CeleryDB: a genomic database for celery

Genomics empowering conservation action and improvement of celery in the face of climate change

MAIN CONCLUSION

Integration of genomic approaches like whole genome sequencing, functional genomics, evolutionary genomics, and CRISPR/Cas9-based genome editing has accelerated the improvement of crop plants including leafy vegetables like celery in the face of climate change. The anthropogenic climate change is a real peril to the existence of life forms on our planet, including human and plant life. Climate change is predicted to be a significant threat to biodiversity and food security in the coming decades and is rapidly transforming global farming systems. To avoid the ghastly future in the face of climate change, the elucidation of shifts in the geographical range of plant species, species adaptation, and evolution is necessary for plant scientists to develop climate-resilient strategies. In the post-genomics era, the increasing availability of genomic resources and integration of multifaceted genomics elements is empowering biodiversity conservation action, restoration efforts, and identification of genomic regions adaptive to climate change. Genomics has accelerated the true characterization of crop wild relatives, genomic variations, and the development of climate-resilient varieties to ensure food security for 10 billion people by 2050. In this review, we have summarized the applications of multifaceted genomic tools, like conservation genomics, whole genome sequencing, functional genomics, genome editing, pangenomics, in the conservation and adaptation of plant species with a focus on celery, an aromatic and medicinal Apiaceae vegetable. We focus on how conservation scientists can utilize genomics and genomic data in conservation and improvement.

AgMYB5, an MYB transcription factor from celery, enhanced β-carotene synthesis and promoted drought tolerance in transgenic Arabidopsis

BACKGROUND

Water shortage caused by global warming seriously affects the yield and quality of vegetable crops. β-carotene, the lipid-soluble natural product with important pharmacological value, is abundant in celery. Transcription factor MYB family extensively disperses in plants and plays regulatory roles in carotenoid metabolism and water scarcity response.

RESULTS

Here, the AgMYB5 gene encoding 196 amino acids was amplified from celery cv. 'Jinnanshiqin'. In celery, the expression of AgMYB5 exhibited transactivation activity, tissue specificity, and drought-condition responsiveness. Further analysis proved that ectopic expression of AgMYB5 increased β-carotene content and promoted drought tolerance in transgenic Arabidopsis thaliana. Moreover, AgMYB5 expression promoted β-carotene biosynthesis by triggering the expression of AtCRTISO and AtLCYB, which in turn increased antioxidant enzyme activities, and led to the decreased contents of H₂O₂ and MDA, and the inhibition of O₂^- generation. Meanwhile, β-carotene accumulation promoted endogenous ABA biosynthesis of transgenic Arabidopsis, which resulted in ABA-induced stomatal closing and delayed water loss. In addition, ectopic expression of AgMYB5 increased expression levels of AtERD1, AtP5CS1, AtRD22, and AtRD29.

CONCLUSIONS

The findings indicated that AgMYB5 up-regulated β-carotene biosynthesis and drought tolerance of Arabidopsis.

Transcriptome profiling of celery petiole tissues reveals peculiarities of the collenchyma cell wall formation

Transcriptome and biochemical analyses are applied to individual plant cell types to reveal potential players involved in the molecular machinery of cell wall formation in specialized cells such as collenchyma. Plant collenchyma is a mechanical tissue characterized by an irregular, thickened cell wall and the ability to support cell elongation. The composition of the collenchyma cell wall resembles that of the primary cell wall and includes cellulose, xyloglucan, and pectin; lignin is absent. Thus, the processes associated with the formation of the primary cell wall in the collenchyma can be more pronounced compared to other tissues due to its thickening. Primary cell walls intrinsic to different tissues may differ in structure and composition, which should be reflected at the transcriptomic level. For the first time, we conducted transcriptome profiling of collenchyma strands isolated from young celery petioles and compared them with other tissues, such as parenchyma and vascular bundles. Genes encoding proteins involved in the primary cell wall formation during cell elongation, such as xyloglucan endotransglucosylase/hydrolases, expansins, and leucine-rich repeat proteins, were significantly activated in the collenchyma. As the key players in the transcriptome orchestra of collenchyma, xyloglucan endotransglucosylase/hydrolase transcripts were characterized in more detail, including phylogeny and expression patterns. The comprehensive approach that included transcriptome and biochemical analyses allowed us to reveal peculiarities of collenchyma cell wall formation and modification, matching the abundance of upregulated transcripts and their potential substrates for revealed gene products. As a result, specific isoforms of multigene families were determined for further functional investigation.

Origin, evolution, breeding, and omics of Apiaceae: a family of vegetables and medicinal plants

Many of the world's most important vegetables and medicinal crops, including carrot, celery, coriander, fennel, and cumin, belong to the Apiaceae family. In this review, we summarize the complex origins of Apiaceae and the current state of research on the family, including traditional and molecular breeding practices, bioactive compounds, medicinal applications, nanotechnology, and omics research. Numerous molecular markers, regulatory factors, and functional genes have been discovered, studied, and applied to improve vegetable and medicinal crops in Apiaceae. In addition, current trends in Apiaceae application and research are also briefly described, including mining new functional genes and metabolites using omics research, identifying new genetic variants associated with important agronomic traits by population genetics analysis and GWAS, applying genetic transformation, the CRISPR-Cas9 gene editing system, and nanotechnology. This review provides a reference for basic and applied research on Apiaceae vegetable and medicinal plants.

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.

A celery transcriptional repressor AgERF8 negatively modulates abscisic acid and salt tolerance

Ethylene response factors (ERFs) widely exist in plants and have been reported to be an important regulator of plant abiotic stress. Celery, a common economic vegetable of Apiaceae, contains lots of ERF transcription factors (TFs) with various functions. AP2/ERF TFs play positive or negative roles in plant growth and stress response. Here, AgERF8, a gene encoding EAR-type AP2/ERF TF, was identified. The AgERF8 mRNA accumulated in response to both abscisic acid (ABA) signaling and salt treatment. AgERF8 was proving to be a nucleus-located protein and could bind to GCC-box. The overexpression of AgERF8 in Arabidopsis repressed the transcription of downstream genes, AtBGL and AtBCH. Arabidopsis overexpressing AgERF8 gene showed inhibited root growth under ABA and NaCl treatments. AgERF8 transgenic lines showed low tolerance to ABA and salt stress than wild-type plants. Low increment in SOD and POD activities, increased accumulation of MDA, and significantly decreased plant fresh weights and chlorophyll levels were detected in AgERF8 hosting lines after treated with ABA and NaCl. Furthermore, the overexpression of AgERF8 also inhibited the levels of ascorbic acid and antioxidant-related genes (AtCAT1, AtSOD1, AtPOD, AtSOS1, AtAPX1, and AtP5CS1) expression in transgenic Arabidopsis. This finding indicated that AgERF8 negatively affected the resistance of transgenic Arabidopsis to ABA and salt stress through regulating downstream genes expression and relevant physiological changes. It will provide a potential sight to further understand the functions of ERF TFs in celery.

Advances in AP2/ERF super-family transcription factors in plant

In the whole life process, many factors including external and internal factors affect plant growth and development. The morphogenesis, growth, and development of plants are controlled by genetic elements and are influenced by environmental stress. Transcription factors contain one or more specific DNA-binding domains, which are essential in the whole life cycle of higher plants. The AP2/ERF (APETALA2/ethylene-responsive element binding factors) transcription factors are a large group of factors that are mainly found in plants. The transcription factors of this family serve as important regulators in many biological and physiological processes, such as plant morphogenesis, responsive mechanisms to various stresses, hormone signal transduction, and metabolite regulation. In this review, we summarized the advances in identification, classification, function, regulatory mechanisms, and the evolution of AP2/ERF transcription factors in plants. AP2/ERF family factors are mainly classified into four major subfamilies: DREB (Dehydration Responsive Element-Binding), ERF (Ethylene-Responsive-Element-Binding protein), AP2 (APETALA2) and RAV (Related to ABI3/VP), and Soloists (few unclassified factors). The review summarized the reports about multiple regulatory functions of AP2/ERF transcription factors in plants. In addition to growth regulation and stress responses, the regulatory functions of AP2/ERF in plant metabolite biosynthesis have been described. We also discussed the roles of AP2/ERF transcription factors in different phytohormone-mediated signaling pathways in plants. Genomic-wide analysis indicated that AP2/ERF transcription factors were highly conserved during plant evolution. Some public databases containing the information of AP2/ERF have been introduced. The studies of AP2/ERF factors will provide important bases for plant regulatory mechanisms and molecular breeding.

Deciphering the high-quality genome sequence of coriander that causes controversial feelings

Coriander (Coriandrum sativum L. 2n = 2x = 22), a plant from the Apiaceae family, also called cilantro or Chinese parsley, is a globally important crop used as vegetable, spice, fragrance and traditional medicine. Here, we report a high-quality assembly and analysis of its genome sequence, anchored to 11 chromosomes, with total length of 2118.68 Mb and N50 scaffold length of 160.99 Mb. We found that two whole-genome duplication events, respectively, dated to ~45-52 and ~54-61 million years ago, were shared by the Apiaceae family after their split from lettuce. Unbalanced gene loss and expression are observed between duplicated copies produced by these two events. Gene retention, expression, metabolomics and comparative genomic analyses of terpene synthase (TPS) gene family, involved in terpenoid biosynthesis pathway contributing to coriander's special flavour, revealed that tandem duplication contributed to coriander TPS gene family expansion, especially compared to their carrot counterparts. Notably, a TPS gene highly expressed in all 4 tissues and 3 development stages studied is likely a major-effect gene encoding linalool synthase and myrcene synthase. The present genome sequencing, transcriptome, metabolome and comparative genomic efforts provide valuable insights into the genome evolution and spice trait biology of Apiaceae and other related plants, and facilitated further research into important gene functions and crop improvement.

Celery and Celeriac: A Critical View on Present and Future Breeding

Cultivated for the crispy petioles and round, fleshy, and flavored hypocotyl celery and celeriac have over two centuries of breeding history in Europe. In this review paper we summarized the most recent advances touching when necessary the historical context of celery and celeriac breeding. In the post genomic era of research, the genome sequence of celery is only partially available. We comprised however in this paper the most important aspects of celery genetics that are available today and have applicability in celery modern cultivars development. We discussed the problems and traits that drive the main celery and celeriac breeding goals, like hybrid seed production, disease resistance, and interesting enlarged hypocotyl and petiole characteristics. Besides the classical breeding traits we covered the potential of integration of existing cultivars as sources for consumer oriented traits like nutraceuticals and health promoting substances. Sustainability is a subject that is continuously growing in popularity and we looked at the genetic base of celery and celeriac that makes them sources for abiotic stress resistance and candidates for phytoremediation. We explored the fundamental concepts gained in various fields of celery and related species research, as resources for future improvement of celery and celeriac germplasm. We forecast what the next years will bring to Apium breeding.

The genome sequence of celery (Apium graveolens L.), an important leaf vegetable crop rich in apigenin in the Apiaceae family

Celery (Apium graveolens L.) is a vegetable crop in the Apiaceae family that is widely cultivated and consumed because it contains necessary nutrients and multiple biologically active ingredients, such as apigenin and terpenoids. Here, we report the genome sequence of celery based on the use of HiSeq 2000 sequencing technology to obtain 600.8 Gb of data, achieving ~189-fold genome coverage, from 68 sequencing libraries with different insert sizes ranging from 180 bp to 10 kb in length. The assembled genome has a total sequence length of 2.21 Gb and consists of 34,277 predicted genes. Repetitive DNA sequences represent 68.88% of the genome sequences, and LTR retrotransposons are the main components of the repetitive sequences. Evolutionary analysis showed that a recent whole-genome duplication event may have occurred in celery, which could have contributed to its large genome size. The genome sequence of celery allowed us to identify agronomically important genes involved in disease resistance, flavonoid biosynthesis, terpenoid metabolism, and other important cellular processes. The comparative analysis of apigenin biosynthesis genes among species might explain the high apigenin content of celery. The whole-genome sequences of celery have been deposited at CeleryDB (http://apiaceae.njau.edu.cn/celerydb). The availability of the celery genome data advances our knowledge of the genetic evolution of celery and will contribute to further biological research and breeding in celery as well as other Apiaceae plants.

Comparative de novo transcriptomics and untargeted metabolomic analyses elucidate complicated mechanisms regulating celery (Apium graveolens L.) responses to selenium stimuli

Presently, concern regarding the effects of selenium (Se) on the environment and organisms worldwide is increasing. Too much Se in the soil is harmful to plants. In this study, Illumina RNA sequencing and the untargeted metabolome of control and Se-treated celery seedlings were analyzed. In total, 297,911,046 clean reads were obtained and assembled into 150,218 transcripts (50,876 unigenes). A total of 36,287 unigenes were annotated using different databases. Additionally, 8,907 differentially expressed genes, including 5,319 up- and 3,588 downregulated genes, were identified between mock and Se-treated plants. “Phenylpropanoid biosynthesis” was the most enriched KEGG pathway. A total of 24 sulfur and selenocompound metabolic unigenes were differentially expressed. Furthermore, 1,774 metabolites and 237 significant differentially accumulated metabolites were identified using the untargeted metabolomic approach. We conducted correlation analyses of enriched KEGG pathways of differentially expressed genes and accumulated metabolites. Our findings suggested that candidate genes and metabolites involved in important biological pathways may regulate Se tolerance in celery. The results increase our understanding of the molecular mechanism responsible for celery’s adaptation to Se stress.

Isolation, purification and characterization of an ascorbate peroxidase from celery and overexpression of the AgAPX1 gene enhanced ascorbate content and drought tolerance in Arabidopsis

BACKGROUND

Celery is a widely cultivated vegetable abundant in ascorbate (AsA), a natural plant antioxidant capable of scavenging free radicals generated by abiotic stress in plants. Ascorbate peroxidase (APX) is a plant antioxidant enzyme that is important in the synthesis of AsA and scavenging of excess hydrogen peroxide. However, the characteristics and functions of APX in celery remain unclear to date.

RESULTS

In this study, a gene encoding APX was cloned from celery and named AgAPX1. The transcription level of the AgAPX1 gene was significantly upregulated under drought stress. AgAPX1 was expressed in Escherichia coli BL21 (DE3) and purified. The predicted molecular mass of rAgAPX1 was 33.16 kDa, which was verified by SDS-PAGE assay. The optimum pH and temperature for rAgAPX1 were 7.0 and 55 °C, respectively. Transgenic Arabidopsis hosting the AgAPX1 gene showed elevated AsA content, antioxidant capacity and drought resistance. Less decrease in net photosynthetic rate, chlorophyll content, and relative water content contributed to the high survival rate of transgenic Arabidopsis lines after drought.

CONCLUSIONS

The characteristics of APX in celery were different from that in other species. The enhanced drought resistance of overexpressing AgAPX1 in Arabidopsis may be achieved by increasing the accumulation of AsA, enhancing the activities of various antioxidant enzymes, and promoting stomatal closure. Our work provides new evidence to understand APX and its response mechanisms to drought stress in celery.

Elevated gibberellin altered morphology, anatomical structure, and transcriptional regulatory networks of hormones in celery leaves

Gibberellins (GAs), as one of the important hormones in regulating the growth and development of higher plants, can significantly promote cell elongation and expansion. Celery is a widely grown leafy vegetable crop with rich nutritional value. However, the effect of gibberellins on celery leaves is unclear. In this paper, the celery variety "Jinnan Shiqin" plants were treated with gibberellic acid (GA₃) and paclobutrazol (PBZ, a gibberellin inhibitor). Our results showed that GA₃ treatment promoted the growth of celery leaves and caused lignification of celery leaf tissue. In addition, the transcript levels of genes associated with gibberellins, auxin, cytokinins, ethylene, jasmonic acid, abscisic acid, and brassinolide were altered in response to increased or decreased exogenous gibberellins or inhibitor. GA₃ may regulate celery growth by interacting with other hormones through crosstalk mechanisms. This study provided a reference for further study of the regulation mechanism of gibberellins metabolism, and exerted effects on understanding the role of gibberellins in the growth and development of celery.

Selection of appropriate reference genes for RT-qPCR analysis under abiotic stress and hormone treatment in celery

Celery is one of the most important vegetable crop and its yield and quality is influenced by many environmental factors. Researches on gene expression not only help to unravel the molecular regulatory mechanism but also identify the key genes in the biological response. RT-qPCR is a commonly used technology to quantify the gene expression. Selecting an appropriate reference gene is an effective approach to improve the accuracy of RT-qPCR assay. To our knowledge, the evaluation of reference genes under different treatments in celery has not been reported yet. In this study, the expression stabilities of eight candidate reference genes (ACTIN, eIF-4α , GAPDH, TBP, TUB-A, UBC, TUB-B, and EF-1α ) under abiotic stresses (heat, cold, drought, and salt) and hormone treatments (SA, MeJA, GA, and ABA) were detected. The expression stabilities of candidate genes were compared and ranked by geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder programs. The results calculated by different programs were not completely consistent. Considering the comprehensive analysis results, ACTIN was the most stable reference gene and TUB-B showed the worst expression stabilities under the selected abiotic stress and hormone treatments in celery. The reliability of reference genes was further confirmed by the normalization of CAT1 gene under drought stress. This study presented evidences and basis to select the appropriate reference genes under different treatments in celery.

Genomic identification of AP2/ERF transcription factors and functional characterization of two cold resistance-related AP2/ERF genes in celery (Apium graveolens L.)

This study analyzed the AP2/ERF transcription factors in celery and showed that two dehydration-responsive-element-binding (DREB) transcription factors, AgDREB1 and AgDREB2, contribute to the enhanced resistance to abiotic stress in transgenic Arabidopsis. The AP2/ERF family is a large family of transcription factors (TFs) in higher plants that plays a central role in plant growth, development, and response to environmental stress. Here, 209 AP2/ERF family members were identified in celery based on genomic and transcriptomic data. The TFs were classified into four subfamilies (i.e., DREB, ERF, RAV, and AP2) and Soloist. Evolution analysis indicated that the AP2/ERF TFs are ancient molecules and have expanded in the long-term evolution process of plants and whole-genome duplication events. AgAP2/ERF proteins may be associated with multiple biological processes as predicted by the interaction network. The expression profiles and sequence alignment analysis of the TFs in the DREB-A1 group showed that eight genes could be divided into four branches. Two genes, AgDREB1 and AgDREB2, from the DREB-A1 group were selected for further analysis. Subcellular localization assay suggested that the two proteins are nuclear proteins. Yeast one hybrid assay demonstrated that the two proteins could bind to the dehydration-responsive element (DRE). The overexpression of AgDREB1 and AgDREB2 in Arabidopsis induced the increased tolerance to cold treatment and the up-regulation of the COR genes expression. AgDREB1 and AgDREB2 might function as transcriptional activators in regulating the downstream genes by binding to corresponding DRE to enhance stress tolerance in celery.

AgMYB2 transcription factor is involved in the regulation of anthocyanin biosynthesis in purple celery (Apium graveolens L.)

This study showed that an R2R3-MYB transcription factor, AgMYB2, functions in anthocyanin biosynthesis and accumulation in purple celery. Anthocyanins are involved in tissue coloration and stress response in plants. Foods containing high anthocyanin content are also beneficial to human health. Purple celery accumulated amounts of anthocyanins in the petioles. The biosynthesis of anthocyanin in plants is mainly regulated by the R2R3-MYB transcription factor (TF). However, the R2R3-MYB TF that controls anthocyanin accumulation in purple celery remains unclear. In this study, an R2R3-MYB TF gene, AgMYB2, was cloned from purple celery and characterized as anthocyanin biosynthetic regulator. Sequence analysis indicated that AgMYB2 contained highly conserved R2R3 domain and two anthocyanin characteristic motifs, ANDV motif and KPRPR[S/T]F motif. The relative expression level of AgMYB2 in purple celery was significantly higher than that in non-purple celery at three developmental stages. Heterologous expression of AgMYB2 in Arabidopsis generated more anthocyanins and resulted in dark-purple leaves and flowers. The expression levels of anthocyanin biosynthetic genes and the antioxidant activity of transgenic Arabidopsis carrying AgMYB2 were up-regulated. The determination of anthocyanin glycosylation activity of Arabidopsis crude enzyme verified the anthocyanin biosynthesis regulatory function of AgMYB2 at the protein level. The interaction between AgMYB2 and bHLH proteins was shown by yeast two-hybrid assay. The results will help to elucidate the molecular mechanism of anthocyanin biosynthesis in purple celery and provide an approach for cultivating plants with high anthocyanin content.

MGH: a genome hub for the medicinal plant maca (Lepidium meyenii)

Maca (Lepidium meyenii), a Brassicaceae herb plant originated from Andean mountains, has attracted wide interests due to its unique health benefits in reproduction and fertility. Because of its adaptation to the 4000 m high-altitude harsh environment, maca is attracting more and more attention from both crop breeders and basic biologists. After our previous release of the maca genome sequence, there's a growing need to store, query, analyze and integrate various maca resources efficiently. Here, we created Maca Genome Hub (MGH), a genomics and genetics database of maca. Currently, the MGH V1.0 harbors the genome sequence, predicted coding sequences and protein sequences, various annotations, markers and expression data. For the maca research community, we also provided the publications, researchers and related news. MGH is designed to enable users' easy access to analyze, retrieve and visualize the genomic or genetic information through a series of online tools, including the Basic Local Alignment Search Tool, the JBrowse, the query system, the synteny tool and the data downloads. These integrated heterogeneous data, tools and interfaces in MGH allow efficient mining of the latest genomics and genetics data. We hope that MGH will accelerate the research and development in maca.