Insights into Taxol® biosynthesis by endophytic fungi.

There have been two hundred reports that endophytic fungi produce Taxol®, but its production yield is often rather low. Although considerable efforts have been made to increase Taxol/taxanes production in fungi by manipulating cocultures, mutagenesis, genome shuffles, and gene overexpression, little is known about the molecular signatures of Taxol biosynthesis and its regulation. It is known that some fungi have orthologs of the Taxol biosynthetic pathway, but the overall architecture of this pathway is unknown. A biosynthetic putative gene homology approach, combined with genomics and transcriptomics analysis, revealed that a few genes for metabolite residues may be located on dispensable chromosomes. This review explores a number of crucial topics (i) finding biosynthetic pathway genes using precursors, elicitors, and inhibitors; (ii) orthologs of the Taxol biosynthetic pathway for rate-limiting genes/enzymes; and (iii) genomics and transcriptomics can be used to accurately predict biosynthetic putative genes and regulators. This provides promising targets for future genetic engineering approaches to produce fungal Taxol and precursors. KEY POINTS: • A recent trend in predicting Taxol biosynthetic pathway from endophytic fungi. • Understanding the Taxol biosynthetic pathway and related enzymes in fungi. • The genetic evidence and formation of taxane from endophytic fungi.

Transcriptome analysis of Euwallacea interjectus reveals differentially expressed unigenes related to developmental stages and egg laying.

Euwallacea interjectus (Curculionidae: Scolytinae) is an ambrosia beetle species in its early stages of research. Therefore, studying the related molecular mechanism associated with the development and egg laid is essential. Transcriptome sequencing was used in this study to compare the gene expression of the beetles at different developmental stages and female adults before and after oviposition. A total of 40,047 annotated unigenes were obtained. There were 4225 differentially expressed unigenes (DEUs) from larva to prepupa stage, 3651 DEUs between prepupa and pupa, 1675 DEUs generated from pupa to adult, and 4762 DEUs between females before and after oviposition. The most significant pathway differences between different development stages and before and after oviposition were selected through functional annotation of DEUs between different stages. Among them, there were many pathways related to protein metabolism including: neuroactive ligand-receptor interaction, endoplasmic reticulum and RNA transport. This study provides valuable information on the molecular regulation mechanism of development and the egg laid of E. interjectus.

Transcriptome analysis of response strategy in Hemerocallis fulva under drought stress.

BACKGROUND: Hemerocallis fulva is an important ground cover plant widely used in urban greening. The analysis of the molecular mechanism underlying the drought response of H. fulva can lay a foundation for improving its adaptability and expanding its planting area. OBJECTIVE: To reveal the drought response mechanisms of H. fulva, identify candidate unigenes associated with drought response, and lay a foundation for further unigenes functional study and drought resistance improvement of H. fulva via genetic engineering. METHODS: RNA was isolated from H. fulva under different experimental conditions. De novo transcriptomic analysis of the samples was performed to screen drought response unigenes. The transcriptional changes of candidate drought response unigenes were verified by quantitative real-time PCR. RESULTS: The differentially expressed unigenes and their functions were analyzed after H. fulva treated by PEG-simulated drought stress and rewatering. The candidate unigenes, associated with H. fulva drought response, were identified after transcriptome analysis. Then, the transcription level of drought response unigenes of H. fulva under different conditions was further verified. Abscisic acid, protein phosphorylation, sterol biosynthesis and ion transport were involved in drought response with quick restore in H. fulva. The response unigenes, involved in hormone (ABA, JA, CK and GA) signaling pathways, defense response, high light response, karrikin response and leaf shaping, can maintain at changed expression levels even after stress withdraw. CONCLUSION: Hemerocallis fulva has unique drought response mechanism. Negative regulation mechanism may play more important roles in drought response of H. fulva. The analysis of candidate unigenes, associated with drought response, lays a foundation for further drought resistance improvement of H. fulva.

RNA-Seq Provides Novel Genomic Resources for Noug (Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome.

Genomic resources and tools are essential for improving crops and conserving their genetic resources. Guizotia abyssinica (noug), an outcrossing edible oilseed crop, has highly limited genomic resources. Hence, RNA-Seq based transcriptome sequencing of 30 noug genotypes was performed to generate novel genomic resources and assess their usefulness. The genotypes include self-compatible and self-incompatible types, which differ in maturity time, photoperiod sensitivity, or oil content and quality. RNA-Seq was performed on Illumina HiSeq 2500 platform, and the transcript was reconstructed de novo, resulting in 409,309 unigenes. The unigenes were characterized for simple sequence repeats (SSRs), and served as a reference for single nucleotide polymorphism (SNP) calling. In total, 40,776 SSRs were identified in 35,639 of the 409,309 unigenes. Of these, mono, di, tri, tetra, penta and hexanucleotide repeats accounted for 55.4, 20.8, 21.1, 2.3, 0.2, and 0.2%, respectively. The average G+C content of the unigenes and their SSRs were 40 and 22.1%, respectively. The vast majority of mononucleotide repeat SSRs (97%) were of the A/T type. AG/CT and CCA/TGG were the most frequent di and trinucleotide repeat SSRs. A different number of single nucleotide polymorphism (SNP) loci were discovered in each genotype, of which 1,687 were common to all 30 genotypes and 5,531 to 28 of them. The mean observed heterozygosity of the 5,531 SNPs was 0.22; 19.4% of them had polymorphism information content above 0.30 while 17.2% deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). In both cluster and principal coordinate analyses, the genotypes were grouped into four major clusters. In terms of population structure, the genotypes are best represented by three genetic populations, with significant admixture within each. Genetic similarity between self-compatible genotypes was higher, due to the narrow genetic basis, than that between self-incompatible genotypes. The genotypes that shared desirable characteristics, such as early maturity, and high oil content were found to be genetically diverse, and hence superior cultivars with multiple desirable traits can be developed through crossbreeding. The genomic resources developed in this study are vital for advancing research in noug, such as genetic linkage mapping and genome-wide association studies, which could lead to genomic-led breeding.

Transcriptome analysis of Holotrichia oblita reveals differentially expressed unigenes related to reproduction and development under different photoperiods.

Holotrichia oblita (Faldermann) (Coleoptera: Scarabaeidae) is an insect whose feeding and mating behaviors occur at night. A scotophase is necessary for H. oblita reproduction. We used RNA sequencing (RNA-seq) to compare the expression patterns of H. oblita at five photoperiods (0:24, 8:16, 12:12, 16:8, and 24:0 h) (L:D). Compared to the control (24:0) (L:D), 161-684 differentially expressed unigenes (DEUs) were found in female samples, while 698-2322 DEUs were found in male samples. For all DEUs, a total of 92-1143 DEUs were allocated to 116-662 categories of gene ontology (GO), and 81-1116 DEUs were assigned into 77-286 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The iPath diagram showed that the DEUs generated by comparing female and male samples with photoperiods of 0:24 and 24:0, respectively, involved multiple metabolic pathways, such as carbohydrate metabolism, lipid metabolism, nucleotide metabolism, purine metabolism and glutathione metabolism. Most of these DEUs were upregulated. Finally, 13 DEUs related to reproduction and development were selected to confirm the consistency of relative expression between RNA-Seq and quantitative real-time polymerase chain reaction (qRT-PCR). Most of these comparison results agreed well, except for some qRT-PCR results that were not detected in male samples due to their low expression. These results provide useful information for understanding the dark-induced reproduction of H. oblita.

The first transcriptome sequencing and data analysis of the Javan mahseer (Tor tambra).

The Javan mahseer (Tor tambra) is one of the most valuable freshwater fish found in Tor species. To date, other than mitogenomic data (BioProject: PRJNA422829), genomic and transcriptomic resources for this species are still lacking which is crucial to understand the molecular mechanisms associated with important traits such as growth, immune response, reproduction and sex determination. For the first time, we sequenced the transcriptome from a whole juvenile fish using Illumina NovaSEQ6000 generating raw paired-end reads. De novo transcriptome assembly generated a draft transcriptome (BUSCO5 completeness of 91.2% [Actinopterygii_odb10 database]) consisting of 259,403 putative transcripts with a total and N50 length of 333,881,215 bp and 2283 bp, respectively. A total count of 77,503 non-redundant protein coding sequences were predicted from the transcripts and used for functional annotation. We mapped the predicted proteins to 304 known KEGG pathways with signal transduction cluster having the highest representation followed by immune system and endocrine system. In addition, transcripts exhibiting significant similarity to previously published growth-and immune-related genes were identified which will facilitate future molecular breeding of Tor tambra.

Comparative Transcriptomic and Metabolic Analyses Reveal the Molecular Mechanism of Ovule Development in the Orchid, Cymbidium sinense.

Ovule development is pivotal to plant reproduction and seed development. Cymbidium sinense (Orchidaceae) has high ornamental value due to its pleasant aroma and elegant floral morphology. The regulatory mechanism underlying ovule development in orchids, especially C. sinense, is largely unknown and information on the C. sinense genome is very scarce. In this study, a combined analysis was performed on the transcriptome and non-targeted metabolomes of 18 C. sinense 'Qi Jian Hei Mo' ovule samples. Transcriptome analysis assembled gene-related information related to six growth stages of C. sinense ovules (S1-S6, equivalent to 30, 35, 42, 46, 53, and 60 days after pollination). Illumina sequencing technology was used to obtain the complete set of transcriptome sequences of the 18 samples. A total of 81,585 unigene sequences were obtained after assembly, 24,860 (30.47%) of which were functionally annotated. Using transcriptome sequencing technology, a total of 9845 differentially expressed unigenes (DEUs) were identified in C. sinense ovules that were assigned to specific metabolic pathways according to the Kyoto Encyclopedia of Genes and Genomes (KEGG). DEUs associated with transcription factors (TFs) and phytohormones were identified and analyzed. The TFs homeobox and MADS-box were associated with C. sinense ovule development. In particular, the phytohormones associated with DEUs such as indole-3-acetic acid (IAA), cytokinin (CK), gibberellin (GA), abscisic acid (ABA), brassinosteroid (BR), and jasmonate (JA), may have important regulatory effects on C. sinense ovule development. Metabolomic analysis showed an inconsistent number of KEGG annotations of differential metabolites across comparisons (S2_vs_S4, S2_vs_S5, and S4_vs_S5 contained 23, 26, and 3 annotations, respectively) in C. sinense ovules. This study provides a valuable foundation for further understanding the regulation of orchid ovule development and formation, and establishes a theoretical background for future practical applications during orchid cultivation.

Global insights to drought stress perturbed genes in oat (Avena sativa L.) seedlings using RNA sequencing.

Oat (Avena sativa L.) is an important crop in northwestern China. Drought stress is the most significant factor affecting oat yield. In the present study, we explored the changes that occur in oats under drought stress conditions at a global genomic level. RNA sequencing was performed using 15-day-old oat seedlings. The differentially expressed transcripts were identified, and their related functions and pathways were investigated. In total, 1,065 unigenes were differentially expressed in oats under drought stress conditions. Of these, 386 unigenes were upregulated and 679 were downregulated. The perturbed transcripts were closely related to the biosynthesis of secondary metabolites, plant hormone signal transduction, and biosynthesis of antibiotics. DN50483_c0_g1_i3, which was annotated as acetyl-CoA carboxylase, was a significant node in the protein-protein interaction network. Biosynthesis of antibiotics and secondary metabolites may be involved in the drought stress response mechanisms of oats. The perturbed transcripts may provide targets for improving plant stress responses.

Prospects of next generation sequencing in lentil breeding.

Lentil is an important food legume crop that has large and complex genome. During past years, considerable attention has been given on the use of next generation sequencing for enriching the genomic resources including identification of SSR and SNP markers, development of unigenes, transcripts, and identification of candidate genes for biotic and abiotic stresses, analysis of genetic diversity and identification of genes/ QTLs for agronomically important traits. However, in other crops including pulses, next generation sequencing has revolutionized the genomic research and helped in genomic assisted breeding rapidly and cost effectively. The present review discuss current status and future prospects of the use NGS based breeding in lentil.

Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing.

Spinibarbus caldwelli is an omnivorous cyprinid fish that is distributed widely in China. To investigate the adaptive evolution of S. caldwelli, the muscle transcriptome was sequenced by Illumina HiSeq 4000 platform. A total of 80,447,367 reads were generated by next-generation sequencing. Also, 211,386 unigenes were obtained by de novo assembly. Additionally, we calculated that the divergence time between S. caldwelli and Sinocyclocheilus grahami is 23.14 million years ago (Mya). And both of them diverged from Ctenopharyngodon idellus 46.95 Mya. Furthermore, 38 positive genes were identified by calculating Ka/Ks ratios from 9225 orthologs. Among them, several immune-related genes were identified as positively selected, such as POLR3B, PIK3C3, TOPORS, FASTKD3, CYPLP1A1, and UACA. Our results throw light on the nature of the natural selection of S. caldwelli and contribute to future immunological and transcriptome studies.

De Novo Assembly and Annotation of the Juvenile Tuber Transcriptome of a Gastrodia elata Hybrid by RNA Sequencing: Detection of SSR Markers.

Gastrodia elata is a traditional Chinese herbal medicine with good therapeutic effect on various nervous and cerebrovascular diseases. In the present study, we generated 20,611,556 raw reads from the young tuber transcriptome of a G. elata hybrid (Gastrodia elata BI.f.elata × Gastrodia elata BI.f.pilifera) by using Illumina HiSeq™ 4000 sequencing platform. De novo assembly and bioinformatics analysis revealed 20,237,474 clean reads, including 2,529,684,250 bp that assembled into 34,323 unigenes with an average length of 695.19 bp. Among them, 24,698 (71.96%) unigenes were annotated by at least one of the Nr, Swiss-Prot, COG and KEGG databases. A total of 4236 (12.34%) unigenes were identified as candidate transcription factors, and 2007 (5.85%) unigenes were found to contain at least one single sequence repeat (SSR). Of these SSRs, AG/CT repeat motif was the most frequent, with a total of 498 (21.67%). This study will enhance our understanding about the molecular mechanism of physiological metabolism, growth and development of G. elata, particularly abundant SSR markers will offer plenty of alternative tools for further studies about molecular genetics, molecular breeding and association analysis.

De novo assembly and characterization of transcriptome in the medicinal plant Euphorbia jolkini.

BACKGROUND: Euphorbia jolkini, a medicinal herb that grows on the warm beaches in Japan and South Korea, is known to be used for traditional medicines to treat a variety of ailments, including bruises, stiffness, indigestion, toothache, and diabetes. OBJECTIVE: It is to analyze the whole transcriptome and identify the genes related to the phenylpropanoid biosynthesis in the medicinally important herb E jolkini. METHODS: Paired-end Illumina HiSeq™ 2500 sequencing technology was employed for cDNA library construction and Illumina sequencing. Public databases like TAIR (The Arabidopsis Information Resource), Swissprot and KEGG (Kyoto Encyclopedia of Genes and Genomes) were used for annotations of unigenes obtained. RESULTS: The transcriptome of E. jolkini generated 139,215 assembled transcripts with an average length of 868 bp and an N50 value of 1460 bp that were further clustered using CD-HIT into 93,801 unigenes with an average length of 847 bp (N50-1410 bp). Sixty-three percent of the coding sequences (CDS) were annotated from the longest open reading frame (ORF). A remarkable percentage of unigenes were annotated against various databases. The differentially expressed gene analysis revealed that the expression of genes related to the terpenoid backbone biosynthesis pathway was higher in the flowers, whereas that of genes related to the phenylpropanoid biosynthesis pathway was both up- and downregulated in flowers and leaves. A search of against the transcription factor domain found 1023 transcription factors (TFs) that were from 54 TF families. CONCLUSION: Assembled sequences of the E. jolkini transcriptome are made available for the first time in this study E. jolkini and lay a foundation for the investigation of secondary metabolite biosynthesis.

De novo transcriptome analysis unravels tissue-specific expression of candidate genes involved in major secondary metabolite biosynthetic pathways of Plumbago zeylanica: implication for pharmacological potential.

KEY MESSAGE: The present study provides comparative transcriptome analysis, besides identifying functional secondary metabolite genes of Plumbago zeylanica with pharmacological potential for future functional genomics, and metabolomic engineering of secondary metabolites from this plant towards diversified biomedical applications. ABSTRACT: Plumbago zeylanica is a widely used medicinal plant of the traditional Indian system of medicine with wide pharmacological potential to treat several disorders. The present study aimed to carry out comparative transcriptome analysis in leaf and root tissue of P. zeylanica using Illumina paired end sequencing to identify tissue-specific functional genes involved in the biosynthesis of secondary metabolites, contributing to its therapeutic efficacy. De novo sequencing assembly resulted in the identification of 62,321 "Unigenes" transcripts with an average size of 1325 bp. Functional annotation using BLAST2GO resulted in the identification of 50,301 annotated transcripts (80.71%) and GO assigned to 18,814 transcripts. KEGG pathway annotation of the "Unigenes" revealed that 2465 transcripts could be assigned to 242 KEGG pathway maps wherein the number of transcripts involved in secondary metabolism was distinct in root and leaf transcriptome. Among the secondary metabolite biosynthesis pathways, the cluster of "Unigenes" encoding enzymes of 'Phenylpropanoid biosynthesis pathway' represents the largest group (84 transcripts) followed by 'Terpenoid Backbone biosynthesis' (48 transcripts). The transcript levels of the candidate unigenes encoding key enzymes of phenylpropanoid (PAL, TAL) and flavanoid biosynthesis (CHS, ANS, FLS) pathways were up-regulated in root, while the expression levels of candidate "Unigenes" transcript for monoterpenoid (DXS, ISPF), diterpenoid biosynthesis (SPS, SDS) and indole alkaloid pathways (STR) were significantly higher in leaf of P. zeylanica. Interestingly, validation of differential gene expression profile by qRT-PCR also confirmed that candidate "Unigenes" enzymes of phenylpropanoid and flavonoid biosynthesis were highly expressed in the root, while the key regulatory enzymes of terpenoid and indole alkaloid compounds were up-regulated in the leaf, suggesting that (differences in) the levels of these functional genes could be attributed to the (differential) pharmacological activity (between root and leaf) in tissues of P. zeylanica.

Comparative transcriptome analysis of differential expression in different tissues of Prunella vulgaris / 中草药

Objective: To compare and analyze the transcriptome of ears, leaves and stems of Prunella vulgaris, and excavate the key enzyme genes related to the secondary metabolism biosynthesis of P. vulgaris. Methods: The transcriptome of ears, leaves and stems of P. vulgaris were sequenced by Illumina high-throughput sequencing technology. Additionally biosynthesis related enzyme gene of secondary metabolism were identified from differentially expressed genes. Results: In the transcripts of three different tissues of P. vulgaris, a total of 8 270 Unigenes differed significantly between at least two tissues. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of genes differentially expressed in different tissues showed that the expression of phenylpropanoid biosynthesis genes varied greatly. A total of 31 triterpenoid biosynthesis-related Unigenes, 16 phenolic acid biosynthesis-related Unigenes, and 113 P450s-related Unigenes were identified in the differentially expressed genes. Conclusion: This study provides a basis for the subsequent discovery of functional genes related to the secondary metabolism synthesis pathway of P. vulgaris, and plays a foundation for the regulation of secondary metabolism biosynthesis of P. vulgaris.

Transcriptome analysis reveals key enzyme genes involved in lignin biosynthesis pathway in Arctium lappa / 中草药

Objective: To obtain the functional genes in Arctium lappa and analyze the key enzyme genes involved in biosynthesis pathway of lignin. Methods: The transcriptome dataset of roots of A. lappa was obtained by using the BGISEQ-500 sequencing platform. Unigenes were de novo assembled and annotated according to the existing nucleic acids and protein databases. The key enzyme genes involved in lignin biosynthesis pathway were analyzed and the three-dimensional model of phenylalanine ammonialyase (AlPAL) was generated by the SWISS-MODEL and PyMol. Results: A total of 54 215 Unigenes were obtained by de novo assembly, and 42 003 Unigenes were annotated in at least one public database. A total of 1 668 Unigenes were identified to be plant transcription factors (TFs), which belong to 54 TF families, and 423 Unigenes were found to be involved in the biosynthesis pathway of lignin. Structure model indicated that AlPAL was a homotypic tetramer, and each monomer was consisted of three domains, including 4-methyl-imidazole-5-ketone (MIO) domain, core domain and shield domain. The MIO domain contained three conserved amino acids (ASG), which formed the catalytic activity center of the enzyme. Conclusion: This study was the first de novo transcriptome assembly of A. lappa, which will lay the foundation for the identification of functional genes, secondary metabolic pathway and the study of regulation mechanism of biosynthesis pathway of lignin in A. lappa in the future.

Transcriptome Analysis and Identification of Insecticide Tolerance-Related Genes after Exposure to Insecticide in Sitobion avenae.

Aphids cause serious losses to the production of wheat. The grain aphid, Sitobion avenae, which is the dominant species of aphid in all wheat regions of China, is resistant to a variety of insecticides, including imidacloprid and chlorpyrifos. However, the resistance and mechanism of insecticide tolerance of S. avenae are still unclear. Therefore, this study employed transcriptome analysis to compare the expression patterns of stress response genes under imidacloprid and chlorpyrifos treatment for 15 min, 3 h, and 36 h of exposure. S. avenae adult transcriptome was assembled and characterized first, after which samples treated with insecticides for different lengths of time were compared with control samples, which revealed 602267 differentially expressed unigenes (DEUs). Among these DEUs, 31-790 unigenes were classified into 66-786 categories of gene ontology (GO) functional groups, and 24-760 DEUs could be mapped into 54-268 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Finally, 11 insecticide-tolerance-related unigenes were chosen to confirm the relative expression by quantitative real-time polymerase chain reaction (qRT-PCR) in each treatment. Most of the results between qRT-PCR and RNA sequencing (RNA-Seq) are well-established. The results presented herein will facilitate molecular research investigating insecticide resistance in S. avenae, as well as in other wheat aphids.

Transcriptome analysis reveals the different compatibility between LAAA × AA and LAAA × LL in Lilium.

To unveil the mechanism of the compatibility of odd-allotetraploid lily (LAAA) as female with diploid male lily, the differences of expressed unigenes in the ovaries and leaves between LAAA × AA and LAAA × LL were investigated using transcriptome analysis. The results showed the fruits of LAAA × AA well developed, while those of LAAA × LL aborted. The number of differentially expressed genes was less in the ovaries of LAAA × AA than those of LAAA × LL, but it showed opposite trend in those of leaves. The unigenes related with auxins, cytokinins, gibberellins, antioxidants, expansins, chlorophylls, carbohydrates, transport proteins were usually up-expressed in the ovaries and leaves of LAAA × AA but not in LAAA × LL; while those of abscisic acid, ethylene, jasmonic acid, and salicylic acid were increased in the ovaries or leaves of LAAA × LL but not in LAAA × AA. The up-expressed unigenes in the ovaries and leaves of LAAA × AA played positive roles in its fruit development because the products of the genes, like phytohormones and antioxidants, had functions protecting leaves from senescence or scavenging ROS, and thus LAAA was compatible with AA, while those of LAAA × LL played negative roles and caused its fruits aborted, and hence LAAA was incompatible with LL.

Genome-wide analysis of developmental stage-specific transcriptome in Bradysia odoriphaga.

Bradysia odoriphaga is a serious pest of the Chinese chive; however, detailed information regarding the developmental stage-specific gene expression patterns of B. odoriphaga is not yet available. In this study, RNA sequencing (RNA-seq) was performed to determine the gene expression patterns of developmental stages including the eggs, second instar larvae, fourth instar larvae, pupae, and adults of B. odoriphaga. Analysis of 15 samples revealed an average of 89.56% of the clean reads could be mapped onto the assembled UniGene database. Cluster tree analysis showed that the expression patterns were stage-specific and that samples of the second and fourth instar larvae clustered in one group, while those of eggs, pupae, and adults clustered in another group. Differential expression unigenes (DEUs) for sequential developmental stages were between 3314 and 10,632. A total of 1910-7756 DEUs of sequential developmental stages were assigned into 45-56 gene ontology categories and 1165-3845 DEUs were mapped into Kyoto Encyclopedia of Genes and Genomes pathways. The expression of DEUs related to growth and development showed that hormone receptors highly expressed in the pupal stage, while chitinases were highly expressed in the larval stage. The results of quantitative real time polymerase chain reaction (qRT-PCR) and RNA-seq expression agreed well for 12 growth- and development-related unigenes. This study identified DEUs for sequential developmental stages of B. odoriphaga. Gene Ontology classifications and KEGG pathway identification of DEUs not only provide information useful for understanding insect growth and development but also for exploring novel approaches to control B. odoriphaga.

De novo transcriptome analysis of Rhododendron molle G. Don flowers by Illumina sequencing.

Rhododendron molle G. Don occupies an important phylogenetic node in the genus rhododendron with unique yellow flower and medicinal functions. However, only limited genetic resources and their genome information are available for the generation of rhododendron flowers. The next generation sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and therefore provide a turning point for rhododendron research. Our goal is to use the genetic information to facilitate the relevant research on flowering and flower color formation in R. molle. In total, 66,026 unigenes were identified, among which 31,298 were annotated in the NCBI non-redundant protein database and 22,410 were annotated in the Swiss-Prot database. Of these annotated unigenes, 9490 and 18,680 unigenes were assigned to clusters of orthologous groups and gene ontology categories, respectively. A total of 7177 genes were mapped to 118 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database. In addition, 8266 simple sequence repeats (SSRs) were detected, and these SSRs will undoubtedly benefit rhododendron breeding work. Metabolic pathway analysis revealed that 32 unigenes were predicted to be involved in carotenoid biosynthesis. Our transcriptome revealed 32 engines that encode key enzymes in the carotenoid biosynthesis pathway, including PSY, PDS, LCYB, LCYE, etc. The content of ß-carotene was much higher than the other carotenoids throughout the flower development. It was consistent with the key genes expression level in the carotenoid biosynthesis pathway by the Illumina expression profile analysis and the qRT-PCR analysis. Our study identified genes associated with carotenoid biosynthesis in R. molle and provides a valuable resource for understanding the flowering and flower color formation mechanisms in R. molle.

Global gene expression and pigment analysis of two contrasting flower color cultivars of Canna.

Development of flower color in plants is a complex process. Among others, it is an important trait for ornamental flowering plants. Canna is a flowering ornamental plant of family Cannaceae. To understand the molecular mechanism of flower color development in Canna, RNA sequencing from flower tissues of two contrasting flower color cultivars, Red President (RP) and Tropical Sunrise (TS) was performed. More than 27.0 million and 19.0 million clean reads were obtained from RP and TS, respectively. The combined clean reads were assembled into 147,295 unigenes. The Canna unigenes showed maximum homology with Populus trichocarpa (26.79%). A total of 2702 unigenes expressed differentially between the two cultivars of which 1972 were up-regulated and 730 were down-regulated in RP. Phenylpropanoid and flavonoid biosynthetic processes were the significant processes in RP. Expression of a vast number of transcription factors including MYB, bHLH, ARF, and WRKY were higher in RP than TS. The expression analysis of RNA sequencing data was validated by qRT-PCR analysis. Further, concentration of measured anthocyanidins and flavonols were very low or absent in TS, corroborating largely with our transcriptome data. These findings may help in understanding flower color development in Canna and in future crop breeding program.