Telomere-to-telomere carrot (Daucus carota) genome assembly reveals carotenoid characteristics

DcMYB62, a transcription factor from carrot, enhanced cadmium tolerance of Arabidopsis by inducing the accumulation of carotenoids and hydrogen sulfide

Cadmium (Cd) is a significant heavy metal contaminant within the environment, carrying a notable level of toxicity that presents a substantial hazard to both plant and human. Carrot (Daucus carota), a significant root vegetable crop globally, have evolved multiple transcriptional regulatory mechanisms to cope with Cd stress, with a crucial involvement of the myeloblastosis (MYB) transcription factor. In this study, the DcMYB62 gene encoding 288 amino acids, localized in the nucleus and demonstrated transcription activation property, was isolated from carrot (cv. 'Kuroda'). There was a positive relationship observed between the levels of DcMYB62 expression and the accumulation patterns of carotenoids in two distinct carrot cultivars. Further investigation revealed that the expression of DcMYB62 improved Cd tolerance of Arabidopsis by increasing seed germination rate, root length, and overall survival rate. The levels of carotenoids in DcMYB62 transgenic Arabidopsis surpassed those in wild type, accompanied by elevated expression levels of 15-cis-phytoene desaturase, zeta-carotene desaturase, and carotenoid isomerase. Meanwhile, the heterologous expression of DcMYB62 promoted the biosynthesis of abscisic acid (ABA) and hydrogen sulfide (H2S), which in turn suppressed the formation of hydrogen peroxide and superoxide anion, while also stimulating stomatal closure. Furthermore, the heterologous expression of DcMYB62 increased the transcription of genes associated with heavy metal resistance in Arabidopsis, notably nicotianamine synthase. Overall, this study contributes to understanding how DcMYB62 promote Cd stress resistance of plants by regulating the biosynthesis pathways of carotenoids, ABA, and H2S, which offers valuable insights into the regulatory mechanism connecting DcMYBs with Cd stress response of carrot.

T2T genomes of carrot and Alternaria dauci and their utility for understanding host-pathogen interactions during carrot leaf blight disease

Carrot (Daucus carota) is one of the most popular and nutritious vegetable crops worldwide. However, significant yield losses occur every year due to leaf blight, a disease caused by a fungal pathogen (Alternaria dauci). Past research on resistance to leaf blight disease in carrots has been slow because of the low-quality genome assemblies of both carrot and the pathogen. Here, we report the greatly improved assemblies and annotations of telomere-to-telomere (T2T) reference genomes of carrot DH13M14 (451.04 Mb) and A. dauci A2016 (34.91 Mb). Compared with the previous carrot genome versions, our assembly featured notable improvements in genome size, continuity, and completeness of centromeres and telomeres. In addition, we generated a time course transcriptomic atlas during the infection of carrots by A. dauci and captured their dynamic gene expression reprogramming during the interaction process. During infection, A. dauci genes encoding effectors and enzymes responsible for the degradation of plant cell wall components, e.g., cellulose and pectin, were identified, which appeared to increase pathogenic ability through upregulation. In carrot, the coordinated gene expression of components of pattern- and effector-triggered immunity (PTI and ETI) in response to A. dauci attack was characterized. The biosynthesis or signal transduction of plant hormones, including JA, SA, and ethylene, was also involved in the carrot response to A. dauci. This work provides a foundation for understanding A. dauci pathogenic progression and carrot defense mechanisms to improve carrot resistance to leaf blight disease. The Carrot Database (CDB) developed also provides a useful resource for the carrot community.

Accumulation characteristics of plant flavonoids and effects of cultivation measures on their biosynthesis: A review

Flavonoids, a kind of secondary metabolites with both edible, medicinal and antioxidant purposes, could be widely used in food, drug processing, forest products, chemical industry and many other fields. Flavonoid production in plant organs were influenced by numerous internal and external factors at various stages, leading to differential gene expression and transcription factors activity. This study reviews the characteristics of major flavonoids categories, their distribution and accumulation in different plant parts and analyzing their molecular mechanisms. The results showed that: (1) Flavonoids exhibited wide distribution in all parts of the plants, with higher concentrations found in shoots system compared to roots sytem, across most species (predominantly accumulated in leaves and flowers). Plant sex, specific growth and development stages are both impacting indicators; (2) Cultivation methods and abiotic stress could affect plants flavonoid biosynthesis, while inappropriate physical treatments and cultivation methods induced stress in plants, prompting the activation of antioxidant mechanisms for flavonoid synthesis as a defence strategy via indirect pathways; (3) Various key genes and transcription factors collaboratively influenced key enzymes activities and regulate flavonoid biosynthesis, forming a complex regulatory network among these genes and transcription factors; (4) Further studies are required to elucidate whether flavonoid synthesis under various cultivation measures follows direct or indirect pathways. Furthermore, exploring methods for flavonoid biosynthesis and accumulation in specific organs or tissues, as well as identifying plant tissues and microorganisms with high efficiency in flavonoid biosynthesis, is essential for achieving targeted cultivation of plants and quantitative flavonoid production.

An anthocyanin activation gene underlies the purple central flower pigmentation in wild carrot

Many organisms have complex pigmentation patterns. However, how these patterns are formed remains largely unknown. In wild carrot (Daucus carota subsp. carota), which is also known as Queen Anne's lace, one or several purple central flowers occur in white umbels. Here, we investigated the unique central flower pigmentation pattern in wild carrot umbels. Using wild and cultivated carrot (D. carota subsp. sativus L.) accessions, transcriptome analysis, protein interaction, stable transformation, and CRISPR/Cas9-mediated knockout, an anthocyanin-activating R2R3-myeloblastosis (MYB) gene, Purple Central Flower (DcPCF), was identified as the causal gene that triggers only central flowers to possess the purple phenotype. The expression of DcPCF was only detected in tiny central flowers. We propose that the transition from purple to nonpurple flowers in the center of the umbel occurred after 3 separate adverse events: insertion of transposons in the promoter region, premature termination of the coding sequence (caused by a C-T substitution in the open reading frame), and the emergence of unknown anthocyanin suppressors. These 3 events could have occurred either consecutively or independently. The intriguing purple central flower pattern and its underlying mechanism may provide evidence that it is a remnant of ancient conditions of the species, reflecting the original appearance of Umbelliferae (also called Apiaceae) when a single flower was present.

Hydrogen sulfide alleviates cadmium stress in germinating carrot seeds by promoting the accumulation of proline

Carrot (Daucus carota L.), a widely cultivated economically vegetable from the Apiaceae family, is grown globally. However, carrots can be adversely impacted by cadmium (Cd) pollution in the soil due to its propensity to accumulate in the fleshy root, thus impeding carrot growth and posing health hazards to consumers. Given the potential of hydrogen sulfide (H2S) to improve plant resistance against Cd stress, we treated germinating carrot seeds with varying concentrations of sodium hydrosulfide (NaHS), aiming to alleviate the toxic impacts of Cd stress on carrot seed germination. The results revealed that carrot seeds treated with a concentration of 0.25 mM NaHS displayed better seed germination-associated characteristics compared to seeds treated with NaHS concentrations of 0.1 mM and 0.5 mM. Further investigation revealed a rise in the expression levels of L-cysteine desulfhydrase and D-cysteine desulfhydrase, along with enhanced activity of L-cysteine desulfhydrase and D-cysteine desulfhydrase among the NaHS treatment group, thereby leading to H2S accumulation. Moreover, NaHS treatment triggered the expression of pyrroline-5-carboxylate synthase and pyrroline-5-carboxylate reductase and promoted the accumulation of endogenous proline, while the contents of soluble sugar and soluble protein increased correspondingly. Interestingly, since the application of exogenous proline did not influence the accumulation of endogenous H2S, suggesting that H2S served as the upstream regulator of proline. Histochemical staining and biochemical indices revealed that NaHS treatment led to elevated antioxidant enzyme activity, alongside a suppression of superoxide anion and hydrogen peroxide generation. Furthermore, high performance liquid chromatography analysis revealed that NaHS treatment reduced Cd2+ uptake, thereby promoting germination rate, seed vitality, and hypocotyl length of carrot seeds under Cd stress. Overall, our findings shed light on the application of NaHS to enhance carrot resistance against Cd stress and lay a foundation for exploring the regulatory role of H2S in plants responding to Cd stress.

The gradual establishment of complex coumarin biosynthetic pathway in Apiaceae

Complex coumarins (CCs) represent characteristic metabolites found in Apiaceae plants, possessing significant medical value. Their essential functional role is likely as protectants against pathogens and regulators responding to environmental stimuli. Utilizing genomes and transcriptomes from 34 Apiaceae plants, including our recently sequenced Peucedanum praeruptorum, we conduct comprehensive phylogenetic analyses to reconstruct the detailed evolutionary process of the CC biosynthetic pathway in Apiaceae. Our results show that three key enzymes - p-coumaroyl CoA 2'-hydroxylase (C2'H), C-prenyltransferase (C-PT), and cyclase - originated successively at different evolutionary nodes within Apiaceae through various means of gene duplications: ectopic and tandem duplications. Neofunctionalization endows these enzymes with novel functions necessary for CC biosynthesis, thus completing the pathway. Candidate genes are cloned for heterologous expression and subjected to in vitro enzymatic assays to test our hypothesis regarding the origins of the key enzymes, and the results precisely validate our evolutionary inferences. Among the three enzymes, C-PTs are likely the primary determinant of the structural diversity of CCs (linear/angular), due to divergent activities evolved to target different positions (C-6 or C-8) of umbelliferone. A key amino acid variation (Ala161/Thr161) is identified and proven to play a crucial role in the alteration of enzymatic activity, possibly resulting in distinct binding forms between enzymes and substrates, thereby leading to different products. In conclusion, this study provides a detailed trajectory for the establishment and evolution of the CC biosynthetic pathway in Apiaceae. It explains why only a portion, not all, of Apiaceae plants can produce CCs and reveals the mechanisms of CC structural diversity among different Apiaceae plants.

BoaBZR1.1 mediates brassinosteroid-induced carotenoid biosynthesis in Chinese kale

Brassinazole resistant 1 (BZR1), a brassinosteroid (BR) signaling component, plays a pivotal role in regulating numerous specific developmental processes. Our study demonstrated that exogenous treatment with 2,4-epibrassinolide (EBR) significantly enhanced the accumulation of carotenoids and chlorophylls in Chinese kale (Brassica oleracea var. alboglabra). The underlying mechanism was deciphered through yeast one-hybrid (Y1H) and dual-luciferase (LUC) assays, whereby BoaBZR1.1 directly interacts with the promoters of BoaCRTISO and BoaPSY2, activating their expression. This effect was further validated through overexpression of BoaBZR1.1 in Chinese kale calli and plants, both of which exhibited increased carotenoid accumulation. Additionally, qPCR analysis unveiled upregulation of carotenoid and chlorophyll biosynthetic genes in the T1 generation of BoaBZR1.1-overexpressing plants. These findings underscored the significance of BoaBZR1.1-mediated BR signaling in regulating carotenoid accumulation in Chinese kale and suggested the potential for enhancing the nutritional quality of Chinese kale through genetic engineering of BoaBZR1.1.

Genomic, transcriptomic, and metabolomic analyses provide insights into the evolution and development of a medicinal plant Saposhnikovia divaricata (Apiaceae)

Saposhnikovia divaricata, 2n = 2x = 16, as a perennial species, is widely distributed in China, Mongolia, Russia, etc. It is a traditional Chinese herb used to treat tetanus, rubella pruritus, rheumatic arthralgia, and other diseases. Here, we assembled a 2.07 Gb and N50 scaffold length of 227.67 Mb high-quality chromosome-level genome of S. divaricata based on the PacBio Sequel II sequencing platform. The total number of genes identified was 42 948, and 42 456 of them were functionally annotated. A total of 85.07% of the genome was composed of repeat sequences, comprised mainly of long terminal repeats (LTRs) which represented 73.7% of the genome sequence. The genome size may have been affected by a recent whole-genome duplication event. Transcriptional and metabolic analyses revealed bolting and non-bolting S. divaricata differed in flavonoids, plant hormones, and some pharmacologically active components. The analysis of its genome, transcriptome, and metabolome helped to provide insights into the evolution of bolting and non-bolting phenotypes in wild and cultivated S. divaricata and lays the basis for genetic improvement of the species.

Construction of high-density genetic map based on SLAF-seq and QTL analysis of major traits in sweetpotato [Ipomoea batatas (L.) Lam.]

Sweetpotato, Ipomoea batatas (L.) Lam., is an important worldwide crop used as feed, food, and fuel. However, its polyploidy, high heterozygosity and self-incompatibility makes it difficult to study its genetics and genomics. Longest vine length (LVL), yield per plant (YPP), dry matter content (DMC), starch content (SC), soluble sugar content (SSC), and carotenoid content (CC) are some of the major agronomic traits being used to evaluate sweetpotato. However limited research has actually examined how these traits are inherited. Therefore, after selecting 212 F1 from a Xin24 × Yushu10 crossing as the mapping population, this study applied specific-locus amplified fragment sequencing (SLAF-seq), at an average sequencing depth of 26.73 × (parents) and 52.25 × (progeny), to detect single nucleotide polymorphisms (SNPs). This approach generated an integrated genetic map of length 2441.56 cM and a mean distance of 0.51 cM between adjacent markers, encompassing 15 linkage groups (LGs). Based on the linkage map, 26 quantitative trait loci (QTLs), comprising six QTLs for LVL, six QTLs for YPP, ten QTLs for DMC, one QTL for SC, one QTL for SSC, and two QTLs for CC, were identified. Each of these QTLs explained 6.3-10% of the phenotypic variation. It is expected that the findings will be of benefit for marker-assisted breeding and gene cloning of sweetpotato.

The high-quality genome of Cryptotaenia japonica and comparative genomics analysis reveals anthocyanin biosynthesis in Apiaceae

Cryptotaenia japonica, a traditional medicinal and edible vegetable crops, is well-known for its attractive flavors and health care functions. As a member of the Apiaceae family, the evolutionary trajectory and biological properties of C. japonica are not clearly understood. Here, we first reported a high-quality genome of C. japonica with a total length of 427 Mb and N50 length 50.76 Mb, was anchored into 10 chromosomes, which confirmed by chromosome (cytogenetic) analysis. Comparative genomic analysis revealed C. japonica exhibited low genetic redundancy, contained a higher percentage of single-cope gene families. The homoeologous blocks, Ks, and collinearity were analyzed among Apiaceae species contributed to the evidence that C. japonica lacked recent species-specific WGD. Through comparative genomic and transcriptomic analyses of Apiaceae species, we revealed the genetic basis of the production of anthocyanins. Several structural genes encoding enzymes and transcription factor genes of the anthocyanin biosynthesis pathway in different species were also identified. The CjANSa, CjDFRb, and CjF3H gene might be the target of Cjaponica_2.2062 (bHLH) and Cjaponica_1.3743 (MYB). Our findings provided a high-quality reference genome of C. japonica and offered new insights into Apiaceae evolution and biology.

Linkage mapping of root shape traits in two carrot populations

This study investigated the genetic basis of carrot root shape traits using composite interval mapping in two biparental populations (n = 119 and n = 128). The roots of carrot F2:3 progenies were grown over 2 years and analyzed using a digital imaging pipeline to extract root phenotypes that compose market class. Broad-sense heritability on an entry-mean basis ranged from 0.46 to 0.80 for root traits. Reproducible quantitative trait loci (QTL) were identified on chromosomes 2 and 6 on both populations. Colocalization of QTLs for phenotypically correlated root traits was also observed and coincided with previously identified QTLs in published association and linkage mapping studies. Individual QTLs explained between 14 and 27% of total phenotypic variance across traits, while four QTLs for length-to-width ratio collectively accounted for up to 73% of variation. Predicted genes associated with the OFP-TRM (OVATE Family Proteins-TONNEAU1 Recruiting Motif) and IQD (IQ67 domain) pathway were identified within QTL support intervals. This observation raises the possibility of extending the current regulon model of fruit shape to include carrot storage roots. Nevertheless, the precise molecular mechanisms through which this pathway operates in roots characterized by secondary growth originating from cambium layers remain unknown.

Technology-enabled great leap in deciphering plant genomes

Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.

Plant Functional Genomics Based on High-Throughput CRISPR Library Knockout Screening: A Perspective

Plant biology studies in the post-genome era have been focused on annotating genome sequences' functions. The established plant mutant collections have greatly accelerated functional genomics research in the past few decades. However, most plant genome sequences' roles and the underlying regulatory networks remain substantially unknown. Clustered, regularly interspaced short palindromic repeat (CRISPR)-associated systems are robust, versatile tools for manipulating plant genomes with various targeted DNA perturbations, providing an excellent opportunity for high-throughput interrogation of DNA elements' roles. This study compares methods frequently used for plant functional genomics and then discusses different DNA multi-targeted strategies to overcome gene redundancy using the CRISPR-Cas9 system. Next, this work summarizes recent reports using CRISPR libraries for high-throughput gene knockout and function discoveries in plants. Finally, this work envisions the future perspective of optimizing and leveraging CRISPR library screening in plant genomes' other uncharacterized DNA sequences.

DcGST1, encoding a glutathione S-transferase activated by DcMYB7, is the main contributor to anthocyanin pigmentation in purple carrot

The color of purple carrot taproots mainly depends on the anthocyanins sequestered in the vacuoles. Glutathione S-transferases (GSTs) are key enzymes involved in anthocyanin transport. However, the precise mechanism of anthocyanin transport from the cytosolic surface of the endoplasmic reticulum (ER) to the vacuoles in carrots remains unclear. In this study, we conducted a comprehensive analysis of the carrot genome, leading to the identification of a total of 41 DcGST genes. Among these, DcGST1 emerged as a prominent candidate, displaying a strong positive correlation with anthocyanin pigmentation in carrot taproots. It was highly expressed in the purple taproot tissues of purple carrot cultivars, while it was virtually inactive in the non-purple taproot tissues of purple and non-purple carrot cultivars. DcGST1, a homolog of Arabidopsis thaliana TRANSPARENT TESTA 19 (TT19), belongs to the GSTF clade and plays a crucial role in anthocyanin transport. Using the CRISPR/Cas9 system, we successfully knocked out DcGST1 in the solid purple carrot cultivar 'Deep Purple' ('DPP'), resulting in carrots with orange taproots. Additionally, DcMYB7, an anthocyanin activator, binds to the DcGST1 promoter, activating its expression. Compared with the expression DcMYB7 alone, co-expression of DcGST1 and DcMYB7 significantly increased anthocyanin accumulation in carrot calli. However, overexpression of DcGST1 in the two purple carrot cultivars did not change the anthocyanin accumulation pattern or significantly increase the anthocyanin content. These findings improve our understanding of anthocyanin transport mechanisms in plants, providing a molecular foundation for improving and enhancing carrot germplasm.

Comprehensive Evaluation of Genome Gap-Filling Tools Utilizing Long Reads

The availability of the complete genome of an organism plays a crucial role in the comprehensive analysis of the entire biological entity. Despite the rapid advancements in sequencing technologies, the inherent complexities of genomes inevitably lead to gaps during genome assembly. To obviate this, numerous genome gap-filling tools utilizing long reads have emerged. However, a comprehensive evaluation of these tools is currently lacking. In this study, we evaluated seven software under various ploidy levels and different data generation methods, and assessing them using QUAST and two additional criteria such as accuracy and completeness. Our findings revealed that the performance of the different tools varied across diverse ploidy levels. Based on accuracy and completeness, FGAP emerged as the top-performing tool, excelling in both haploid and tetraploid scenarios. This evaluation of commonly used genome gap-filling tools aims to provide users with valuable insights for tool selection, assisting them in choosing the most suitable genome gap-filling tool for their specific needs.

The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis

BACKGROUND

Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant constituents praeruptorin (A-E), are the active constituents in the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies have attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understanding of genetic traits and thus the development of better breeding strategies.

RESULTS

A telomere-to-telomere (T2T) genome was assembled for P. praeruptorum by combining PacBio HiFi, ONT ultra-long, and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes with genome completeness >98%. Comparative genomic analysis suggested that P. praeruptorum experienced 2 whole-genome duplication events. By the transcriptomic and metabolomic analysis of the coumarin metabolic pathway, we presented coumarins' spatial and temporal distribution and the expression patterns of critical genes for its biosynthesis. Notably, the COSY and cytochrome P450 genes showed tandem duplications on several chromosomes, which may be responsible for the high accumulation of coumarins.

CONCLUSIONS

A T2T genome for P. praeruptorum was obtained, providing molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome is an essential resource for designing engineering strategies for improving the production of these valuable compounds.

A chromosome-scale genome of Peucedanum praeruptorum provide insights into Apioideae evolution and medicinal ingredient biosynthesis

Peucedanum praeruptorum Dunn, a traditional Chinese medicine rich in coumarin, belongs to the Apiaceae family. A high-quality assembled genome of P. praeruptorum is lacking, which has posed obstacles to functional identification and molecular evolution studies of genes associated with coumarin production. Here, a chromosome-scale reference genome of P. praeruptorum, an important medicinal and aromatic plant, was first sequenced and assembled using Oxford Nanopore Technologies and Hi-C sequencing. The final assembled genome size was 1.83 Gb, with a contig N50 of 11.12 Mb. The entire BUSCO evaluation and second-generation read comparability rates were 96.0 % and 99.31 %, respectively. Furthermore, 99.91 % of the genome was anchored to 11 pseudochromosomes. The comparative genomic study revealed the presence of 18,593 orthogroups, which included 476 species-specific orthogroups and 1211 expanded gene families. Two whole-genome duplication (WGD) events and one whole-genome triplication (WGT) event occurred in P. praeruptorum. In addition to the γ-WGT shared by core eudicots or most eudicots, the first WGD was shared by Apiales, while the most recent WGD was unique to Apiaceae. Our study demonstrated that WGD events that occurred in Apioideae highlighted the important role of tandem duplication in the biosynthesis of coumarins and terpenes in P. praeruptorum. Additionally, the expansion of the cytochrome P450 monooxygenase, O-methyltransferase, ATP-binding cassette (ABC) transporter, and terpene synthase families may be associated with the abundance of coumarins and terpenoids. Moreover, we identified >170 UDP-glucosyltransferase members that may be involved in the glycosylation post-modification of coumarins. Significant gene expansion was observed in the ABCG, ABCB, and ABCC subgroups of the ABC transporter family, potentially facilitating the transmembrane transport of coumarins after bolting. The P. praeruptorum genome provides valuable insights into the machinery of coumarin biosynthesis and enhances our understanding of Apiaceae evolution.