De novo transcriptome of safflower and the identification of putative genes for oleosin and the biosynthesis of flavonoids

Integrated Proteomics and Metabolomics of Safflower Petal Wilting and Seed Development

Safflower (Carthamus tinctorius L.) is an ancient oilseed crop of interest due to its diversity of end-use industrial and food products. Proteomic and metabolomic profiling of its organs during seed development, which can provide further insights on seed quality attributes to assist in variety and product development, has not yet been undertaken. In this study, an integrated proteome and metabolic analysis have shown a high complexity of lipophilic proteins and metabolites differentially expressed across organs and tissues during seed development and petal wilting. We demonstrated that these approaches successfully discriminated safflower reproductive organs and developmental stages with the identification of 2179 unique compounds and 3043 peptides matching 724 unique proteins. A comparison between cotyledon and husk tissues revealed the complementarity of using both technologies, with husks mostly featuring metabolites (99%), while cotyledons predominantly yielded peptides (90%). This provided a more complete picture of mechanisms discriminating the seed envelope from what it protected. Furthermore, we showed distinct molecular signatures of petal wilting and colour transition, seed growth, and maturation. We revealed the molecular makeup shift occurring during petal colour transition and wilting, as well as the importance of benzenoids, phenylpropanoids, flavonoids, and pigments. Finally, our study emphasizes that the biochemical mechanisms implicated in the growing and maturing of safflower seeds are complex and far-reaching, as evidenced by AraCyc, PaintOmics, and MetaboAnalyst mapping capabilities. This study provides a new resource for functional knowledge of safflower seed and potentially further enables the precision development of novel products and safflower varieties with biotechnology and molecular farming applications.

De novo sequencing, assembly, and characterization of Asparagus racemosus transcriptome and analysis of expression profile of genes involved in the flavonoid biosynthesis pathway

Asparagus racemosus is known for its diverse content of secondary metabolites, i.e., saponins, alkaloids, and a wide range of flavonoids. Flavonoids, including phenols and polyphenols, have a significant role in plant physiology and are synthesized in several tissues. Despite the diverse role of flavonoids, genetic information is limited for flavonoid biosynthesis pathways in A. racemosus. The current study explores full-scale functional genomics information of A. racemosus by de novo transcriptome sequencing using Illumina paired-end sequencing technology to elucidate the genes involved in flavonoid biosynthesis pathways. The de novo assembly of high-quality paired-end reads resulted in ∼2.3 million high-quality reads with a pooled transcript of 45,647 comprising ∼76 Mb transcriptome with a mean length (bp) of 1,674 and N50 of 1,868bp. Furthermore, the coding sequence (CDS) prediction analysis from 45,647 pooled transcripts resulted in 45,444 CDS with a total length and mean length of 76,398,686 and 1,674, respectively. The Gene Ontology (GO) analysis resulted in a high number of CDSs assigned to 25,342 GO terms, which grouped the predicted CDS into three main domains, i.e., Biological Process (19,550), Molecular Function (19,873), and Cellular Component (14,577). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database was used to categorize 6,353 CDS into 25 distinct biological pathway categories, in which the majority of mapped CDS were shown to be related to translation (645), followed by signal transduction (532), carbohydrate metabolism (524), folding, sorting, and degradation (522). Among these, only ∼64 and 14 CDSs were found to be involved in the phenylpropanoid and flavonoid biosynthesis pathways, respectively. Quantitative Real-time PCR was used to check the expression profile of fourteen potential flavonoid biosynthesis pathway genes. The qRT-PCR analysis result matches the transcriptome sequence data validating the Illumina sequence results. Moreover, a large number of genes associated with the flavonoids biosynthesis pathway were found to be upregulated under the induction of methyl jasmonate. The present-day study on transcriptome sequence data of A. racemosus can be utilized for characterizing genes involved in flavonoid biosynthesis pathways and for functional genomics analysis in A. racemosus using the reverse genetics approach (CRISPR/Cas9 technology).

Molecular Characterization of an Isoflavone 2'-Hydroxylase Gene Revealed Positive Insights into Flavonoid Accumulation and Abiotic Stress Tolerance in Safflower

Flavonoids with significant therapeutic properties play an essential role in plant growth, development, and adaptation to various environments. The biosynthetic pathway of flavonoids has long been studied in plants; however, its regulatory mechanism in safflower largely remains unclear. Here, we carried out comprehensive genome-wide identification and functional characterization of a putative cytochrome P45081E8 gene encoding an isoflavone 2'-hydroxylase from safflower. A total of 15 CtCYP81E genes were identified from the safflower genome. Phylogenetic classification and conserved topology of CtCYP81E gene structures, protein motifs, and cis-elements elucidated crucial insights into plant growth, development, and stress responses. The diverse expression pattern of CtCYP81E genes in four different flowering stages suggested important clues into the regulation of secondary metabolites. Similarly, the variable expression of CtCYP81E8 during multiple flowering stages further highlighted a strong relationship with metabolite accumulation. Furthermore, the orchestrated link between transcriptional regulation of CtCYP81E8 and flavonoid accumulation was further validated in the yellow- and red-type safflower. The spatiotemporal expression of CtCYP81E8 under methyl jasmonate, polyethylene glycol, light, and dark conditions further highlighted its likely significance in abiotic stress adaption. Moreover, the over-expressed transgenic Arabidopsis lines showed enhanced transcript abundance in OE-13 line with approximately eight-fold increased expression. The upregulation of AtCHS, AtF3'H, and AtDFR genes and the detection of several types of flavonoids in the OE-13 transgenic line also provides crucial insights into the potential role of CtCYP81E8 during flavonoid accumulation. Together, our findings shed light on the fundamental role of CtCYP81E8 encoding a putative isoflavone 2'-hydroxylase via constitutive expression during flavonoid biosynthesis.

Screening of stable internal reference gene of Quinoa under hormone treatment and abiotic stress

Real-time quantitative polymerase chain reaction is the most commonly used method to accurately detect gene expression patterns. The method requires stable internal reference genes to standardize the data. However, studies have shown that there is no stable expression of internal reference genes in different tissues and under different treatments. Therefore, in order to study the optimal reference genes of quinoa under different hormones and abiotic stress, leaves and stems from quinoa seedlings treated with low temperature (4 °C), salt (200 mmol/L) and abscisic acid (200 mmol/L) were used as experimental materials. Using ACT-1, eIF, EF1α, GAPDH, TUA, TUB-9, TUB-1, H2A and L8-1 as candidate reference genes, the expression stability of these 9 quinoa candidate reference genes under different hormone treatment and abiotic stress was evaluated by using geNorm, NormFinder and BestKeeper software. The results showed that TUB-1 gene under salt stress, L8-1 gene under low temperature stress, EF-1α gene induced by ABA. PLIM2c WLIM1and WLIM2b were selected to verify the candidate internal reference genes, and finally the expression of GAPDH was most unstable under the three treatments, which was not suitable to be the internal reference gene of quinoa under specific conditions, while EF1α showed good stability under the three different treatments and was suitable to be used as the internal reference gene. In conclusion, the results of this study could provide an important reference for quantifying the expression level of reference genes in quinoa.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01094-z.

Temporal transcriptome profiling of developing seeds reveals candidate genes involved in oil accumulation in safflower (Carthamus tinctorius L.)

BACKGROUND

The investigation of molecular mechanisms involved in lipid metabolism plays a critical role for the genetic engineering of safflower (Carthamus tinctorius L.) to increase the oil accumulation level or to change the oil composition. Although transcript sequences are currently available for the leaves and flowers of safflower, a wide range scan of temporal transcripts at different stages of seed development has not been conducted for safflower.

RESULTS

In this study, temporal transcriptome sequencing was executed at 10, 14, 18, and 22 days after flowering (DAF) to uncover the molecular networks concerned in the biosynthesis of unsaturated fatty acids (USFAs). The results revealed that the biosynthesis of fatty acids is a dominant cellular process from 10 to 14 DAF, while degradation mainly happens after 18 DAF. Significant expression changes of two genes, stearoyl-[acyl-carrier-protein] 9-desaturase gene (SAD) from 10 to 14 DAF and oleate desaturase (FAD2-1) from 14 to 18 DAF, were detected at the transcriptomic levels, and the temporal expression patterns revealed by the transcriptomic analysis were confirmed using quantitative real-time PCR experiments. In addition, 13 candidate transcription factors (TFs) involved in regulating the expression level of the FAD2-1 gene were identified.

CONCLUSIONS

These results create a link between fatty acid biosynthesis and gene expression at different developmental stages of the seeds, provide insight into the underlying lipid metabolism, and meanwhile lay an important foundation for the genetic engineering of safflower varieties. We have identified novel candidate genes, including TFs, that are worthy of further exploration.

Reference gene selection for expression studies in the reproductive axis tissues of Magang geese at different reproductive stages under light treatment

In quantitative PCR research, appropriate reference genes are key to determining accurate mRNA expression levels. In order to screen the reference genes suitable for detecting gene expression in tissues of the reproductive axis, a total of 420 (males and females = 1:5) 3-year-old Magang geese were selected and subjected to light treatment. The hypothalamus, pituitary and testicular tissues were subsequently collected at different stages. Ten genes including HPRT1, GAPDH, ACTB, LDHA, SDHA, B2M, TUBB4, TFRC, RPS2 and RPL4 were selected as candidate reference genes. The expression of these genes in goose reproductive axis tissues was detected by real-time fluorescent quantitative PCR. The ΔCT, geNorm, NormFinder and BestKeeper algorithms were applied to sort gene expression according to stability. The results showed that ACTB and TUBB4 were the most suitable reference genes for the hypothalamic tissue of Magang goose in the three breeding stages; HPRT1 and RPL4 for pituitary tissue; and HPRT1 and LDHA for testicular tissue. For all three reproductive axis tissues, ACTB was the most suitable reference gene, whereas the least stable reference gene was GAPDH. Altogether, these results can provide references for tissue expression studies in geese under light treatment.

Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L

The basic leucine zipper (bZIP) is a widely known transcription factors family in eukaryotes. In plants, the role of bZIP proteins are crucial in various biological functions such as plant growth and development, seed maturation, response to light signal and environmental stress. To date, bZIP protein family has been comprehensively identified in Arabidopsis, castor, rice, ramie, soybean and other plant species, however, the complete genome-wide investigation of Carthamus tinctorius-bZIP family still remains unexplained. Here, we identified 52 putative bZIP genes from Carthamus tinctorius using a draft genome assembly and further analyzed their evolutionary classification, physicochemical properties, Conserved domain analysis, functional differentiation and the investigation of expression level in different tissues. Based on the common bZIP domain, CtbZIP family were clustered into 12 subfamilies renamed as (A-J, S, X), of which the X is a unique subfamily to Carthamus tinctorius. A total of 20 conserved protein motifs were found in CtbZIP proteins. The expression profiling of CtbZIP genes deciphered their tissue-specific pattern. Furthermore, the changes in CtbZIP transcript abundance suggested that their transcription regulation could be highly influenced by light intensity and hormones. Collectively, this study highlights all functional and regulatory elements of bZIP transcription factors family in Carthamus tinctorius which may serve as potential candidates for functional characterization in future.

RNA-seq Profiling Showed Divergent Carbohydrate-Active Enzymes (CAZymes) Expression Patterns in Lentinula edodes at Brown Film Formation Stage Under Blue Light Induction

Lentinula edodes (shiitake mushroom) is one of the most important edible mushrooms worldwide. The L. edodes cultivation cycle includes a unique developing stage called brown film formation that directly affects the development of primordium and the quality of fruiting body. Brown film formation is induced by light, especially blue light. To promote our understanding of the role of blue light in brown film formation mechanisms of L. edodes, we used RNA-seq and compared the transcriptomes of L. edodes grown under blue light and in dark, and validated the expression profiles using qRT-PCR. Blue light stimulated the formation of brown film and increased the content of polysaccharides in L. edodes. Blue light also promoted L. edodes to absorb more polysaccharides by enhancing the activities of enzymes. Among the 730 differentially expressed genes (DEGs), 433 genes were up-regulated and 297 were down-regulated. Most of the DEGs were in the oxidoreductase activity group. Pentose and glucuronic acid conversion and starch and sucrose metabolism were the most important pathways in the formation of brown film. A total of 79 genes of DEGs were identified as genes encoding carbohydrate-active enzymes (CAZymes). Fifty-one of the CAZymes genes were up-regulated, suggesting that CAZymes play important roles in brown film formation to provide sufficient nutrition for L. edodes. The results will facilitate future functional investigations of the genes involved in the developmental control of L. edodes.

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas

Background

Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronomic performance, a two-step approach was performed in six different maturation stages of seeds: 1) generation of the entire transcriptome of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels using a custom Agilent 8x60K oligonucleotide microarray.

Results

A total of 793,875 high-quality reads were assembled into 19,382 unique full-length contigs, of which 13,507 could be annotated with Gene Ontology (GO) terms. Microarray data analysis identified 9111 probes (out of 57,842 probes), which were differentially expressed between the six maturation stages. The expression results were validated for 75 selected transcripts based on expression levels, predicted function, pathway, and length.

Result from cluster analyses showed that transcripts associated with fatty acid, flavonoid, and phenylpropanoid biosynthesis were over-represented in the early stages, while those of lipid storage were over-represented in the late stages. Expression analyses of different maturation stages of J. curcas seed showed that most changes in transcript abundance occurred between the two last stages, suggesting that the timing of metabolic pathways during seed maturation in J. curcas occurs in late stages. The co-expression results showed that the hubs (CB5-D, CDR1, TT8, DFR, HVA22) with the highest number of edges, associated with fatty acid and flavonoid biosynthesis, are showing a decrease in their expression during seed maturation. Furthermore, seed development and hormone pathways are significantly well connected.

Conclusion

The obtained results revealed differentially expressed sequences (DESs) regulating important pathways related to seed maturation, which could contribute to the understanding of the complex regulatory network during seed maturation with the focus on lipid, flavonoid and phenylpropanoid biosynthesis. This study provides detailed information on transcriptional changes during J. curcas seed maturation and provides a starting point for a genomic survey of seed quality traits. The results highlighted specific genes and processes relevant to the molecular mechanisms involved in Jatropha seed maturation. These data can also be utilized regarding other Euphorbiaceae species.

Metabolome and Transcriptome Analysis of Hexaploid Solidago canadensis Roots Reveals its Invasive Capacity Related to Polyploidy

Polyploid plants are more often invasive species than their diploid counterparts. As the invasiveness of a species is often linked to its production of allelopathic compounds, we hypothesize that differences in invasive ability between cytotypes may be due to their different ability to synthesize allelopathic metabolites. We test this using two cytotypes of Solidago canadensis as the model and use integrated metabolome and transcriptome data to resolve the question. Metabolome analysis identified 122 metabolites about flavonoids, phenylpropanoids and terpenoids, of which 57 were differentially accumulated between the two cytotypes. Transcriptome analysis showed that many differentially expressed genes (DEGs) were enriched in ‘biosynthesis of secondary metabolites’, ‘plant hormone signal transduction’, and ‘MAPK signaling’, covering most steps of plant allelopathic metabolite synthesis. Importantly, the differentially accumulated flavonoids, phenylpropanoids and terpenoids were closely correlated with related DEGs. Furthermore, 30 miRNAs were found to be negatively associated with putative targets, and they were thought to be involved in target gene expression regulation. These miRNAs probably play a vital role in the regulation of metabolite synthesis in hexaploid S. canadensis. The two cytotypes of S. canadensis differ in the allelopathic metabolite synthesis and this difference is associated with regulation of expression of a range of genes. These results suggest that changes in gene expression may underlying the increased invasive potential of the polyploidy.

De novo transcriptome sequencing of radish (Raphanus sativus L.) fleshy roots: analysis of major genes involved in the anthocyanin synthesis pathway

Background

The HongXin radish (Raphanus sativus L.), which contains the natural red pigment (red radish pigment), is grown in the Fuling district of Chongqing City. However, the molecular mechanisms underlying anthocyanin synthesis for the formation of natural red pigment in the fleshy roots of HongXin radish are not well studied.

Results

De novo transcriptome of HX-1 radish, as well as that of the advanced inbred lines HX-2 and HX-3 were characterized using next generation sequencing (NGS) technology. In total, approximately 66.22 million paired-end reads comprising 34, 927 unigenes (N50 = 1, 621 bp) were obtained. Based on sequence similarity search with known proteins, total of 30, 127 (about 86.26%) unigenes were identified. Additionally, functional annotation and classification of these unigenes indicated that most of the unigenes were predominantly enriched in the metabolic process-related terms, especially for the biosynthetic pathways of secondary metabolites. Moreover, majority of the anthocyanin biosynthesis-related genes (ABRGs) involved in the regulation of anthocyanin biosynthesis were identified by targeted search for their annotation. Subsequently, the expression of 15 putative ABRGs involved in the anthocyanin synthesis-related pathways were validated using quantitative real-time polymerase chain reaction (qRT-PCR). Of those, RsPAL2, RsCHS-B2, RsDFR1, RsDFR2, RsFLS, RsMT3 and RsUFGT73B2-like were identified significantly associated with anthocyanin biosynthesis. Especially for RsDFR1, RsDFR2 and RsFLS, of those, RsDFR1 and RsDFR2 were highest enriched in the HX-3 and WG-3, but RsFLS were down-regulated in HX-3 and WG-3. We proposed that the transcripts of RsDFR1, RsDFR2 and RsFLS might be act as key regulators in anthocyanin biosynthesis pathway.

Conclusions

The assembled radish transcript sequences were analysed to identify the key ABRGs involved in the regulation of anthocyanin biosynthesis. Additionally, the expression patterns of candidate ABRGs involved in the anthocyanin biosynthetic pathway were validated by qRT-PCR. We proposed that the transcripts of RsDFR1, RsDFR2 and RsFLS might be acted as key regulators in anthocyanin biosynthesis pathway. This study will enhance our understanding of the biosynthesis and metabolism of anthocyanin in radish.

Integrating molecular characterization and metabolites profile revealed CtCHI1's significant role in Carthamus tinctorius L

BACKGROUND

As a traditional Chinese herb, safflower (Carthamus tinctorius L.) is valued for its florets to prevent cardiovascular and cerebrovascular diseases. Basing on previous chemical analysis, the main active compounds are flavonoids in its florets. Although flavonoid biosynthetic pathway has been well-documented in many model species, unique biosynthetic pathway remains to be explored in safflower. Of note, as an important class of transitional enzymes, chalcone isomerase (CHI) has not been characterized in safflower.

RESULTS

According to our previous research, CHIs were identified in a safflower transcriptome library built by our lab. To characterize CHI in safflower, a CHI gene named CtCHI1 was identified. A multiple sequences alignment and phylogenetic tree demonstrate that CtCHI1 shares 92% amino acid identity and close relationship with CHI to Saussurea medusa. Additionally, subcellular localization analysis indicated CtCHI1-GFP fusion protein was mainly in the cell nucleus. Further, we purified CtCHI1 protein from E. coli which can effectively catalyze isomerization of 2',4',4,6'-tetrahydroxychalcone into naringenin in vitro. Via genetic engineer technology, we successfully obtained transgenic tobacco and safflower lines. In transgenic tobacco, overexpression of CtCHI1 significantly inhibited main secondary metabolites accumulation, including quercetin (~ 79.63% for ovx-5 line) and anthocyanins (~ 64.55% for ovx-15 line). As shown in transgenic safflower, overexpression of CtCHI1 resulted in upstream genes CtPAL3 and CtC4H1 increasing dramatically (up to ~ 3.9fold) while Ct4CL3, CtF3H and CtDFR2 were inhibited. Also, comparing the whole metabolomics database by PCA and PLS-DA between transgenic and control group, 788 potential differential metabolites were marked and most of them displayed up-regulated trends. In parallel, some isolated secondary metabolites, such as hydroxysafflor yellow A (HSYA), rutin, kaempferol-3-O-β-rutinoside and dihydrokaempferol, accumulated in transgenic safflower plants.

CONCLUSIONS

In this study, we found that CtCHI1 is an active, functional, catalytic protein. Moreover, CtCHI1 can negatively and competitively regulate anthocyanins and quercetin pathway branches in tobacco. By contrast, CtCHI1 can positively regulate flavonol and chalcone metabolic flow in safflower. This research provides some clues to understand CHI's differential biochemical functional characterization involving in flavonoid pathway. More molecular mechanisms of CHI remain to be explored in the near future.

Genome-Wide Identification, Expression Profiling, and Functional Validation of Oleosin Gene Family in Carthamus tinctorius L

Carthamus tinctorius L., commonly known as safflower, is an important oilseed crop containing oil bodies. Oil bodies are intracellular organelles in plant cells for storing triacylglycerols (TAGs) and sterol esters. Oleosins are the most important surface proteins of the oil bodies. We predicted and retrieved the sequences of eight putative C. tinctorius oleosin (Ctoleosin) genes from the genome database of safflower. The bioinformatics analyses revealed the size of their open reading frames ranging from 414 to 675 bp, encoding 137 to 224 aa polypeptides with predicted molecular weights of 14.812 to 22.155 kDa, all containing the typical "proline knot" motif. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) determined the spatiotemporal expression pattern of Ctoleosin genes, which gradually increased and peaked during flowering and seed ripening, and decreased thereafter. To validate their role in plant development, we transformed and overexpressed these eight putative Ctoleosin genes in Arabidopsis. Overexpressing Ctoleosins did not affect leaf size, although silique length was altered. Arabidopsis transformed with Ctoleosin3, 4, and 5 grew longer siliques than did the wild-type plants, without altering seed quantity. The 100-grain weight of the transgenic Arabidopsis seeds was slightly more than that of the wild-type seeds. The seed germination rates of the plants overexpressing Ctoleosin4 and 6 were slightly lower as compared with that of the wild-type Arabidopsis, whereas that in the other transgenic lines were higher than that in the wild-type plants. The overexpression of Ctoleosin genes elevated the oil content in the seeds of transgenic Arabidopsis. Our findings not only provide an approach for increasing the oil content, but also for elucidating the intricate mechanisms of oil body synthesis.

Full-length transcriptome sequences and the identification of putative genes for flavonoid biosynthesis in safflower

Background

The flower of the safflower (Carthamus tinctorius L.) has been widely used in traditional Chinese medicine for the ability to improve cerebral blood flow. Flavonoids are the primary bioactive components in safflower, and their biosynthesis has attracted widespread interest. Previous studies mostly used second-generation sequencing platforms to survey the putative flavonoid biosynthesis genes. For a better understanding of transcription data and the putative genes involved in flavonoid biosynthesis in safflower, we carry our study.

Results

High-quality RNA was extracted from six types of safflower tissue. The RNAs of different tissues were mixed equally and used for multiple size-fractionated libraries (1–2, 2–3 and 3-6 k) library construction. Five cells were carried (2 cells for 1–2 and for 2-3 k libraries and 1 cell for 3-6 k libraries). 10.43Gb clean data and 38,302 de-redundant sequences were captured. 44 unique isoforms were annotated as encoding enzymes involved in flavonoid biosynthesis. The full length flavonoid genes were characterized and their evolutional relationship and expressional pattern were analyzed. They can be divided into eight families, with a large differences in the tissue expression. The temporal expressions under MeJA treatment were also measured, 9 genes are significantly up-regulated and 2 genes are significantly down-regulated. The genes involved in flavonoid synthesis in safflower were predicted in our study. Besides, the SSR and lncRNA are also analyzed in our study.

Conclusions

Full-length transcriptome sequences were used in our study. The genes involved in flavonoid synthesis in safflower were predicted in our study. Combined the determination of flavonoids, CtC4H2, CtCHS3, CtCHI3, CtF3H3, CtF3H1 are mainly participated in MeJA promoting the synthesis of flavonoids. Our results also provide a valuable resource for further study on safflower.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4946-9) contains supplementary material, which is available to authorized users.

Blood transcriptomics of captive forest musk deer (Moschus berezovskii) and possible associations with the immune response to abscesses

Forest musk deer (Moschus berezovskii; FMD) are both economically valuable and highly endangered. A problem for FMD captive breeding programs has been the susceptibility of FMD to abscesses. To investigate the mechanisms of abscess development in FMD, the blood transcriptomes of three purulent and three healthy individuals were generated. A total of ~39.68 Gb bases were generated using Illumina HiSeq 4000 sequencing technology and 77,752 unigenes were identified after assembling. All the unigenes were annotated, with 63,531 (81.71%) mapping to at least one database. Based on these functional annotations, 45,798 coding sequences (CDS) were detected, along with 12,697 simple sequence repeats (SSRs) and 65,536 single nucleotide polymorphisms (SNPs). A total of 113 unigenes were found to be differentially expressed between healthy and purulent individuals. Functional annotation indicated that most of these differentially expressed genes were involved in the regulation of immune system processes, particularly those associated with parasitic and bacterial infection pathways.

Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids

BACKGROUND

Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have been extensively studied due to its culinary and medicinal properties. There are only a few transcriptome sequences available for species from this important family of medicinal plants. The limited genetic information from the public expressed sequences tag (EST) library hinders further study on molecular mechanisms underlying secondary metabolite production.

METHODS

In this study, we performed a hybrid assembly of 454 and Illumina sequencing reads from Polygonum minus root and leaf tissues, respectively, to generate a combined transcriptome library as a reference.

RESULTS

A total of 34.37 million filtered and normalized reads were assembled into 188,735 transcripts with a total length of 136.67 Mbp. We performed a similarity search against all the publicly available genome sequences and found similarity matches for 163,200 (86.5%) of Polygonum minus transcripts, largely from Arabidopsis thaliana (58.9%). Transcript abundance in the leaf and root tissues were estimated and validated through RT-qPCR of seven selected transcripts involved in the biosynthesis of phenylpropanoids and flavonoids. All the transcripts were annotated against KEGG pathways to profile transcripts related to the biosynthesis of secondary metabolites.

DISCUSSION

This comprehensive transcriptome profile will serve as a useful sequence resource for molecular genetics and evolutionary research on secondary metabolite biosynthesis in Polygonaceae family. Transcriptome assembly of Polygonum minus can be accessed at http://prims.researchfrontier.org/index.php/dataset/transcriptome.

De novo Transcriptome Assembly of Chinese Kale and Global Expression Analysis of Genes Involved in Glucosinolate Metabolism in Multiple Tissues

Chinese kale, a vegetable of the cruciferous family, is a popular crop in southern China and Southeast Asia due to its high glucosinolate content and nutritional qualities. However, there is little research on the molecular genetics and genes involved in glucosinolate metabolism and its regulation in Chinese kale. In this study, we sequenced and characterized the transcriptomes and expression profiles of genes expressed in 11 tissues of Chinese kale. A total of 216 million 150-bp clean reads were generated using RNA-sequencing technology. From the sequences, 98,180 unigenes were assembled for the whole plant, and 49,582~98,423 unigenes were assembled for each tissue. Blast analysis indicated that a total of 80,688 (82.18%) unigenes exhibited similarity to known proteins. The functional annotation and classification tools used in this study suggested that genes principally expressed in Chinese kale, were mostly involved in fundamental processes, such as cellular and molecular functions, the signal transduction, and biosynthesis of secondary metabolites. The expression levels of all unigenes were analyzed in various tissues of Chinese kale. A large number of candidate genes involved in glucosinolate metabolism and its regulation were identified, and the expression patterns of these genes were analyzed. We found that most of the genes involved in glucosinolate biosynthesis were highly expressed in the root, petiole, and in senescent leaves. The expression patterns of ten glucosinolate biosynthetic genes from RNA-seq were validated by quantitative RT-PCR in different tissues. These results provided an initial and global overview of Chinese kale gene functions and expression activities in different tissues.

Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower

Carthami flos, the dried petal of safflower (Carthamus tinctorius L.) has been widely used in traditional Chinese medicine to treat cardiovascular and cerebrovascular diseases, in which quinochalcone glucosides such as hydrosafflower yellow A (HSYA), carthamin are uniquely present and have been identified as active compounds. In the present study, through sequencing of a safflower floret cDNA library and subsequent microarray analysis, we found 23 unigenes (5 PALs, 1 C4Hs, 5 4CLs, 6 CHSs, 2 CHIs, 2 DFRs, 2 FLSs) involved in flavonoid pathway, of which 4 were up-regulated differentially during quinochalcone glucosides accumulation with the floret developing stage. The up-regulated genes were verified by PCR methods. Considering chalcone synthase are entry enzyme in flavonoid biosynthesis, CHS1 was focused on target gene to verify its function furtherly. Bioinformation analysis showed that CHS1 shared 86.94% conserved residues with CHS from other plants. Subcellular localization showed that CtCHS1 was localized in cytoplasm in onion epidermal cells. The transgenic safflower plant with overexpression CtCHS1 by Agrobacterium-mediated pollen-tube pathway method was firstly generated. The results present that expression of PAL2, PAL3, CHS1, CHS4, CHS6 increased and expression of CHI1 and CHI2 decreased in the transgenic plant floret. Meanwhile, the accumulation of quinochalcone glucosides increased by ∼20-30% and accumulation of quercetin-3-β-D-glucoside and quercetin decreased by 48 and 63% in the transgenic plant floret. These results suggested that CtCHS1 played an important role in quinochalcone glucosides biosynthesis rather than flavonol biosynthesis. These results also demonstrated that the pollen-tube pathway method was an efficient method for gene transformation in safflower. Our study will provide a deep understanding of potential synthetic genes involved in quinochalcone biosynthetic pathway.

De novo transcriptome sequencing of black pepper (Piper nigrum L.) and an analysis of genes involved in phenylpropanoid metabolism in response to Phytophthora capsici

BACKGROUND

Piper nigrum L., or "black pepper", is an economically important spice crop in tropical regions. Black pepper production is markedly affected by foot rot disease caused by Phytophthora capsici, and genetic improvement of black pepper is essential for combating foot rot diseases. However, little is known about the mechanism of anti- P. capsici in black pepper. The molecular mechanisms underlying foot rot susceptibility were studied by comparing transcriptome analysis between resistant (Piper flaviflorum) and susceptible (Piper nigrum cv. Reyin-1) black pepper species.

RESULTS

116,432 unigenes were acquired from six libraries (three replicates of resistant and susceptible black pepper samples), which were integrated by applying BLAST similarity searches and noted by adopting Kyoto Encyclopaedia of Genes and Gene Ontology (GO) genome orthology identifiers. The reference transcriptome was mapped using two sets of digital gene expression data. Using GO enrichment analysis for the differentially expressed genes, the majority of the genes associated with the phenylpropanoid biosynthesis pathway were identified in P. flaviflorum. In addition, the expression of genes revealed that after susceptible and resistant species were inoculated with P. capsici, the majority of genes incorporated in the phenylpropanoid metabolism pathway were up-regulated in both species. Among various treatments and organs, all the genes were up-regulated to a relatively high degree in resistant species. Phenylalanine ammonia lyase and peroxidase enzyme activity increased in susceptible and resistant species after inoculation with P. capsici, and the resistant species increased faster. The resistant plants retain their vascular structure in lignin revealed by histochemical analysis.

CONCLUSIONS

Our data provide critical information regarding target genes and a technological basis for future studies of black pepper genetic improvements, including transgenic breeding.

Molecular characterization of flavanone 3-hydroxylase gene and flavonoid accumulation in two chemotyped safflower lines in response to methyl jasmonate stimulation

BACKGROUND

Among secondary metabolites, flavonoids are particularly crucial for plant growth, development, and reproduction, as well as beneficial for maintenance of human health. As a flowering plant, safflower has synthesized a striking variety of flavonoids with various pharmacologic properties. However, far less research has been carried out on the genes involved in the biosynthetic pathways that generate these amazing flavonoids, especially characterized quinochalcones. In this study, we first cloned and investigated the participation of a presumed flavanone 3-hydroxylase gene (F3H) from safflower (CtF3H) in a flavonoid biosynthetic pathway.

RESULTS

Bioinformation analysis showed that CtF3H shared high conserved residues and confidence with F3H from other plants. Subcellular localization uncovered the nuclear and cytosol localization of CtF3H in onion epidermal cells. The functional expressions of CtF3H in Escherichia coli BL21(DE3)pLysS cells in the pMAL-C5x vector led to the production of dihydrokaempferol when naringenin was the substrate. Furthermore, the transcriptome expression of CtF3H showed a diametrically opposed expression pattern in a quinochalcone-type safflower line (with orange-yellow flowers) and a flavonol-type safflower line (with white flowers) under external stimulation by methyl jasmonate (MeJA), which has been identified as an elicitor of flavonoid metabolites. Further metabolite analysis showed the increasing tendency of quinochalcones and flavonols, such as hydroxysafflor yellow A, kaempferol-3-O-β-D-glucoside, kaempferol-3-O-β-rutinoside, rutin, carthamin, and luteolin, in the quinochalcone-type safflower line. Also, the accumulation of kaempferol-3-O-β-rutinoside and kaempferol-3-O-β-D-glucoside in flavonols-typed safflower line showed enhanced accumulation pattern after MeJA treatment. However, other flavonols, such as kaempferol, dihydrokaempferol and quercetin-3-O-β-D-glucoside, in flavonols-typed safflower line presented down accumulation respond to MeJA stimulus.

CONCLUSIONS

Our results showed that the high expression of CtF3H in quinochalcone-type safflower line was associated with the accumulation of both quinochalcones and flavonols, whereas its low expression did not affect the increased accumulation of glycosylated derivatives (kaempferol-3-O-β-rutinoside and rutin) in flavonols-typed safflower line but affect the upstream precursors (D-phenylalanine, dihydrokaempferol, kaempferol), which partly revealed the function of CtF3H in different phenotypes and chemotypes of safflower lines.

Characterization of Glycolytic Pathway Genes Using RNA-Seq in Developing Kernels of Eucommia ulmoides

Eucommia ulmoides Oliver, the only member of the Eucommiaceae family, is a rare and valuable tree used to produce a highly valued traditional Chinese medicine and contains α-linolenic acid (ALA) up to 60% of the total fatty acids in the kernels (embryos). Glycolysis provides both cellular energy and the intermediates for other biosynthetic processes. However, nothing was known about the molecular basis of the glycolytic pathway in E. ulmoides kernels. The purposes of this study were to identify novel genes of E. ulmoides related to glycolytic metabolism and to analyze the expression patterns of selected genes in the kernels. Transcriptome sequencing based on the Illumina platform generated 96,469 unigenes in four cDNA libraries constructed using RNAs from 70 and 160 days after flowering kernels of both low- and high-ALA varieties. We identified and characterized the digital expression of 120 unigenes coding for 24 protein families involved in kernel glycolytic pathway. The expression levels of glycolytic genes were generally higher in younger kernels than in more mature kernels. Importantly, several unigenes from kernels of the high-ALA variety were expressed more than those from the low-ALA variety. The expression of 10 unigenes encoding key enzymes in the glycolytic pathway was validated by qPCR using RNAs from six kernel stages of each variety. The qPCR data were well consistent with their digital expression in transcriptomic analyses. This study identified a comprehensive set of genes for glycolytic metabolism and suggests that several glycolytic genes may play key roles in ALA accumulation in the kernels of E. ulmoides.

De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species

Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa "Yaan" and H. altissima "1110." Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for "Yaan" and "1110," respectively. In addition, a total of 86,731 "Yaan" and 48,645 "1110" unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11-87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.

Transcriptome Analysis Revealed Highly Expressed Genes Encoding Secondary Metabolite Pathways and Small Cysteine-Rich Proteins in the Sclerotium of Lignosus rhinocerotis

Lignosus rhinocerotis (Cooke) Ryvarden (tiger milk mushroom) has long been known for its nutritional and medicinal benefits among the local communities in Southeast Asia. However, the molecular and genetic basis of its medicinal and nutraceutical properties at transcriptional level have not been investigated. In this study, the transcriptome of L. rhinocerotis sclerotium, the part with medicinal value, was analyzed using high-throughput Illumina HiSeq^TM platform with good sequencing quality and alignment results. A total of 3,673, 117, and 59,649 events of alternative splicing, novel transcripts, and SNP variation were found to enrich its current genome database. A large number of transcripts were expressed and involved in the processing of gene information and carbohydrate metabolism. A few highly expressed genes encoding the cysteine-rich cerato-platanin, hydrophobins, and sugar-binding lectins were identified and their possible roles in L. rhinocerotis were discussed. Genes encoding enzymes involved in the biosynthesis of glucans, six gene clusters encoding four terpene synthases and one each of non-ribosomal peptide synthetase and polyketide synthase, and 109 transcribed cytochrome P450 sequences were also identified in the transcriptome. The data from this study forms a valuable foundation for future research in the exploitation of this mushroom in pharmacological and industrial applications.

De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis

Background

Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to AsA biosynthesis.

Results

In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs.

Conclusions

This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with the empirically observed capability of M. dubia to synthesize and accumulate AsA and other important molecules, and adds to our current knowledge of the molecular biology and biochemistry of their production in plants. By providing insights into the mechanisms underpinning these metabolic processes, these results can be used to direct efforts to genetically manipulate this organism in order to enhance the production of these bioactive phytochemicals.

The accumulation of AsA precursor and discovery of genes associated with their biosynthesis and metabolism in M. dubia is intriguing and worthy of further investigation. The sequences and pathways produced here present the genetic framework required for further studies. Quantitative transcriptomics in concert with studies of the genome, proteome, and metabolome under conditions that stimulate production and accumulation of AsA and their precursors are needed to provide a more comprehensive view of how these pathways for AsA metabolism are regulated and linked in this species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2225-6) contains supplementary material, which is available to authorized users.

De Novo Sequencing and Analysis of the Safflower Transcriptome to Discover Putative Genes Associated with Safflor Yellow in Carthamus tinctorius L

Safflower (Carthamus tinctorius L.), an important traditional Chinese medicine, is cultured widely for its pharmacological effects, but little is known regarding the genes related to the metabolic regulation of the safflower’s yellow pigment. To investigate genes related to safflor yellow biosynthesis, 454 pyrosequencing of flower RNA at different developmental stages was performed, generating large databases.In this study, we analyzed 454 sequencing data from different flowering stages in safflower. In total, 1,151,324 raw reads and 1,140,594 clean reads were produced, which were assembled into 51,591 unigenes with an average length of 679 bp and a maximum length of 5109 bp. Among the unigenes, 40,139 were in the early group, 39,768 were obtained from the full group and 28,316 were detected in both samples. With the threshold of “log2 ratio ≥ 1”, there were 34,464 differentially expressed genes, of which 18,043 were up-regulated and 16,421 were down-regulated in the early flower library. Based on the annotations of the unigenes, 281 pathways were predicted. We selected 12 putative genes and analyzed their expression levels using quantitative real time-PCR. The results were consistent with the 454 sequencing results. In addition, the expression of chalcone synthase, chalcone isomerase and anthocyanidin synthase, which are involved in safflor yellow biosynthesis and safflower yellow pigment (SYP) content, were analyzed in different flowering periods, indicating that their expression levels were related to SYP synthesis. Moreover, to further confirm the results of the 454 pyrosequencing, full-length cDNA of chalcone isomerase (CHI) and anthocyanidin synthase (ANS) were cloned from safflower petal by RACE (Rapid-amplification of cDNA ends) method according to fragment of the transcriptome.

Transcriptome Analysis Comparison of Lipid Biosynthesis in the Leaves and Developing Seeds of Brassica napus

Brassica napus seed is a lipid storage organ containing approximately 40% oil, while its leaves contain many kinds of lipids for many biological roles, but the overall amounts are less than in seeds. Thus, lipid biosynthesis in the developing seeds and the leaves is strictly regulated which results the final difference of lipids. However, there are few reports about the molecular mechanism controlling the difference in lipid biosynthesis between developing seeds and leaves. In this study, we tried to uncover this mechanism by analyzing the transcriptome data for lipid biosynthesis. The transcriptome data were de novo assembled and a total of 47,216 unigenes were obtained, which had an N50 length and median of 1271 and 755 bp, respectively. Among these unigenes, 36,368 (about 77.02%) were annotated and there were 109 up-regulated unigenes and 72 down-regulated unigenes in the developing seeds lipid synthetic pathway after comparing with leaves. In the oleic acid pathway, 23 unigenes were up-regulated and four unigenes were down-regulated. During triacylglycerol (TAG) synthesis, the key unigenes were all up-regulated, such as phosphatidate phosphatase and diacylglycerol O-acyltransferase. During palmitic acid, palmitoleic acid, stearic acid, linoleic acid and linolenic acid synthesis in leaves, the unigenes were nearly all up-regulated, which indicated that the biosynthesis of these particular fatty acids were more important in leaves. In the developing seeds, almost all the unigenes in the ABI3VP1, RKD, CPP, E2F-DP, GRF, JUMONJI, MYB-related, PHD and REM transcript factor families were up-regulated, which helped us to discern the regulation mechanism underlying lipid biosynthesis. The differential up/down-regulation of the genes and TFs involved in lipid biosynthesis in developing seeds and leaves provided direct evidence that allowed us to map the network that regulates lipid biosynthesis, and the identification of new TFs that are up-regulated in developing seeds will help us to further elucidate the lipids biosynthesis pathway in developing seeds and leaves.

De novo transcriptome sequencing in Pueraria lobata to identify putative genes involved in isoflavones biosynthesis

Using Illumina sequencing technology, we have generated the large-scale transcriptome sequencing data and indentified many putative genes involved in isoflavones biosynthesis in Pueraria lobata. Pueraria lobata, a member of the Leguminosae family, is a traditional Chinese herb which has been used since ancient times. P. lobata root has extensive clinical usages, because it contains a rich source of isoflavones, including daidzin and puerarin. However, the knowledge of isoflavone metabolism and the characterization of corresponding genes in such a pathway remain largely unknown. In this study, de novo transcriptome of P. lobata root and leaf was sequenced using the Solexa sequencing platform. Over 140 million high-quality reads were assembled into 163,625 unigenes, of which about 43.1% were aligned to the Nr protein database. Using the RPKM (reads per kilo bases per million reads) method, 3,148 unigenes were found to be upregulated, and 2,011 genes were downregulated in the leaf as compared to those in the root. Towards a further understanding of these differentially expressed genes, Gene ontology enrichment and metabolic pathway enrichment analyses were performed. Based on these results, 47 novel structural genes were identified in the biosynthesis of isoflavones. Also, 22 putative UDP glycosyltransferases and 45 O-methyltransferases unigenes were identified as the candidates most likely to be involved in the tailoring processes of isoflavonoid downstream pathway. Moreover, MYB transcription factors were analyzed, and 133 of them were found to have higher expression levels in the roots than in the leaves. In conclusion, the de novo transcriptome investigation of these unique transcripts provided an invaluable resource for the global discovery of functional genes related to isoflavones biosynthesis in P. lobata.

Transciptome analysis reveals flavonoid biosynthesis regulation and simple sequence repeats in yam (Dioscorea alata L.) tubers

Background

Yam (Dioscorea alata L.) is an important tuber crop and purple pigmented elite cultivar has recently become popular because of associated health benefits. Identifying candidate genes responsible for flavonoid biosynthesis pathway (FBP) will facilitate understanding the molecular mechanism of controlling pigment formation in yam tubers. Here, we used Illumina sequencing to characterize the transcriptome of tubers from elite purple-flesh cultivar (DP) and conventional white-flesh cultivar (DW) of yam. In this process, we also designed high quality molecular markers to assist molecular breeding for tuber trait improvement.

Results

A total of 125,123 unigenes were identified from the DP and DW cDNA libraries, of which about 49.5% (60,020 unigenes) were annotated by BLASTX analysis using the publicly available protein database. These unigenes were further annotated functionally and subject to biochemical pathway analysis. 511 genes were identified to be more than 2-fold (FDR < 0.05) differentially expressed between the two yam cultivars, of which 288 genes were up-regulated and 223 genes were down-regulated in the DP tubers. Transcriptome analysis detected 61 unigenes encoding multiple well-known enzymes in the FBP. Furthermore, the unigenes encoding chalcone isomerase (CHS), flavanone 3-hydroxylase (F3H), flavonoid 3′-monooxygenase (F3’H), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin dioxygenase (LDOX), and flavonol 3-O-glucosyltransferase (UF3GT) were found to be significantly up-regulated in the DP, implying that these genes were potentially associated with tuber color formation in this elite cultivar. The expression of these genes was further confirmed by qRT-PCR. Finally, 11,793 SSRs were successfully identified with these unigenes and 6,082 SSR markers were developed using Primer 3.

Conclusions

This study provides the first comprehensive transcriptomic dataset for yam tubers, which will significantly contribute to genomic research of this and other related species. Some key genes associated with purple-flesh trait were successfully identified, thus providing valuable information about molecular process of regulating pigment accumulation in elite yam tubers. In the future, this information might be directly used to genetically manipulate the conventional white-fleshed tuber cultivars to enable them to produce purple flesh. In addition, our SSR marker sets will facilitate identification of QTLs for various tuber traits in yam breeding programs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1547-8) contains supplementary material, which is available to authorized users.

The complete chloroplast genome sequence of Safflower (Carthamus tinctorius L.)

Safflower (Carthamus tinctorius L.) is a traditional medical plants of Asia. In this study, the complete chloroplast genome of safflower was presented. The total genome size was 153,675 bp in length, containing a pair of inverted repeats (IRs) of 25,407 bp, separated by large single copy (LSC) and small single copy (SSC) of 83,606 bp and 19,156 bp, respectively. Overall GC content of the genome was 37.4%. The chloroplast genome harbored 127 annotated genes, including 89 protein coding genes, 30 tRNA genes and 8 rRNA genes. A total of 7 of these genes were duplicated in the inverted repeat regions. Twelve genes contained one intron.

Transcriptome analysis reveals in vitro cultured Withania somnifera leaf and root tissues as a promising source for targeted withanolide biosynthesis

Background

The production of metabolites via in vitro culture is promoted by the availability of fully defined metabolic pathways. Withanolides, the major bioactive phytochemicals of Withania somnifera, have been well studied for their pharmacological activities. However, only a few attempts have been made to identify key candidate genes involved in withanolide biosynthesis. Understanding the steps involved in withanolide biosynthesis is essential for metabolic engineering of this plant to increase withanolide production.

Results

Transcriptome sequencing was performed on in vitro adventitious root and leaf tissues using the Illumina platform. We obtained a total of 177,156 assembled transcripts with an average unigene length of 1,033 bp. About 13% of the transcripts were unique to in vitro adventitious roots but no unique transcripts were observed in in vitro-grown leaves. A putative withanolide biosynthetic pathway was deduced by mapping the assembled transcripts to the KEGG database, and the expression of candidate withanolide biosynthesis genes -were validated by qRT PCR. The accumulation pattern of withaferin A and withanolide A varied according to the type of tissue and the culture period. Further, we demonstrated that in vitro leaf extracts exhibit anticancer activity against human gastric adenocarcinoma cell lines at sub G1 phase.

Conclusions

We report here a validated large-scale transcriptome data set and the potential biological activity of in vitro cultures of W. somnifera. This study provides important information to enhance tissue-specific expression and accumulation of secondary metabolites, paving the way for industrialization of in vitro cultures of W. somnifera.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1214-0) contains supplementary material, which is available to authorized users.

Polyploidy and the petal transcriptome of Gossypium

Background

Genes duplicated by polyploidy (homoeologs) may be differentially expressed in plant tissues. Recent research using DNA microarrays and RNAseq data have described a cacophony of complex expression patterns during development of cotton fibers, petals, and leaves. Because of its highly canalized development, petal tissue has been used as a model tissue for gene expression in cotton. Recent advances in cotton genome annotation and assembly now permit an enhanced analysis of duplicate gene deployment in petals from allopolyploid cotton.

Results

Homoeologous gene expression levels were quantified in diploid and tetraploid flower petals of Gossypium using the Gossypium raimondii genome sequence as a reference. In the polyploid, most homoeologous genes were expressed at equal levels, though a subset had an expression bias of A_T and D_T copies. The direction of gene expression bias was conserved in natural and recent polyploids of cotton. Conservation of direction of bias and additional comparisons between the diploids and tetraploids suggested different regulation mechanisms of gene expression. We described three phases in the evolution of cotton genomes that contribute to gene expression in the polyploid nucleus.

Conclusions

Compared to previous studies, a surprising level of expression homeostasis was observed in the expression patterns of polyploid genomes. Conserved expression bias in polyploid petals may have resulted from cis-acting modifications that occurred prior to polyploidization. Some duplicated genes were intriguing exceptions to general trends. Mechanisms of gene regulation for these and other genes in the cotton genome warrants further investigation.

De novo transcriptome analysis of an imminent biofuel crop, Camelina sativa L. using Illumina GAIIX sequencing platform and identification of SSR markers

Camelina sativa L. is an emerging biofuel crop with potential applications in industry, medicine, cosmetics and human nutrition. The crop is unexploited owing to very limited availability of transcriptome and genomic data. In order to analyse the various metabolic pathways, we performed de novo assembly of the transcriptome on Illumina GAIIX platform with paired end sequencing for obtaining short reads. The sequencing output generated a FastQ file size of 2.97 GB with 10.83 million reads having a maximum read length of 101 nucleotides. The number of contigs generated was 53,854 with maximum and minimum lengths of 10,086 and 200 nucleotides respectively. These trancripts were annotated using BLAST search against the Aracyc, Swiss-Prot, TrEMBL, gene ontology and clusters of orthologous groups (KOG) databases. The genes involved in lipid metabolism were studied and the transcription factors were identified. Sequence similarity studies of Camelina with the other related organisms indicated the close relatedness of Camelina with Arabidopsis. In addition, bioinformatics analysis revealed the presence of a total of 19,379 simple sequence repeats. This is the first report on Camelina sativa L., where the transcriptome of the entire plant, including seedlings, seed, root, leaves and stem was done. Our data established an excellent resource for gene discovery and provide useful information for functional and comparative genomic studies in this promising biofuel crop.

De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism

Background

Radish (Raphanus sativus L.), is an important root vegetable crop worldwide. Glucosinolates in the fleshy taproot significantly affect the flavor and nutritional quality of radish. However, little is known about the molecular mechanisms underlying glucosinolate metabolism in radish taproots. The limited availability of radish genomic information has greatly hindered functional genomic analysis and molecular breeding in radish.

Results

In this study, a high-throughput, large-scale RNA sequencing technology was employed to characterize the de novo transcriptome of radish roots at different stages of development. Approximately 66.11 million paired-end reads representing 73,084 unigenes with a N50 length of 1,095 bp, and a total length of 55.73 Mb were obtained. Comparison with the publicly available protein database indicates that a total of 67,305 (about 92.09% of the assembled unigenes) unigenes exhibit similarity (e –value ≤ 1.0e^-5) to known proteins. The functional annotation and classification including Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the main activated genes in radish taproots are predominately involved in basic physiological and metabolic processes, biosynthesis of secondary metabolite pathways, signal transduction mechanisms and other cellular components and molecular function related terms. The majority of the genes encoding enzymes involved in glucosinolate (GS) metabolism and regulation pathways were identified in the unigene dataset by targeted searches of their annotations. A number of candidate radish genes in the glucosinolate metabolism related pathways were also discovered, from which, eight genes were validated by T-A cloning and sequencing while four were validated by quantitative RT-PCR expression profiling.

Conclusions

The ensuing transcriptome dataset provides a comprehensive sequence resource for molecular genetics research in radish. It will serve as an important public information platform to further understanding of the molecular mechanisms involved in biosynthesis and metabolism of the related nutritional and flavor components during taproot formation in radish.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-836) contains supplementary material, which is available to authorized users.

Molecular analysis of the processes of surface brown spot (SBS) formation in pear fruit (Pyrus bretschneideri Rehd. cv. Dangshansuli) by de novo transcriptome assembly

Browning disorder, which usually occurs post-harvest in pears subjected to long-term storage, can cause browning of the pear flesh and/or core. In 2011, investigators in China found a novel type of brown spot (designated as surface brown spot, SBS) in pre-harvest ‘Dangshansuli’ pears (Pyrus bretschneideri Rehd.). SBS has a large impact on the exterior quality of the pears. Interestingly, the brown coloration was only found on the peel and not the flesh or the core. In this paper, de novo transcriptome analysis of the exocarp of pears with SBS using Illumina sequencing showed that SBS up-regulated the expression of genes related to oxidative phosphorylation, phenolic compound synthesis and polyphenoloxidase (PPO), and SBS was associated with inhibition of primary and secondary metabolism genes. Ca²⁺-sensor proteins might be involved in the signal transduction that occurs during the process of SBS formation, and this signaling is likely to be regulated by H₂O₂, abscisic acid (ABA) and gibberellic acid (GA₃). Phytohormone and mineral element analyses confirmed that GA₃, ABA, H₂O₂ and Ca²⁺ contribute to SBS formation. In addition to the seasonal characteristics, low levels of O₂ and Ca²⁺ in the fruit are potential causes of the browning response due to exposure to oxidative stress, oxidative-reductive imbalance and the accumulation of reactive oxygen species (ROS), which affected the membrane integrity. Disruption of the membranes allows for PPO and phenolic compounds to come into contact, and the phenolic compounds are oxidized to form the browning pigments.

Transcriptome analysis of yellow horn (Xanthoceras sorbifolia Bunge): a potential oil-rich seed tree for biodiesel in China

Background

Yellow horn (Xanthoceras sorbifolia Bunge) is an oil-rich seed shrub that grows well in cold, barren environments and has great potential for biodiesel production in China. However, the limited genetic data means that little information about the key genes involved in oil biosynthesis is available, which limits further improvement of this species. In this study, we describe sequencing and de novo transcriptome assembly to produce the first comprehensive and integrated genomic resource for yellow horn and identify the pathways and key genes related to oil accumulation. In addition, potential molecular markers were identified and compiled.

Methodology/Principal Findings

Total RNA was isolated from 30 plants from two regions, including buds, leaves, flowers and seeds. Equal quantities of RNA from these tissues were pooled to construct a cDNA library for 454 pyrosequencing. A total of 1,147,624 high-quality reads with total and average lengths of 530.6 Mb and 462 bp, respectively, were generated. These reads were assembled into 51,867 unigenes, corresponding to a total of 36.1 Mb with a mean length, N50 and median of 696, 928 and 570 bp, respectively. Of the unigenes, 17,541 (33.82%) were unmatched in any public protein databases. We identified 281 unigenes that may be involved in de novo fatty acid (FA) and triacylglycerol (TAG) biosynthesis and metabolism. Furthermore, 6,707 SSRs, 16,925 SNPs and 6,201 InDels with high-confidence were also identified in this study.

Conclusions

This transcriptome represents a new functional genomics resource and a foundation for further studies on the metabolic engineering of yellow horn to increase oil content and modify oil composition. The potential molecular markers identified in this study provide a basis for polymorphism analysis of Xanthoceras, and even Sapindaceae; they will also accelerate the process of breeding new varieties with better agronomic characteristics.

Transcriptome analysis of artificial hybrid pufferfish Jiyan-1 and its parental species: implications for pufferfish heterosis

Jiyan-1 puffer, the F1 hybrid of Takifugu rubripes and Takifugu flavidus, displays obvious heterosis in the growth performance, flavor and stress tolerance. In the present study, comparative analysis for the transcriptomes of T. rubripes, T. flavidus and Jiyan-1 was performed aiming to reveal the possible mechanisms of heterosis in pufferfish. Whole transcriptomes were sequenced using the SOLiD4 platform, and a total of 44,305 transcripts corresponding to 18,164 genes were identified collectively. A total of 14,148 transcripts were differentially expressed. By comparing the gene expression patterns of the three samples, the coexistence of overdominance, dominance, underdominance and additivity was observed in the gene action modes of Jiyan-1. There were 2,237 transcripts in the intersection of the differentially expressed transcripts from Jiyan-1 versus T. rubripes and Jiyan-1 versus T. flavidus, among which 213 transcripts were also in the T. rubripes versus T. flavidus. The potential functions of the remaining 2,024 transcripts were mainly associated with metabolic process, nucleotide binding and catalytic activity. The enrichment results indicated metabolism was the most activated biological function in the heterosis. In addition, 35 KEGG pathways were retrieved as affiliated with more than three differentially expressed transcripts and 8,579 potentially novel transcript isoforms were identified for Jiyan-1. The present study revealed the coexistence of multiple gene actions in the hybrid puffer, indicated the importance of metabolism, ion binding function and kinase activity, as well as provided a list of candidate genes and pathways for heterosis. It could be helpful for the better understanding of the determination and regulation mechanisms of heterosis.

De novo sequencing and characterization of the floral transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)

Background

Transcriptome sequencing can be used to determine gene sequences and transcript abundance in non-model species, and the advent of next-generation sequencing (NGS) technologies has greatly decreased the cost and time required for this process. Transcriptome data are especially desirable in bamboo species, as certain members constitute an economically and culturally important group of mostly semelparous plants with remarkable flowering features, yet little bamboo genomic research has been performed. Here we present, for the first time, extensive sequence and transcript abundance data for the floral transcriptome of a key bamboo species, Dendrocalamus latiflorus, obtained using the Illumina GAII sequencing platform. Our further goal was to identify patterns of gene expression during bamboo flower development.

Results

Approximately 96 million sequencing reads were generated and assembled de novo, yielding 146,395 high quality unigenes with an average length of 461 bp. Of these, 80,418 were identified as putative homologs of annotated sequences in the public protein databases, of which 290 were associated with the floral transition and 47 were related to flower development. Digital abundance analysis identified 26,529 transcripts differentially enriched between two developmental stages, young flower buds and older developing flowers. Unigenes found at each stage were categorized according to their putative functional categories. These sequence and putative function data comprise a resource for future investigation of the floral transition and flower development in bamboo species.

Conclusions

Our results present the first broad survey of a bamboo floral transcriptome. Although it will be necessary to validate the functions carried out by these genes, these results represent a starting point for future functional research on D. latiflorus and related species.