Notably, the expression levels of UGT1A1 in the gonads of the hybrid F1 were significantly higher than those in C. idella and S. curriculus. These results provide a scientific basis for further research on the gonadal differentiation mechanism of hybrid F1 offspring.

Extensive transcriptome data providing great efficacy in genetic research and adaptive gene discovery: a case study of Elymus sibiricus L. (Poaceae, Triticeae)

Genetic markers play a central role in understanding genetic diversity, speciation, evolutionary processes, and how species respond to environmental stresses. However, conventional molecular markers are less effective when studying polyploid species with large genomes. In this study, we compared gene expression levels in 101 accessions of Elymus sibiricus, a widely distributed allotetraploid forage species across the Eurasian continent. A total of 20,273 high quality transcriptomic SNPs were identified. In addition, 72,344 evolutionary information loci of these accessions of E. sibiricus were identified using genome skimming data in conjunction with the assembled composite genome. The population structure results suggest that transcriptome SNPs were more effective than SNPs derived from genome skimming data in revealing the population structure of E. sibiricus from different locations, and also outperformed gene expression levels. Compared with transcriptome SNPs, the investigation of population-specifically-expressed genes (PSEGs) using expression levels revealed a larger number of locally adapted genes mainly involved in the ion response process in the Sichuan, Inner Mongolia, and Xizang geographical groups. Furthermore, we performed the weighted gene co-expression network analysis (WGCNA) and successfully identified potential regulators of PSEGs. Therefore, for species lacking genomic information, the use of transcriptome SNPs is an efficient approach to perform population structure analysis. In addition, analyzing genes under selection through nucleotide diversity and genetic differentiation index analysis based on transcriptome SNPs, and exploring PSEG through expression levels is an effective method for analyzing locally adaptive genes.

Population genetics analysis of Diospyrosmun A.Chev. ex Lecomte (Ebenaceae) based on EST-SSR markers derived from a novel transcriptome

Diospyrosmun A.Chev. ex Lecomte (Ebenaceae), a native evergreen tree in Vietnam, has important economic and ecological values. The absence of effective and reliable molecular markers has hampered the study of D.mun's genetic diversity and population structure, even though it is an endemic and endangered species. Therefore, significant enrichment of genomic resources is urgently needed to uncover and better understand the genetic architecture of D.mun. This study aims to demonstrate an efficient and reliable tool to explore the polymorphism within D.mun germplasm. It provides a valuable platform for the breeding and conservation of this species and other endangered species worldwide. The Illumina HiSeq™ 4000 sequencing technology was applied for the transcriptomic analysis, genetic differentiation and population structure of D.mun in Vietnam. In this study, the transcriptomes of D.mun were analysed using the Illumina HiSeqTM 4000 sequencing system and a total of 5,588,615,700 base pairs were generated. De novo assembly indicated that 91,134 unigenes were generated (average length = 645.55 bp, N50 = 957 bp, Q20 = 98.08% and Q30 = 94.51%). A total of 92,798 and 21,134 unigenes had significant similarities amongst Nr and Swiss-Prot, respectively. In the GO database, 19,929 unigenes were annotated and these genes were divided into three major categories and 50 subcategories. In the KOG analysis, 18,499 unigenes were annotated and divided into 25 gene function categories. In the KEGG analysis, 12,017 unigenes were annotated. According to the related pathways involved, they could be classified into 56 subclasses. In this study, we have identified a total of 9,391 EST-SSR markers. Ten microsatellite loci were employed to assess the genetic diversity and structure of 82 adult D.mun trees across three populations in Vietnam. The results indicated moderate levels of genetic diversity with PIC = 0.77, NA = 3.9, NE = 2.8, Ho = 0.56 and HE = 0.58 and the fixation index value was recorded as positive for three populations (NS, NH and CP). Genetic differentiation among populations was low (FST = 0.045), suggesting limited gene flow (Nm = 5.34). This result indicates gene exchange between the populations of ancient D.mun from different geographical areas and regions. The analysis of molecular variance (AMOVA) showed that high genetic variation existed within individuals (91%) compared to amongst populations (4%). Genetic structure analysis, DAPC and the NJ tree indicated that the three populations were divided into three main clusters. With this study, we provide a molecular resoureces for the breeding and conservation of D.mun.

Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations

Moso bamboo (Phyllostachys edulis), an ecologically and economically important forest species in East Asia, plays vital roles in carbon sequestration and climate change mitigation. However, intensifying climate change threatens moso bamboo survival. Here we generate high-quality haplotype-based pangenome assemblies for 16 representative moso bamboo accessions and integrated these assemblies with 427 previously resequenced accessions. Characterization of the haplotype-based pangenome reveals extensive genetic variation, predominantly between haplotypes rather than within accessions. Many genes with allele-specific expression patterns are implicated in climate responses. Integrating spatiotemporal climate data reveals more than 1050 variations associated with pivotal climate factors, including temperature and precipitation. Climate-associated variations enable the prediction of increased genetic risk across the northern and western regions of China under future emissions scenarios, underscoring the threats posed by rising temperatures. Our integrated haplotype-based pangenome elucidates moso bamboo's local climate adaptation mechanisms and provides critical genomic resources for addressing intensifying climate pressures on this essential bamboo. More broadly, this study demonstrates the power of long-read sequencing in dissecting adaptive traits in climate-sensitive species, advancing evolutionary knowledge to support conservation.

Whole transcriptome RNA sequencing provides novel insights into the molecular dynamics of ovarian development in mud crab, Scylla paramamosain after mating

Ovarian development in animals is a complicated biological process, requiring the simultaneous coordination among various genes and pathways. To understand the dynamic changes and molecular regulatory mechanisms of ovarian development in mud crab (Scylla paramamosain), both histological observation and whole transcriptome sequencing of ovarian tissues at different mating stages were implemented in this study. The histological results revealed that ovarian development was delayed in unmated females (60 days after courtship behavior but not mating), who exhibited an oocyte diameter of 56.38 ± 15.17 μm. Conversely, mated females exhibited accelerated the ovarian maturation process, with females reaching ovarian stage III (proliferative stage) 23 days after mating and attained an average oocyte diameter of 132.19 ± 15.07 μm. Thus, mating process is essential in promoting the rapid ovarian development in mud crab. Based on the whole transcriptome sequencing analysis, a total of 518 mRNAs, 1502 lncRNAs, 18 circRNAs and 151 miRNAs were identified to be differentially expressed between ovarian tissues at different mating stages. Notably, six differentially expressed genes (DEGs) associated with ovarian development were identified, including ovary development-related protein, red pigment concentrating hormone receptor, G2/mitotic-specific cyclin-B3-like, lutropin-chorio gonadotropic hormone receptor, renin receptor, and SoxB2. More importantly, both DEGs and targets of differentially expressed non-coding RNAs (DEncRNAs) were enriched in renin-angiotensin system, TGF-β signaling, cell adhesion molecules, MAPK signaling pathway, and ECM-receptor interaction, suggesting that these pathways may play significant roles in the ovarian development of mud crabs. Moreover, competition endogenous RNA (ceRNA) networks were constructed while mRNAs were differentially expressed between mating stages were involved in Gene Ontology (GO) biological processes such as developmental process, reproduction, and growth. These findings could provide solid foundations for the future development of female mud crab maturation enhancement strategy, and improve the understanding of the ovarian maturation process in crustaceans.

Antioxidant Capacity, Enzyme Activities Related to Energy Metabolism, and Transcriptome Analysis of Crassostrea hongkongensis Exposed to Hypoxia

Crassostrea hongkongensis (C. hongkongensis) is one of the three most commonly cultivated oyster species in China. Seasonal hypoxia is one of the most serious threats to its metabolism, reproductive behavior, and survival. To investigate the effects of hypoxia stress on the antioxidant capacity and energy metabolism of C. hongkongensis, the total antioxidant capacity (T-AOC), glycogen content, and enzyme activities (phosphofructokinase, PFK; pyruvate kinase, PK; phosphoenolpyruvate carboxykinase, PEPCK) of oysters were determined under normoxic (DO 6 ± 0.2 mg/L) and hypoxic (DO 1.5 mg/L) conditions at 0 h, 6 h, 48 h, and 72 h. We also determined the T-AOC, glycogen content, and enzyme activities of oysters under reoxygenation (recovered to normoxia for 24 h). To further examine the potential molecular regulatory mechanism of hypoxic adaptation, a transcriptome analysis was conducted on the gill of C. hongkongensis under normoxia (N, 72 h), hypoxia (H, 72 h), and reoxygenation (R). After being exposed to hypoxia for 6 h, the T-AOC, glycogen content, and enzyme activities of PK, PFK, and PEPCK in C. hongkongensis were significantly decreased. However, after prolonging the duration of hypoxia exposure for 72 h, the T-AOC, glycogen content, and enzyme activities increased compared to that of 48 h. After 24 h reoxygenation, the T-AOC, glycogen content, and enzyme activity of PK and PFK returned to close to initial levels. In addition, a transcriptome analysis discovered 6097 novel genes by mapping the C. hongkongensis genome with the clean reads. In total, 352 differentially expressed genes (DEGs) were identified in the H vs. N comparison group (235 upregulated and 117 downregulated genes). After recovery to normoxia, 292 DEGs (134 upregulated and 158 downregulated genes) were identified in the R vs. N comparison group, and 632 DEGs were identified (253 upregulated and 379 downregulated genes) in the R vs. H comparison group. The DEGs included some hypoxia-tolerant genes, such as phosphoenolpyruvate carboxykinase (PEPCK), mitochondrial (AOX), tyramine beta-hydroxylase (TBH), superoxide dismutase (SOD), glutathione S-transferase (GST), and egl nine homolog 1 isoform X2 (EGLN1). Additionally, DEGs were significantly enriched in the KEGG pathways that are involved in hypoxia tolerance, including the metabolism of xenobiotics by cytochrome P450 pathways and the HIF-1 signaling pathway. Then, we selected the five hypoxic-tolerant candidate DEGs for real-time quantitative polymerase chain reaction (RT-qPCR) validation, and the results were consistent with the transcriptome sequencing data. These discoveries have increased our understanding of hypoxia tolerance, recovery ability after reoxygenation, and molecular mechanisms governing the responses to hypoxia in C. hongkongensis.

Transcriptome analysis provides new insight into the mechanism of Bombyx mori under zinc exposure

Zinc is a significant source of heavy metal pollution that poses risks to both human health and biodiversity. Excessive concentrations of zinc can hinder the growth and development of insects and trigger cell death through oxidative damage. The midgut is the main organ affected by exposure to heavy metals. The silkworm, a prominent insect species belonging to the Lepidoptera class and widely used in China, serves as a model for studying the genetic response to heavy metal stress. In this study, high-throughput sequencing technology was employed to investigate detoxification-related genes in the midgut that are induced by zinc exposure. A total of 11,320 unigenes and 14,723 transcripts were identified, with 553 differentially expressed genes (DEGs) detected, among which 394 were up-regulated and 159 were down-regulated. The Gene Ontology (GO) analysis revealed that 452 DEGs were involved in 18 biological process subclasses, 14 cellular component subclasses and 8 molecular functional subclasses. Furthermore, the KEGG analysis demonstrated enrichment in pathways such as Protein digestion, absorption and Lysosome. Validation of the expression levels of 9 detoxification-related DEGs through qRT-PCR confirmed the accuracy of the RNA-seq results. This study not only contributes new insights into the detoxification mechanisms mechanism of silkworms against zinc contamination, but also serves as a foundation basis for understanding the molecular detoxification processes in lepidopteran insects.

Differential Strategies of Ectomycorrhizal Development between Suillus luteus and Pinus massoniana in Response to Nutrient Changes

Ectomycorrhizal fungi employ different strategies for mycelial growth and host colonization under varying nutrient conditions. However, key genes associated with mycorrhizal interaction should be influenced solely by the inoculation treatment and not by nutrient variations. To utilize subtle nutrient differences and rapidly screen for key genes related to the interaction between Suillus luteus and Pinus massoniana, we performed an inoculation experiment using culture bottles containing high- and low-nutrient media. Interestingly, S. luteus LS88 promoted the growth of P. massoniana seedlings without mature ectomycorrhiza, and the impact of LS88 inoculation on P. massoniana roots was greater than that of nutrient changes. In this study, the resequenced genome of the LS88 strain was utilized for transcriptome analysis of the strain. The analysis indicated that a unique gene encoding glutathione S-transferase (GST) in LS88 is likely involved in colonizing P. massoniana roots. In this study, the GST gene expression was independent of nutrient levels. It was probably induced by P. massoniana and could be used as a marker for S. luteus colonization degree.

Molecular and physiological responses of two quinoa genotypes to drought stress

Quinoa is an important economic food crop. However, quinoa seedlings are susceptible to drought stress, and the molecular mechanism of drought tolerance remains unclear. In this study, we compared transcriptomic and physiological analyses of drought-tolerant (L1) and susceptible (HZ1) genotypes exposed to 20% PEG for 3 and 9 days at seedling stage. Compared with HZ1, drought stress had less damage to photosynthetic system, and the contents of SOD, POD and CAT were higher and the contents of H2O2 and O2 -were lower in L1 leaves. Based on the RNA-seq method, we identified 2423, 11856, 1138 and 3903 (HZ1-C3-VS-T3, HZ1-C9-vs-T9, L1-C3-vs-T3 and L1-C9-vs-T9) annotated DEGs. Go enrichment was shown in terms of Biological Process: DEGs involved in biological processes such as metabolic process, cellular process, and single-organism process were most abundant in all four comparison treatments. In Molecular Function: the molecular functions of catalytic activity, binding and transporter activity have the most DEGs in all four processes. Cellular Component: membrane, membrane part, and cell have the most DEGs in each of the four processes. These DEGs include AP2/ERF, MYB, bHLH, b-ZIP, WRKY, HD-ZIP, NAC, C3h and MADS, which encode transcription factors. In addition, the MAPK pathway, starch and sucrose metabolism, phenylpropanoid biosynthesis and plant hormone signal transduction were significantly induced under drought stress, among them, G-hydrolases-66, G-hydrolases-81, G-hydrolases-78, Su-synthase-02, Su-synthase-04, Su-synthase-06, BRI1-20 and bHLH17 were all downregulated at two drought stress points in two genotypes, PP2C01, PP2C03, PP2C05-PP2C07, PP2C10, F-box01 and F-box02 were upregulated at two drought stress points in two genotypes. These results agree with the physiological responses and RNA-seq results. Collectively, these findings may lead to a better understanding of drought tolerance, and some of the important DEGs detected in this study could be targeted for future research. And our results will provide a comprehensive basis for the molecular network that mediates drought tolerance in quinoa seedlings and promote the breeding of drought-resistant quinoa varieties.

Two high-quality Prototheca zopfii genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity

The majority of the nearly 10,000 described species of green algae are photoautotrophs; however, some species have lost their ability to photosynthesize and become obligate heterotrophs that rely on parasitism for survival. Two high-quality genomes of the heterotrophic algae Prototheca zopfii Pz20 and Pz23 were obtained using short- and long-read genomic as well as transcriptomic data. The genome sizes were 31.2 Mb and 31.3 Mb, respectively, and contig N50 values of 1.99 Mb and 1.26 Mb. Although P. zopfii maintained its plastid genome, the transition to heterotrophy led to a reduction in both plastid and nuclear genome size, including the loss of photosynthesis-related genes from both the nuclear and plastid genomes and the elimination of genes encoding for carotenoid oxygenase and pheophorbide an oxygenase. The loss of genes, including basic leucine-zipper (bZIP) transcription factors, flavin adenine dinucleotide-linked oxidase, and helicase, could have played a role in the transmission of autotrophy to heterotrophs and in the processes of abiotic stress resistance and pathogenicity. A total of 66 (1.37%) and 73 (1.49%) genes were identified as potential horizontal gene transfer events in the two P. zopfii genomes, respectively. Genes for malate synthase and isocitrate lyase, which are horizontally transferred from bacteria, may play a pivotal role in carbon and nitrogen metabolism as well as the pathogenicity of Prototheca and non-photosynthetic organisms. The two high-quality P. zopfii genomes provide new insights into their evolution as obligate heterotrophs and pathogenicity.

IMPORTANCE

The genus Prototheca, characterized by its heterotrophic nature and pathogenicity, serves as an exemplary model for investigating pathobiology. The limited understanding of the protothecosis infectious disease is attributed to the lack of genomic resources. Using HiFi long-read sequencing, both nuclear and plastid genomes were generated for two strains of P. zopfii. The findings revealed a concurrent reduction in both plastid and nuclear genome size, accompanied by the loss of genes associated with photosynthesis, carotenoid oxygenase, basic leucine-zipper (bZIP) transcription factors, and others. The analysis of horizontal gene transfer revealed the presence of 1.37% and 1.49% bacterial genes, including malate synthase and isocitrate lyase, which play crucial roles in carbon and nitrogen metabolism, as well as pathogenicity and obligate heterotrophy. The two high-quality P. zopfii genomes represent valuable resources for investigating their adaptation and evolution as obligate heterotrophs, as well as for developing future prevention and treatment strategies against protothecosis.

Identification of pine wood nematode (Bursaphelenchus xylophilus) loading response genes in Japanese pine sawyer (Monochamus alternatus) through comparative genomics and transcriptomics

BACKGROUND

Pine wood nematode (PWN; Bursaphelenchus xylophilus) is the causative agent of pine wilt disease (PWD), which is considered the most dangerous biohazard to conifer trees globally. The transmission of PWN relies on insect vectors, particularly the Japanese pine sawyer (JPS; Monochamus alternatus). However, the molecular mechanism underlying PWN-JPS assembly remains largely unknown.

RESULTS

Here, we found that both geographical and gender could significantly affect the PCA (PWN carrying amount) of JPS; thus, JPS transcriptomes from diverse locations and genders were explored regard to PWN loading. Due to the shortage of genomes, we developed a full-length reference transcriptome for analyzing next-generation sequencing data. A comparative genomic study was performed, and 11 248 potential PWN-carrying associate genes (β) were nominated in JPS by using the reported genomes of PWN and non-PWN carrier insect species. Then, 151 differentially expressed transcripts (DETs), 28 of them overlapped with β, correlated with the PCA of JPS were nominated by RNA-Seq, and found that fatty acid β-oxidation might be the key factor that affected the PCA of JPS. Furthermore, JPS fatty acid β-oxidation rates were experimentally decreased using the inhibitor Etomoxir, leading to an increased PCA of JPS. Meanwhile, silencing MaCPT1 in JPS by RNA interference led to a decreased fatty acid β-oxidation rate and increased PCA of JPS.

CONCLUSIONS

In conclusion, MaCPT1 was able to decrease the PWN-JPS assembly formation through the fatty acid β-oxidation of JPS. These results provide new insights for exploring the impact of PWN invasion on JPS. © 2024 Society of Chemical Industry.

Establishment of Novel Simple Sequence Repeat (SSR) Markers from Chimonanthus praecox Transcriptome Data and Their Application in the Identification of Varieties

Chimonanthus praecox, a member of the Calycanthaceae family, is a unique, traditional, and famous flowering economic tree species in China. Despite the existence of several varieties, only a few cultivars have been formally named. Currently, expression sequence tag-simple sequence repeat (EST-SSR) markers are extensively used to identify different species and varieties; a large number of microsatellites can be identified from transcriptome databases. A total of 162,638 unigenes were assembled using RNA-seq; 82,778 unigenes were annotated using the Nr, Nt, Swiss-Prot, Pfam, GO, KOG, and KEGG databases. In total, 13,556 SSR loci were detected from 11,691 unigenes, with trinucleotide repeat motifs being the most abundant among the six repeat motifs. To develop the markers, 64,440 pairs of SSR primers with polymorphism potential were designed, and 75 pairs of primers were randomly selected for amplification. Among these markers, seven pairs produced amplified fragments of the expected size with high polymorphism. Using these markers, 12 C. praecox varieties were clustered into two monophyletic clades. Microsatellites in the transcriptome of C. praecox exhibit rich types, strong specificity, and great polymorphism potential. These EST-SSR markers serve as molecular technical methods for identifying different varieties of C. praecox and facilitate the exploration of a large number of candidate genes associated with important traits.

Full-length agave transcriptome reveals candidate glycosyltransferase genes involved in hemicellulose biosynthesis

Agave species are typical crassulacean acid metabolism (CAM) plants commonly cultivated to produce beverages, fibers, and medicines. To date, few studies have examined hemicellulose biosynthesis in Agave H11648, which is the primary cultivar used for fiber production. We conducted PacBio sequencing to obtain full-length transcriptome of five agave tissues: leaves, shoots, roots, flowers, and fruits. A total of 41,807 genes were generated, with a mean length of 2394 bp and an annotation rate of 97.12 % using public databases. We identified 42 glycosyltransferase genes related to hemicellulose biosynthesis, including mixed-linkage glucan (1), glucomannan (5), xyloglucan (16), and xylan (20). Their expression patterns were examined during leaf development and fungal infection, together with hemicellulose content. The results revealed four candidate glycosyltransferase genes involved in xyloglucan and xylan biosynthesis, including glucan synthase (CSLC), xylosyl transferase (XXT), xylan glucuronyltransferase (GUX), and xylan α-1,3-arabinosyltransferase (XAT). These genes can be potential targets for manipulating xyloglucan and xylan traits in agaves, and can also be used as candidate enzymatic tools for enzyme engineering. We have provided the first full-length transcriptome of agave, which will be a useful resource for gene identification and characterization in agave species. We also elucidated the hemicellulose biosynthesis machinery, which will benefit future studies on hemicellulose traits in agave.