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.

A MYB activator, DcMYB11c, regulates carrot anthocyanins accumulation in petiole but not taproot.

The first domesticated carrots were thought to be purple carrots rich in anthocyanins. The anthocyanins biosynthesis in solid purple carrot taproot was regulated by DcMYB7 within P3 region containing a gene cluster of six DcMYBs. Here, we described a MYB gene within the same region, DcMYB11c, which was highly expressed in the purple pigmented petioles. Overexpression of DcMYB11c in 'Kurodagosun' (KRDG , orange taproot carrot with green petioles) and 'Qitouhuang' (QTHG , yellow taproot carrot with green petioles) resulted in deep purple phenotype in the whole carrot plants indicating anthocyanins accumulation. Knockout of DcMYB11c in 'Deep Purple' (DPPP , purple taproot carrot with purple petioles) through CRISPR/Cas9-based genome editing resulted in pale purple phenotype due to the dramatic decrease of anthocyanins content. DcMYB11c could induce the expression of DcbHLH3 and anthocyanins biosynthesis genes to jointly promote anthocyanins biosynthesis. Yeast one-hybrid assay (Y1H) and dual-luciferase reporter assay (LUC) revealed that DcMYB11c bound to the promoters of DcUCGXT1 and DcSAT1 and directly activated the expression of DcUCGXT1 and DcSAT1 responsible for anthocyanins glycosylation and acylation, respectively. Three transposons were present in the carrot cultivars with purple petioles but not in the carrot cultivars with green petioles. We revealed the core factor, DcMYB11c, involved in anthocyanins pigmentation in carrot purple petioles. This study provides new insights into precise regulation mechanism underlying anthocyanins biosynthesis in carrot. The orchestrated regulation mechanism in carrot might be conserved across the plant kingdom and useful for other researchers working on anthocyanins accumulation in different tissues.

DcCCD4 catalyzes the degradation of α-carotene and ß-carotene to affect carotenoid accumulation and taproot color in carrot.

Carotenoids are important natural pigments that give bright colors to plants. The difference in the accumulation of carotenoids is one of the key factors in the formation of various colors in carrot taproots. Carotenoid cleavage dioxygenases (CCDs), including CCD and 9-cis epoxycarotenoid dioxygenase, are the main enzymes involved in the cleavage of carotenoids in plants. Seven CCD genes have been annotated from the carrot genome. In this study, through expression analysis, we found that the expression level of DcCCD4 was significantly higher in the taproot of white carrot (low carotenoid content) than orange carrot (high carotenoid content). The overexpression of DcCCD4 in orange carrots caused the taproot color to be pale yellow, and the contents of α- and ß-carotene decreased sharply. Mutant carrot with loss of DcCCD4 function exhibited yellow color (the taproot of the control carrot was white). The accumulation of ß-carotene was also detected in taproot. Functional analysis of the DcCCD4 enzyme in vitro showed that it was able to cleave α- and ß-carotene at the 9, 10 (9', 10') double bonds. In addition, the number of colored chromoplasts in the taproot cells of transgenic carrots overexpressing DcCCD4 was significantly reduced compared with that in normal orange carrots. Results showed that DcCCD4 affects the accumulation of carotenoids through cleavage of α- and ß-carotene in carrot taproot.

AgMYB12, a novel R2R3-MYB transcription factor, regulates apigenin biosynthesis by interacting with the AgFNS gene in celery.

KEY MESSAGE: Overexpression of AgMYB12 in celery improved the accumulation of apigenin by interacting with the AgFNS gene. Celery is a common vegetable, and its essential characteristic is medicine food homology. A natural flavonoid and a major pharmacological component in celery, apigenin plays an important role in human health. In this study, we isolated a novel R2R3-MYB transcription factor that regulates apigenin accumulation from the celery cultivar 'Jinnan Shiqin' through yeast one-hybrid screening and designated it as AgMYB12. The AgMYB12 protein was located in the nucleus. It showed transcriptional activation activity and bound specifically to the promoter of AgFNS, a gene involved in apigenin biosynthesis. Phylogenetic tree analysis demonstrated that AgMYB12 belongs to the flavonoid branch. It contains two flavonoid-related motifs, SG7 and SG7-2, and shared a highly conserved R2R3 domain with flavonoid-related MYBs. The homologous overexpression of AgMYB12 induced the up-regulation of AgFNS gene expression and accumulation of apigenin and luteolin in celery. Additionally, the expression levels of apigenin biosynthesis-related genes, including AgPAL, AgCHI, AgCHS, Ag4CL, and AgC4H, increased in transgenic celery plants. These results indicated that AgMYB12 acted as a positive regulator of apigenin biosynthesis and activated the expression of AgFNS gene. The current study provides new information about the regulation mechanism of apigenin metabolism in celery and offers a strategy for cultivating the plants with high apigenin content.

Genome-Wide Identification and Evolution Analysis of R2R3-MYB Gene Family Reveals S6 Subfamily R2R3-MYB Transcription Factors Involved in Anthocyanin Biosynthesis in Carrot.

The taproot of purple carrot accumulated rich anthocyanin, but non-purple carrot did not. MYB transcription factors (TFs) condition anthocyanin biosynthesis in many plants. Currently, genome-wide identification and evolution analysis of R2R3-MYB gene family and their roles involved in conditioning anthocyanin biosynthesis in carrot is still limited. In this study, a total of 146 carrot R2R3-MYB TFs were identified based on the carrot transcriptome and genome database and were classified into 19 subfamilies on the basis of R2R3-MYB domain. These R2R3-MYB genes were unevenly distributed among nine chromosomes, and Ka/Ks analysis suggested that they evolved under a purified selection. The anthocyanin-related S6 subfamily, which contains 7 MYB TFs, was isolated from R2R3-MYB TFs. The anthocyanin content of rhizodermis, cortex, and secondary phloem in 'Black nebula' cultivar reached the highest among the 3 solid purple carrot cultivars at 110 days after sowing, which was approximately 4.20- and 3.72-fold higher than that in the 'Deep purple' and 'Ziwei' cultivars, respectively. The expression level of 7 MYB genes in purple carrot was higher than that in non-purple carrot. Among them, DcMYB113 (DCAR_008994) was specifically expressed in rhizodermis, cortex, and secondary phloem tissues of 'Purple haze' cultivar, with the highest expression level of 10,223.77 compared with the control 'DPP' cultivar at 70 days after sowing. DcMYB7 (DCAR_010745) was detected in purple root tissue of 'DPP' cultivar and its expression level in rhizodermis, cortex, and secondary phloem was 3.23-fold higher than that of secondary xylem at 110 days after sowing. Our results should be useful for determining the precise role of S6 subfamily R2R3-MYB TFs participating in anthocyanin biosynthesis in carrot.

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.

AgNAC1, a celery transcription factor, related to regulation on lignin biosynthesis and salt tolerance.

The NAC transcription factor participates in various biotic and abiotic stress responses and plays a critical role in plant development. Lignin is a water-insoluble dietary fiber, but it is second only to cellulose in abundance. Celery is the main source of dietary fiber, but its quality and production are limited by various abiotic stresses. Here, AgNAC1 containing the NAM domain was identified from celery. AgNAC1 was found to be a nuclear protein. Transgenic Arabidopsis thaliana plants hosting AgNAC1 have longer root lengths and stomatal axis lengths than the wide type (WT). The evidence from lignin determination and expression levels of lignin-related genes indicated that AgNAC1 plays a vital role in lignin biosynthesis. Furthermore, the results of the physiological characterization and the drought and salt treatments indicate that AgNAC1-overexpressing plants are significantly resistive to salt stress. Under drought and salt treatments, the AgNAC1 transgenic Arabidopsis thaliana plants presented increased superoxide dismutase (SOD) and peroxidase (POD) activities and decreased malondialdehyde (MDA) content and size of stomatal apertures relatively to the WT plants. The AgNAC1 served as a positive regulator in inducing the expression of stress-responsive genes. Overall, the overexpressing AgNAC1 enhanced the plants' resistance to salt stress and played a regulatory role in lignin accumulation.

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.

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.

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

MAIN CONCLUSION: 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.).

MAIN CONCLUSION: 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.

Generating colorful carrot germplasm through metabolic engineering of betalains pigments.

Betalains are tyrosine-derived plant pigments exclusively found in the Caryophyllales order and some higher fungi and generally classified into two groups: red-violet betacyanins and yellow-orange betaxanthins. Betalains attract great scientific and economic interest because of their relatively simple biosynthesis pathway, attractive colors and health-promoting properties. Co-expressing two core genes BvCYP76AD1 and BvDODA1 with or without a glycosyltransferase gene MjcDOPA5GT allowed the engineering of carrot (an important taproot vegetable) to produce a palette of unique colors. The highest total betalains content, 943.2 µg·g-1 DW, was obtained in carrot taproot transformed with p35S:RUBY which produces all of the necessary enzymes for betalains synthesis. Root-specific production of betalains slightly relieved tyrosine consumption revealing the possible bottleneck in betalains production. Furthermore, a unique volcano-like phenotype in carrot taproot cross-section was created by vascular cambium-specific production of betalains. The betalains-fortified carrot in this study is thus anticipated to be used as functional vegetable and colorful carrot germplasm in breeding to promote health.

Differential hydroxylation efficiency of the two non-heme carotene hydroxylases: DcBCH1, rather than DcBCH2, plays a major role in carrot taproot.

Carotene hydroxylase plays an important role in catalyzing the hydroxylation of carotene to xanthopylls, including two types: non-heme carotene hydroxylase (BCH type) and heme-containing cytochrome P450 hydroxylase (P450 type). Two BCH-encoding genes were annotated in the carrot genome. However, the role of BCHs and whether there are functional interactions between the duplicated BCHs in carrot remains unclear. In this study, two BCH encoding genes, DcBCH1 and DcBCH2, were cloned from carrot. The relative expression level of DcBCH1 was much higher than that of DcBCH2 in carrot taproots with different carotene accumulation levels. Overexpression of DcBCH1 in 'KRD' (high carotene accumulated) carrot changed the taproot color from orange to yellow, accompanied by substantial reductions in α-carotene and ß-carotene. There was no obvious change in taproot color between transgenic 'KRD' carrot overexpressing DcBCH2 and control carrot. Simultaneously, the content of α-carotene in the taproot of DcBCH2-overexpressing carrot decreased, but the content of ß-carotene did not change significantly in comparison with control carrot. Using the CRISPR/Cas9 system to knock out DcBCH1 in 'KRD' carrot lightened the taproot color from orange to pink-orange; the content of α-carotene in the taproot increased slightly, while the ß-carotene content was still significantly decreased, compared with control carrot. In DcBCH1-knockout carrot, the transcript level of DcBCH2 was significantly increased. These results indicated that in carrot taproot, DcBCH1 played the main function of BCH enzyme, which could hydroxylate α-carotene and ß-carotene; DcBCH1 and DcBCH2 had functional redundancy, and these two DcBCHs could partially compensate for each other.

AgGMP encoding GDP-D-mannose pyrophosphorylase from celery enhanced the accumulation of ascorbic acid and resistance to drought stress in Arabidopsis.

Ascorbic acid (AsA) is an important nutrient in celery, the conversion of D-mannose-1-P to GDP-D-mannose catalyzed by GDP-D-mannose pyrophosphorylase (GMPase) represents the first committed step in the biosynthesis of AsA. To clarify the function of the AgGMP gene of celery, the AgGMP gene was cloned from celery cv. 'Jinnan Shiqin' . It contains an open reading frame (ORF) with the length of 1,086 bp, encoding 361 amino acids. AgGMP protein was highly conserved among different plant species. Phylogenetic analysis demonstrated that the GMP proteins from celery and carrot belonged to the same branch. AgGMP protein was mainly composed of three α-helixes and certain random coils. No signal peptide was found in the AgGMP protein. The subcellular localization indicated that the AgGMP protein was located in the cytoplasm. The relative expression levels of AgGMP in 'Jinnan Shiqin' were significantly up-regulated at 2 h and 4 h under drought stress treatments. AsA contents in transgenic Arabidopsis lines hosting AgGMP gene were higher than that in wild type plants, and the root lengths were also longer in the MS medium containing 300 mM mannitol. The present study provides useful evidence for the functional involvement of AgGMP in regulating AsA accumulation and response to drought stress in celery.

Exogenous melatonin positively regulates lignin biosynthesis in Camellia sinensis.

Melatonin (MT) is a bioactive molecule that can regulate various developmental processes. Changes in lignin content play important roles in plant growth and development. Herein, quantitative analysis and histochemical staining showed that lignin content significantly increased over time, and melatonin treatment triggered the lignification at 8 and 16 d in tea leaves. The POD activity participated in lignin formation had also been significantly improved. The effect of melatonin on the increase of lignin content was attenuation over time. Sequencing results based on transcriptome at 8 and 16 d showed that 5273 and 3019 differentially expressed genes (DEGs) were identified in CK1 vs. MT1 and CK2 vs. MT2, respectively. A total of 67 DEGs were annotated to lignin biosynthesis, and 38 and 9 genes were significantly up-regulated under melatonin treatment, respectively. Some transcription factor genes such as MYB were also identified among the two pairwise comparisons, which might relate to lignin metabolism. Melatonin increased the degree of lignification in tea leaves by modifying the enzyme genes expression involved in lignin synthesis pathway. These results provide a reference for further study on the molecular mechanism of the dynamic changes of lignin content induced by melatonin treatment in tea plants.

AgZDS, a gene encoding ζ-carotene desaturase, increases lutein and ß-carotene contents in transgenic Arabidopsis and celery.

ζ-Carotene desaturase (ZDS) is one of the key enzymes regulating carotenoids biosynthesis and accumulation. Celery transgenic efficiency is low and it is difficult to obtain transgenic plants. The study on ZDS was limited in celery. Here, the AgZDS gene was cloned from celery and overexpressed in Arabidopsis thaliana and celery to verify its function. The AgZDS has typical characteristic of ZDS protein and is highly conserved in higher plants. Phylogenetic analysis showed that AgZDS has the closest evolutionary relationship with ZDSs from Solanum lycopersicum, Capsicum annuum and Tagetes erecta. Overexpression of AgZDS gene in A. thaliana and celery resulted in increased accumulations of lutein and ß-carotene and up-regulated the expression levels of the genes involved in carotenoids biosynthesis. The contents of lutein and ß-carotene in two lines, AtL1 and AgL5, were the highest in transgenic A. thaliana and celery, respectively. The relative expression levels of 5 genes (AtPDS, AtZISO, AtZEP, AtNCED3, and AtCCD4) were up-regulated compared to the wild type plants. The relative expression levels of most genes in carotenoids biosynthesis pathway, such as AgPDS, AgCRTISO1, and AgZISO, were up-regulated in transgenic celery plants. The antioxidant capacity of A. thaliana and photosynthetic capacity of celery were also enhanced. This research is the first report on the function of structure gene related to carotenoid biosynthesis in transgenic celery plants. The findings in this study demonstrated the roles of AgZDS in regulating carotenoids metabolism of celery, which laid a potential foundation for quality improvement of celery.

Integrative genome, transcriptome, microRNA, and degradome analysis of water dropwort (Oenanthe javanica) in response to water stress.

Water dropwort (Liyang Baiqin, Oenanthe javanica (BI.) DC.) is an aquatic perennial plant from the Apiaceae family with abundant protein, dietary fiber, vitamins, and minerals. It usually grows in wet soils and can even grow in water. Here, whole-genome sequencing of O. javanica via HiSeq 2000 sequencing technology was reported for the first time. The genome size was 1.28 Gb, including 42,270 genes, of which 93.92% could be functionally annotated. An online database of the whole-genome sequences of water dropwort, Water dropwortDB, was established to share the results and facilitate further research on O. javanica (database homepage: http://apiaceae.njau.edu.cn/waterdropwortdb ). Water dropwortDB offers whole-genome and transcriptome sequences and a Basic Local Alignment Search Tool. Comparative analysis with other species showed that the evolutionary relationship between O. javanica and Daucus carota was the closest. Twenty-five gene families of O. javanica were found to be expanded, and some genetic factors (such as genes and miRNAs) related to phenotypic and anatomic differentiation in O. javanica under different water conditions were further investigated. Two miRNA and target gene pairs (miR408 and Oja15472, miR171 and Oja47040) were remarkably regulated by water stress. The obtained reference genome of O. javanica provides important information for future work, thus making in-depth genetic breeding and gene editing possible. The present study also provides a foundation for the understanding of the O. javanica response to water stress, including morphological, anatomical, and genetic differentiation.

The Accumulation of Lutein and ß-Carotene and Transcript Profiling of Genes Related to Carotenoids Biosynthesis in Yellow Celery.

Carotenoids are the general term of natural pigments. The formation of plant color is probably related to the components of carotenoids. As the yellow variety of celery, it is rich in the composition and content of carotenoids. However, the transcript profiling and roles of the genes related to carotenoids biosynthesis in yellow celery remain unclear. In this study, three yellow celery cultivars at different growth stages were used to analyze the content and composition of carotenoids and transcriptional changes of carotenoid biosynthesis-related genes. The lutein and ß-carotene were detected in yellow celery cultivar, while α-carotene and lycopene were not detected. The contents of lutein and ß-carotene were higher in leaf blades than in petioles. During the growth and development, the contents of lutein and ß-carotene gradually decreased in celery. Compared with the other two cultivars, the contents of lutein and ß-carotene were the highest in 'Huangtaiji' of 65 days after sowing (DAS) and 85 DAS and 'Liuhehuangxinqin' of 105 DAS, respectively. The expression levels of AgLCYB and AgPSY2 genes were significantly correlated with lutein and ß-carotene contents. This work provided a reference for the further study on carotenoid metabolisms in yellow celery and also made sense on the way of cultivating yellow celery with high carotenoids content.

NAC Family Transcription Factors in Carrot: Genomic and Transcriptomic Analysis and Responses to Abiotic Stresses.

Carrot is an annual or biennial herbaceous plant of the Apiaceae family. Carrot is an important vegetable, and its fresh taproot, which contains rich nutrients, is the main edible part. In the life cycle of carrot, NAC family transcription factors (TFs) are involved in almost all physiological processes. The function of NAC TFs in carrot remains unclear. In this study, 73 NAC family TF members in carrot were identified and characterized using transcriptome and genome databases. These members were divided into 14 subfamilies. Multiple sequence alignment was performed, and the conserved domains, common motifs, phylogenetic tree, and interaction network of DcNAC proteins were predicted and analyzed. Results showed that the same group of NAC proteins of carrot had high similarity. Eight DcNAC genes were selected to detect their expression profiles under abiotic stress treatments. The expression levels of the selected DcNAC genes significantly increased under treatments with low temperature, high temperature, drought, and salt stress. Results provide potentially useful information for further analysis of the roles of DcNAC transcription factors in carrot.

Genome-wide analysis of NAC transcription factors and their response to abiotic stress in celery (Apium graveolens L.).

In plants, NAC (NAM, ATAF, CUC) is a class of transcription factors (TFs) involved in growth regulation and is associated with abiotic stress, morphogenesis, and metabolism. Celery (Apium graveolens L.) is an important leafy vegetable and its yield and quality are considerably influenced by environmental factors. Currently, the characterization of NAC genes in celery is still limited. In this study, a total of 111 putative NAC TFs were determined based on the celery transcriptome and genome database. They were divided into 18 subfamilies on the basis of their NAC domain. NAC TFs in celery account for a moderate number compared with other species, similar to that in carrot. Real-time quantitative PCR (RT-qPCR) showed that some AgNAC genes were differentially expressed under adverse conditions (heat, cold, drought, and salt). AgNAC63 (ortholog of ANAC072/RD26) was highly induced by heat, cold, and salt conditions. The expression levels of AgNAC47 in leaf blades were 105.25- and 123.14-fold those of petioles and roots, respectively. AgNAC63 and AgNAC47 showed significant tissue specificity, high expression in leaves, and varying degrees of response under the four treatments. This study provides a basis for the improved investigation of the structure and function of AgNAC TFs and celery stress resistance.