RNA-Seq for transcriptome analysis in non-model plants

Integrating Transcriptome and Chemical Analyses to Provide Insights into Biosynthesis of Terpenoids and Flavonoids in the Medicinal Industrial Crop Andrographis paniculate and Its Antiviral Medicinal Parts

Andrographis paniculata is a medicinal plant traditionally used to produce diterpene lactones and flavonoids, which possess various biological activities. Widely distributed in China, India, and other Southeast Asia countries, A. paniculata has become an important economic crop, significantly treating SARS-CoV-2, and is being cultivated on a large scale in southern China. The biosynthesis of active ingredients in A. paniculata are regulated and controlled by genes, but their specific roles are still not fully understood. To further explore the growth regulation factors and utilization of its medicinal parts of this industrial crop, chemical and transcriptome analyses were conducted on the roots, stems, and leaves of A. paniculata to identify the biosynthesis pathways and related candidate genes of the active ingredients. The chemical analysis revealed that the main components of A. paniculata were diterpene lactones and flavonoids, which displayed potential ability to treat SARS-CoV-2 through molecular docking. Moreover, the transcriptome sequencing annotated a total of 40,850 unigenes, including 7962 differentially expressed genes. Among these, 120 genes were involved in diterpene lactone biosynthesis and 60 genes were involved in flavonoid biosynthesis. The expression of diterpene lactone-related genes was the highest in leaves and the lowest in roots, consistent with our content determination results. It is speculated that these highly expressed genes in leaves may be involved in the biosynthesis pathway of diterpenes. Furthermore, two class Ⅰ terpene synthases in A. paniculata transcriptome were also annotated, providing reference for the downstream pathway of the diterpene lactone biosynthesis. With their excellent market value, our experiments will promote the study of the biosynthetic genes for active ingredients in A. paniculata and provide insights for subsequent in vitro biosynthesis.

Allantoin improves salinity tolerance in Arabidopsis and rice through synergid activation of abscisic acid and brassinosteroid biosynthesis

Soil salinity stress is one of the major bottlenecks for crop production. Although, allantoin is known to be involved in nitrogen metabolism in plants, yet several reports in recent time indicate its involvement in various abiotic stress responses including salinity stress. However, the detail mechanism of allantoin involvement in salinity stress tolerance in plants is not studied well. Moreover, we demonstrated the role of exogenous application of allantoin as well as increased concentration of endogenous allantoin in rendering salinity tolerance in rice and Arabidopsis respectively, via., induction of abscisic acid (ABA) and brassinosteroid (BR) biosynthesis pathways. Exogenous application of allantoin (10 µM) provides  salt-tolerance to salt-sensitive rice genotype (IR-29). Transcriptomic data after exogenous supplementation of allantoin under salinity stress showed induction of ABA (OsNCED1) and BR (Oscytochrome P450) biosynthesis genes in IR-29. Further, the key gene of allantoin biosynthesis pathway i.e., urate oxidase of the halophytic species Oryza coarctata was also found to induce ABA and BR biosynthesis genes when over-expressed in transgenic Arabidopsis. Thus, indicating that ABA and BR biosynthesis pathways were involved in allantoin mediated salinity tolerance in both rice and Arabidopsis. Additionally, it has been found that several physio-chemical parameters such as biomass, Na⁺/K⁺ ratio, MDA, soluble sugar, proline, allantoin and chlorophyll contents were also associated with the allantoin-mediated salinity tolerance in urate oxidase overexpressed lines of Arabidopsis. These findings depicted the functional conservation of allantoin for salinity tolerance in both plant clades.

RNA-Seq and genetic diversity analysis of faba bean (Vicia faba L.) varieties in China

Background

Faba bean (Vicia faba L) is one of the most important legumes in the world. However, there is relatively little genomic information available for this species owing to its large genome. The lack of data impedes the discovery of molecular markers and subsequent genetic research in faba bean. The objective of this study was to analyze the faba bean transcriptome, and to develop simple sequence repeat (SSR) markers to determine the genetic diversity of 226 faba bean varieties derived from different regions in China.

Methods

Faba bean varieties with different phenotype were used in transcriptome analysis. The functions of the unigenes were analyzed using various database. SSR markers were developed and the polymorphic markers were selected to conduct genetic diversity analysis.

Results

A total of 92.43 Gb of sequencing data was obtained in this study, and 133,487 unigene sequences with a total length of 178,152,541 bp were assembled. A total of 5,200 SSR markers were developed on the basis of RNA-Seq analysis. Then, 200 SSR markers were used to evaluate polymorphisms. In total, 103 (51.5%) SSR markers showed significant and repeatable bands between different faba bean varieties. Clustering analysis revealed that 226 faba bean materials were divided into five groups. Genetic diversity analysis revealed that the relationship between different faba beans in China was related, especially in the same region. These results provided a valuable data resource for annotating genes to different categories and developing SSR markers.

An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea

Large-scale transcriptome analysis can provide a systems-level understanding of biological processes. To accelerate functional genomic studies in chickpea, we perform a comprehensive transcriptome analysis to generate full-length transcriptome and expression atlas of protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs) from 32 different tissues/organs via deep sequencing. The high-depth RNA-seq dataset reveal expression dynamics and tissue-specificity along with associated biological functions of PCGs and lncRNAs during development. The coexpression network analysis reveal modules associated with a particular tissue or a set of related tissues. The components of transcriptional regulatory networks (TRNs), including transcription factors, their cognate cis-regulatory motifs, and target PCGs/lncRNAs that determine developmental programs of different tissues/organs, are identified. Several candidate tissue-specific and abiotic stress-responsive transcripts associated with quantitative trait loci that determine important agronomic traits are also identified. These results provide an important resource to advance functional/translational genomic and genetic studies during chickpea development and environmental conditions.

A full-length transcriptome and expression atlas of protein-coding genes and long non-coding RNAs is generated in chickpea. Components of transcriptional regulatory networks and candidate tissue-specific transcripts associated with quantitative trait loci are identified.

Transcriptome profiles of yellowish-white and fuchsia colored flowers in the Rheum palmatum complex reveal genes related to color polymorphism

Flower color variation is ubiquitous in many plant species, and several studies have been conducted to elucidate the underlying molecular mechanism. There are two flower color variants (yellowish-white and fuchsia) in the Rheum palmatum complex, however, few studies have investigated this phenomenon. Here, we used transcriptome sequencing of the two color variants to shed light on the molecular and biochemical basis for these color morphs. Comparison of the two transcriptomes identified 9641 differentially expressed unigenes (DEGs), including 6477 up-regulated and 3163 down-regulated genes. Functional analyses indicated that several DEGs were related to the anthocyanin biosynthesis pathway, and the expression profiles of these DEGs were coincident with the qRT-PCR validation results, indicating that expression levels of structural genes have a profound effect on the color variation in the R. palmatum complex. Our results suggested that the interaction of transcription factors (MYB, bHLH and WRKY) also regulated the anthocyanin biosynthesis in the R. palmatum complex. Estimation of selection pressures using the dN/dS ratio showed that 1106 pairs of orthologous genes have undergone positive selection. Of these positively selected genes, 21 were involved in the anthocyanin biosynthetic pathway, indicating that they may encode the proteins for structural alteration and affect flower color in the R. palmatum complex.

Comparative Transcriptome Analysis of Two Kalanchoë Species during Plantlet Formation

Few species in the Kalanchoë genus form plantlets on their leaf margins as an asexual reproduction strategy. The limited molecular studies on plantlet formation show that an organogenesis ortholog, SHOOTMERISTEMLESS (STM) and embryogenesis genes, such as LEAFY COTYLEDON1 (LEC1) and FUSCA3 are recruited during plantlet formation. To understand the mechanisms of two Kalanchoë plantlet-forming species with different modes of plantlet formation, RNA-sequencing analysis was performed. Differentially expressed genes between the developmental stages were clustered in K. daigremontiana (Raym.-Hamet and H. Perrier) and K. pinnata (Lam. Pers.), respectively. Of these gene clusters, GO terms that may be involved in plantlet formation of both species, such as signaling, response to wounding, reproduction, regulation of hormone level, and response to karrikin were overrepresented. Compared with the common GO terms, there were more unique GO terms overrepresented during the plantlet formation of each species. A more in-depth investigation is required to understand how these pathways are participating in plantlet formation. Nonetheless, this transcriptome analysis is presented as a reliable basis for future studies on plantlet formation and development in two Kalanchoë plantlet-forming species.

Draft genome sequence of Indian mulberry (Morus indica) provides a resource for functional and translational genomics

Mulberry is an important crop plant for the sericulture industry. Here, we report high-quality genome sequence of a cultivated Indian mulberry (Morus indica cv K2) obtained by combining data from four different technologies, including Illumina, single-molecule real-time sequencing, chromosome conformation capture and optical mapping, with a gene completeness of 96.5%. Based on the genome sequence, we identified 49.2% of repetitive DNA and 27,435 high-confidence protein-coding genes with >90% of them supported by transcript evidence. A comparative analysis with other plant genomes identified 4.8% of species-specific genes in the M. indica genome. Transcriptome profiling revealed tissue-specific and differential expression across multiple accessions of ~4.7% and 2-5% of protein-coding genes, respectively, implicated in diverse biological processes. Whole genome resequencing of 21 accessions/species revealed ~2.5 million single nucleotide polymorphisms and ~ 0.2 million insertions/deletions. These data and results provide a comprehensive resource to accelerate the genomics research in mulberry for its improvement.

Omics Path to Increasing Productivity in Less-Studied Crops Under Changing Climate-Lentil a Case Study

Conventional breeding techniques for crop improvement have reached their full potential, and hence, alternative routes are required to ensure a sustained genetic gain in lentils. Although high-throughput omics technologies have been effectively employed in major crops, less-studied crops such as lentils have primarily relied on conventional breeding. Application of genomics and transcriptomics in lentils has resulted in linkage maps and identification of QTLs and candidate genes related to agronomically relevant traits and biotic and abiotic stress tolerance. Next-generation sequencing (NGS) complemented with high-throughput phenotyping (HTP) technologies is shown to provide new opportunities to identify genomic regions and marker-trait associations to increase lentil breeding efficiency. Recent introduction of image-based phenotyping has facilitated to discern lentil responses undergoing biotic and abiotic stresses. In lentil, proteomics has been performed using conventional methods such as 2-D gel electrophoresis, leading to the identification of seed-specific proteome. Metabolomic studies have led to identifying key metabolites that help differentiate genotypic responses to drought and salinity stresses. Independent analysis of differentially expressed genes from publicly available transcriptomic studies in lentils identified 329 common transcripts between heat and biotic stresses. Similarly, 19 metabolites were common across legumes, while 31 were common in genotypes exposed to drought and salinity stress. These common but differentially expressed genes/proteins/metabolites provide the starting point for developing high-yielding multi-stress-tolerant lentils. Finally, the review summarizes the current findings from omic studies in lentils and provides directions for integrating these findings into a systems approach to increase lentil productivity and enhance resilience to biotic and abiotic stresses under changing climate.

Transcriptome repository of North-Western Himalayan endangered medicinal herbs: a paramount approach illuminating molecular perspective of phytoactive molecules and secondary metabolism

Medicinal plants of the North-Western Himalayan region are known for their unprecedented biodiversity and valuable secondary metabolites that are unique to this dynamic geo-climatic region. From ancient times these medicinal herbs have been used traditionally for their therapeutic potentials. But from the last 2 decades increasing pharmaceutical demand, illegal and unorganized trade of these medicinal plants have accelerated the rate of over-exploitation in a non-scientific manner. In addition, climate change and anthropogenic activities also affected their natural habitat and driving most of these endemic plant species to critically endangered that foresee peril of mass extinction from this eco-region. Hence there is an urgent need for developing alternative sustainable approaches and policies to utilize this natural bioresource ensuring simultaneous conservation. Hither, arise the advent of sequencing-based transcriptomic studies significantly contributes to better understand the background of important metabolic pathways and related genes/enzymes of high-value medicinal herbs, in the absence of genomic information. The use of comparative transcriptomics in conjunction with biochemical techniques in North-Western Himalayan medicinal plants has resulted in significant advances in the identification of the molecular players involved in the production of secondary metabolic pathways over the last decade. This information could be used to further engineer metabolic pathways and breeding programs, ultimately leading to the development of in vitro systems dedicated to the production of pharmaceutically important secondary metabolites at the industrial level. Collectively, successful adoption of these approaches can certainly ensure the sustainable utilization of Himalayan bioresource by reducing the pressure on the wild population of these critically endangered medicinal herbs. This review provides novel insight as a transcriptome-based bioresource repository for the understanding of important secondary metabolic pathways genes/enzymes and metabolism of endangered high-value North-Western Himalayan medicinal herbs, so that researchers across the globe can effectively utilize this information for devising effective strategies for the production of pharmaceutically important compounds and their scale-up for sustainable usage and take a step forward in omics-based conservation genetics.

Comparative transcriptome analysis of roots, stems, and leaves of Pueraria lobata (Willd.) Ohwi: identification of genes involved in isoflavonoid biosynthesis

BACKGROUND

Pueraria lobata (Willd.) Ohwi is a valuable herb used in traditional Chinese medicine. Isoflavonoids are the major bioactive compounds in P. lobata, namely puerarin, daidzin, glycitin, genistin, daidzein, and glycitein, which have pharmacological properties of anti-cardiovascular, anti-hypertension, anti-inflammatory, and anti-arrhythmic.

METHODS

To characterize the corresponding genes of the compounds in the isoflavonoid pathway, RNA sequencing (RNA-Seq) analyses of roots, stems, and leaves of P. lobata were carried out on the BGISEQ-500 sequencing platform.

RESULTS

We identified 140,905 unigenes in total, of which 109,687 were annotated in public databases, after assembling the transcripts from all three tissues. Multiple genes encoding key enzymes, such as IF7GT and transcription factors, associated with isoflavonoid biosynthesis were identified and then further analyzed. Quantitative real-time PCR (qRT-PCR) results of some genes encoding key enzymes were consistent with our RNA-Seq analysis. Differentially expressed genes (DEGs) were determined by analyzing the expression profiles of roots compared with other tissues (leaves and stems). This analysis revealed numerous DEGs that were either uniquely expressed or up-regulated in the roots. Finally, quantitative analyses of isoflavonoid metabolites occurring in the three P. lobata tissue types were done via high-performance liquid-chromatography and tandem mass spectrometry methodology (HPLC-MS/MS). Our comprehensive transcriptome investigation substantially expands the genomic resources of P. lobata and provides valuable knowledge on both gene expression regulation and promising candidate genes that are involved in plant isoflavonoid pathways.

Transcriptome Analysis of Melocactus glaucescens (Cactaceae) Reveals Metabolic Changes During in vitro Shoot Organogenesis Induction

Melocactus glaucescens is an endangered cactus highly valued for its ornamental properties. In vitro shoot production of this species provides a sustainable alternative to overharvesting from the wild; however, its propagation could be improved if the genetic regulation underlying its developmental processes were known. The present study generated de novo transcriptome data, describing in vitro shoot organogenesis induction in M. glaucescens. Total RNA was extracted from explants before (control) and after shoot organogenesis induction (treated). A total of 14,478 unigenes (average length, 520 bases) were obtained using Illumina HiSeq 3000 (Illumina Inc., San Diego, CA, USA) sequencing and transcriptome assembly. Filtering for differential expression yielded 2,058 unigenes. Pairwise comparison of treated vs. control genes revealed that 1,241 (60.3%) unigenes exhibited no significant change, 226 (11%) were downregulated, and 591 (28.7%) were upregulated. Based on database analysis, more transcription factor families and unigenes appeared to be upregulated in the treated samples than in controls. Expression of WOUND INDUCED DEDIFFERENTIATION 1 (WIND1) and CALMODULIN (CaM) genes, both of which were upregulated in treated samples, was further validated by real-time quantitative PCR (RT-qPCR). Differences in gene expression patterns between control and treated samples indicate substantial changes in the primary and secondary metabolism of M. glaucescens after the induction of shoot organogenesis. These results help to clarify the molecular genetics and functional genomic aspects underlying propagation in the Cactaceae family.

Optimized combination methods for exploring and verifying disease-resistant transcription factors in melon

A large amount of omics data and number of bioinformatics tools has been produced. However, the methods for further exploring omics data are simple, in particular, to mine key regulatory genes, which are a priority concern in biological systems, and most of the specific functions are still unknown. First, raw data of two genotypes of melon (susceptible and resistant) were obtained by transcriptome analysis. Second, 391 transcription factors (TFs) were identified from the plant transcription factor database and cucurbit genomics database. Then, functional enrichment analysis indicated that these genes were mainly annotated in the process of transcription regulation. Third, 243 and 230 module-specific TFs were screened by weighted gene coexpression network analysis and short time series expression miner, respectively. Several TF genes, such as WRKYs and bHLHs, were regarded as key regulatory genes according to the values of significantly different modules. The coexpression network showed that these TF genes were significant correlated with resistance (R) genes, such as DRP2, RGA3, DRP1 and NB-ARC. Fourth, cis-acting element analysis illustrated that these R genes may bind to WRKY and bHLH. Finally, the expression of WRKY genes was verified by quantitative reverse transcription PCR (RT-qPCR). Phylogenetic analysis was carried out to further confirm that these TFs may play a critical role in Curcurbitaceae disease resistance. This study provides a new optimized combination strategy to explore the functions of TFs in a wide spectrum of biological processes. This strategy may also effectively predict potential relationships in the interactions of essential genes.

Transcriptional responses to water stress and recovery in a drought-tolerant fescue wild grass (Festuca ovina; Poaceae)

Water stress associated with drought-like conditions is a major factor limiting plant growth and impacts productivity of natural plant communities and agricultural crops. Molecular responses of plants to water stress have been studied most extensively in model species and crops, few of which have evolved natural drought tolerance. In the current study, we examined physiological and transcriptomic responses at multiple timepoints during increasing water stress and following initial recovery from stress in a drought-tolerant C₃ species, Festuca ovina. Results demonstrated non-linear transcriptomic changes during increasing stress, but largely linear declines in physiological measurements during this same period. Transcription factors represented approximately 12.7% of all differentially expressed genes. In total, 117 F. ovina homologs of previously identified and molecularly characterized drought-responsive plant genes were identified. This information will be valuable for further investigations of the molecular mechanisms involved in drought tolerance in C₃ plants.

Functional Markers for Precision Plant Breeding

Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.

Fine mapping and gene cloning in the post-NGS era: advances and prospects

Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genome-wide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.

Differential gene expression among three sex types reveals a MALE STERILITY 1 (CpMS1) for sex differentiation in papaya

BACKGROUND

Carica papaya is a trioecious plant species with a genetic sex-determination system defined by sex chromosomes. Under unfavorable environmental conditions male and hermaphrodite exhibit sex-reversal. Previous genomic research revealed few candidate genes for sex differentiation in this species. Nevertheless, more analysis is still needed to identify the mechanism responsible for sex flower organ development in papaya.

RESULTS

The aim of this study was to identify differentially expressed genes among male, female and hermaphrodite flowers in papaya during early (pre-meiosis) and later (post-meiosis) stages of flower development. RNA-seq was used to evaluate the expression of differentially expressed genes and RT-qPCR was used to verify the results. Putative functions of these genes were analyzed based on their homology with orthologs in other plant species and their expression patterns. We identified a Male Sterility 1 gene (CpMS1) highly up-regulated in male and hermaphrodite flower buds compared to female flower buds, which expresses in small male flower buds (3-8 mm), and that might be playing an important role in male flower organ development due to its homology to MS1 genes previously identified in other plants. This is the first study in which the sex-biased expression of genes related to tapetum development in the anther developmental pathway is being reported in papaya. Besides important transcription factors related to flower organ development and flowering time regulation, we identified differential expression of genes that are known to participate in ABA, ROS and auxin signaling pathways (ABA-8-hydroxylases, AIL5, UPBEAT 1, VAN3-binding protein).

CONCLUSIONS

CpMS1 was expressed in papaya male and hermaphrodite flowers at early stages, suggesting that this gene might participate in male flower organ development processes, nevertheless, this gene cannot be considered a sex-determination gene. Due to its homology with other plant MS1 proteins and its expression pattern, we hypothesize that this gene participates in anther development processes, like tapetum and pollen development, downstream gender specification. Further gene functional characterization studies in papaya are required to confirm this hypothesis. The role of ABA and ROS signaling pathways in papaya flower development needs to be further explored as well.

Transcriptome Landscape Variation in the Genus Thymus

Among the Lamiaceae family, the genus Thymus is an economically important genera due to its medicinal and aromatic properties. Most Thymus molecular research has focused on the determining the phylogenetic relationships between different species, but no published work has focused on the evolution of the transcriptome across the genus to elucidate genes involved in terpenoid biosynthesis. Hence, in this study, the transcriptomes of five different Thymus species were generated and analyzed to mine putative genes involved in thymol and carvacrol biosynthesis. High-throughput sequencing produced ~43 million high-quality reads per sample, which were assembled de novo using several tools, then further subjected to a quality evaluation. The best assembly for each species was used as queries to search within the UniProt, KEGG (Kyoto Encyclopedia of Genes and Genomes), COG (Clusters of Orthologous Groups) and TF (Transcription Factors) databases. Mining the transcriptomes resulted in the identification of 592 single-copy orthogroups used for phylogenetic analysis. The data showed strongly support a close genetic relationship between Thymus vulgaris and Thymus daenensis. Additionally, this study dates the speciation events between 1.5–2.1 and 9–10.2 MYA according to different methodologies. Our study provides a global overview of genes related to the terpenoid pathway in Thymus, and can help establish an understanding of the relationship that exists among Thymus species.

De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway

Oroxylum indicum (L.) Kurz is a medicinally important and rare tree species of the family Bignoniaceae. It is rich in flavonoid content and its mature roots are extensively used in Ayurvedic formulations. O. indicum specific flavonoids like oroxylin B, prunetin and oroxindin possess antibacterial, antiproliferative, antioxidant and anticancerous properties, signifying its importance in modern medicine. In the present study, de novo transcriptome analysis of O. indicum root was performed to elucidate the genes involved in flavonoid metabolism. A total of 24,625,398 high quality reads were assembled into 121,286 transcripts with N50 value 1783. The BLASTx search of 81,002 clustered transcripts against Viridiplantae Uniprot database led to annotation of 46,517 transcripts. Furthermore, Gene ontology (GO) revealed that 34,231 transcripts mapped to 3049 GO terms and KEGG analysis demonstrated that 4570 transcripts plausibly involved in 132 biosynthetic pathways. The transcriptome data indicated that cinnamyl-alcohol dehydrogenase (OinCAD) was abundant in phenylpropanoid pathway genes while; naringenin chalcone synthase (OinCHS), flavone synthase (OinFNS) and flavonoid 3', 5'-methyltransferase (OinF35 MT) were abundant in flavonoid, isoflavonoid, flavone and flavonol biosynthesis pathways, respectively. Transcription factor analysis demonstrated the abundance of MYB, bHLH and WD40 transcription factor families, which regulate the flavonoid biosynthesis. Flavonoid pathway genes displayed differential expression in young and old roots of O. indicum. The transcriptome led to the identification of 31 diverse full length Cytochrome P450 (CYP450) genes which may be involved in biosynthesis of specialized metabolites and flavonoids like baicalein and baicalin. Thus, the information obtained in this study will be a valuable tool for identifying genes and developing system biology approaches for in vitro synthesis of specialized O. indicum metabolites.

Legume genetic resources and transcriptome dynamics under abiotic stress conditions

Grain legumes are an important source of nutrition and income for billions of consumers and farmers around the world. However, the low productivity of new legume varieties, due to the limited genetic diversity available for legume breeding programmes and poor policymaker support, combined with an increasingly unpredictable global climate is resulting in a large gap between current yields and the increasing demand for legumes as food. Hence, there is a need for novel approaches to develop new high-yielding legume cultivars that are able to cope with a range of environmental stressors. Next-generation technologies are providing the tools that could enable the more rapid and cost-effective genomic and transcriptomic studies for most major crops, allowing the identification of key functional and regulatory genes involved in abiotic stress resistance. In this review, we provide an overview of the recent achievements regarding abiotic stress resistance in a wide range of legume crops and highlight the transcriptomic and miRNA approaches that have been used. In addition, we critically evaluate the availability and importance of legume genetic resources with desirable abiotic stress resistance traits.

Comparison of Gene Expression Profiles in Nonmodel Eukaryotic Organisms with RNA-Seq

With recent advances of next-generation sequencing technology, RNA-Sequencing (RNA-Seq) has emerged as a powerful approach for the transcriptomic profiling. RNA-Seq has been used in almost every field of biological studies, and has greatly extended our view of transcriptomic complexity in different species. In particular, for nonmodel organisms which are usually without high-quality reference genomes, the de novo transcriptome assembly from RNA-Seq data provides a solution for their comparative transcriptomic study. In this chapter, we focus on the comparative transcriptomic analysis of nonmodel organisms. Two analysis strategies (without or with reference genome) are described step-by-step, with the differentially expressed genes explored.

Molecular insights into photosynthesis and carbohydrate metabolism in Jatropha curcas grown under elevated CO2 using transcriptome sequencing and assembly

Jatropha curcas L. (Family - Euphorbiaceae) is a perennial tree of special interest due to its potential as a biofuel plant with high carbon sequestration. In this study, physiological investigations coupled with transcriptomics in relation to photosynthesis were evaluated in Jatropha grown under ambient (395 ppm) and elevated (550 ppm) CO2 atmosphere. Morphophysiological analysis revealed that Jatropha sustained enhanced photosynthesis during its growth under elevated CO2 for one year which might be linked to improved CO2 assimilation physiology and enhanced sink activity. We sequenced and analyzed the leaf transcriptome of Jatropha after one year of growth in both conditions using Illumina HiSeq platform. After optimized assembly, a total of 69,581 unigenes were generated. The differential gene expression (DGE) analysis revealed 3013 transcripts differentially regulated in elevated CO2 conditions. The photosynthesis regulatory genes were analysed for temporal expression patterns at four different growth phases which highlighted probable events contributing to enhanced growth and photosynthetic capacity including increased reducing power, starch synthesis and sucrose mobilization under elevated CO2. Overall, our data on physiological and transcriptomic analyses suggest an optimal resource allocation to the available and developing sink organs thereby sustaining improved photosynthetic rates during long-term growth of Jatropha under CO2 enriched environment.

Unravelling a stearidonic acid-rich triacylglycerol biosynthetic pathway in the developing seeds of Buglossoides arvensis: A transcriptomic landscape

Buglossoides arvensis is an emerging oilseed crop that is rich in stearidonic acid (SDA) and has several potential applications in human health and nutrition. The molecular basis of SDA biosynthesis in this plant remains unknown due to lack of genomic information. To unravel key genes involved in SDA-rich triacylglycerol (TAG) biosynthesis, we performed transcriptome sequencing of pooled mRNA from five different developmental stages of B. arvensis seeds using Illumina NextSeq platform. De novo transcriptome assembly generated 102,888 clustered transcripts from 39.83 million high-quality reads. Of these, 62.1% and 55.54% of transcripts were functionally annotated using Uniprot-Viridiplantae and KOG databases, respectively. A total of 10,021 SSR-containing sequences were identified using the MISA tool. Deep mining of transcriptome assembly using in silico tools led to the identification of genes involved in fatty acid and TAG biosynthesis. Expression profiling of 17 key transcripts involved in fatty acid desaturation and TAG biosynthesis showed expression patterns specific to the development stage that positively correlated with polyunsaturated fatty acid accumulation in the developing seeds. This first comprehensive transcriptome analysis provides the basis for future research on understanding molecular mechanisms of SDA-rich TAG accumulation in B. arvensis and aids in biotechnological production of SDA in other oilseed crops.

Integration of omics approaches to understand oil/protein content during seed development in oilseed crops

Oilseed crops, especially soybean (Glycine max) and canola/rapeseed (Brassica napus), produce seeds that are rich in both proteins and oils and that are major sources of energy and nutrition worldwide. Most of the nutritional content in the seed is accumulated in the embryo during the seed filling stages of seed development. Understanding the metabolic pathways that are active during seed filling and how they are regulated are essential prerequisites to crop improvement. In this review, we summarize various omics studies of soybean and canola/rapeseed during seed filling, with emphasis on oil and protein traits, to gain a systems-level understanding of seed development. Currently, most (80-85%) of the soybean and rapeseed reference genomes have been sequenced (950 and 850 megabases, respectively). Parallel to these efforts, extensive omics datasets from different seed filling stages have become available. Transcriptome and proteome studies have detected preponderance of starch metabolism and glycolysis enzymes to be the possible cause of higher oil in B. napus compared to other crops. Small RNAome studies performed during the seed filling stages have revealed miRNA-mediated regulation of transcription factors, with the suggestion that this interaction could be responsible for transitioning the seeds from embryogenesis to maturation. In addition, progress made in dissecting the regulation of de novo fatty acid synthesis and protein storage pathways is described. Advances in high-throughput omics and comprehensive tissue-specific analyses make this an exciting time to attempt knowledge-driven investigation of complex regulatory pathways.

Generation and Characterisation of a Reference Transcriptome for Lentil (Lens culinaris Medik.)

RNA-Seq using second-generation sequencing technologies permits generation of a reference unigene set for a given species, in the absence of a well-annotated genome sequence, supporting functional genomics studies, gene characterisation and detailed expression analysis for specific morphophysiological or environmental stress response traits. A reference unigene set for lentil has been developed, consisting of 58,986 contigs and scaffolds with an N50 length of 1719 bp. Comparison to gene complements from related species, reference protein databases, previously published lentil transcriptomes and a draft genome sequence validated the current dataset in terms of degree of completeness and utility. A large proportion (98%) of unigenes were expressed in more than one tissue, at varying levels. Candidate genes associated with mechanisms of tolerance to both boron toxicity and time of flowering were identified, which can eventually be used for the development of gene-based markers. This study has provided a comprehensive, assembled and annotated reference gene set for lentil that can be used for multiple applications, permitting identification of genes for pathway-specific expression analysis, genetic modification approaches, development of resources for genotypic analysis, and assistance in the annotation of a future lentil genome sequence.

Transcriptome and metabolome analysis in shoot and root of Valeriana fauriei

BACKGROUND

Valeriana fauriei is commonly used in the treatment of cardiovascular diseases in many countries. Several constituents with various pharmacological properties are present in the roots of Valeriana species. Although many researches on V. fauriei have been done since a long time, further studies in the discipline make a limit due to inadequate genomic information. Hence, Illumina HiSeq 2500 system was conducted to obtain the transcriptome data from shoot and root of V. fauriei.

RESULTS

A total of 97,595 unigenes were noticed from 346,771,454 raw reads after preprocessing and assembly. Of these, 47,760 unigens were annotated with Uniprot BLAST hits and mapped to COG, GO and KEGG pathway. Also, 70,013 and 88,827 transcripts were expressed in root and shoot of V. fauriei, respectively. Among the secondary metabolite biosynthesis, terpenoid backbone and phenylpropanoid biosynthesis were large groups, where transcripts was involved. To characterize the molecular basis of terpenoid, carotenoid, and phenylpropanoid biosynthesis, the levels of transcription were determined by qRT-PCR. Also, secondary metabolites content were measured using GC/MS and HPLC analysis for that gene expression correlated with its accumulation respectively between shoot and root of V. fauriei.

CONCLUSIONS

We have identified the transcriptome using Illumina HiSeq system in shoot and root of V. fauriei. Also, we have demonstrated gene expressions associated with secondary metabolism such as terpenoid, carotenoid, and phenylpropanoid.

Full-length de novo assembly of RNA-seq data in pea (Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species

Next-generation sequencing technologies allow an almost exhaustive survey of the transcriptome, even in species with no available genome sequence. To produce a Unigene set representing most of the expressed genes of pea, 20 cDNA libraries produced from various plant tissues harvested at various developmental stages from plants grown under contrasting nitrogen conditions were sequenced. Around one billion reads and 100 Gb of sequence were de novo assembled. Following several steps of redundancy reduction, 46 099 contigs with N50 length of 1667 nt were identified. These constitute the 'Caméor' Unigene set. The high depth of sequencing allowed identification of rare transcripts and detected expression for approximately 80% of contigs in each library. The Unigene set is now available online (http://bios.dijon.inra.fr/FATAL/cgi/pscam.cgi), allowing (i) searches for pea orthologs of candidate genes based on gene sequences from other species, or based on annotation, (ii) determination of transcript expression patterns using various metrics, (iii) identification of uncharacterized genes with interesting patterns of expression, and (iv) comparison of gene ontology pathways between tissues. This resource has allowed identification of the pea orthologs of major nodulation genes characterized in recent years in model species, as a major step towards deciphering unresolved pea nodulation phenotypes. In addition to a remarkable conservation of the early transcriptome nodulation apparatus between pea and Medicago truncatula, some specific features were highlighted. The resource provides a reference for the pea exome, and will facilitate transcriptome and proteome approaches as well as SNP discovery in pea.

Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

Elms, especially Ulmus minor and U. americana, are carrying out a hard battle against Dutch elm disease (DED). This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and conservation programmes have identified a reduced number of DED tolerant genotypes. In this study, three U. minor genotypes with contrasted levels of tolerance to DED were exposed to several biotic and abiotic stresses in order to (i) obtain a de novo assembled transcriptome of U. minor using 454 pyrosequencing, (ii) perform a functional annotation of the assembled transcriptome, (iii) identify genes potentially involved in the molecular response to environmental stress, and (iv) develop gene-based markers to support breeding programmes. A total of 58,429 putative unigenes were identified after assembly and filtering of the transcriptome. 32,152 of these unigenes showed homology with proteins identified in the genome from the most common plant model species. Well-known family proteins and transcription factors involved in abiotic, biotic or both stresses were identified after functional annotation. A total of 30,693 polymorphisms were identified in 7,125 isotigs, a large number of them corresponding to single nucleotide polymorphisms (SNPs; 27,359). In a subset randomly selected for validation, 87% of the SNPs were confirmed. The material generated may be valuable for future Ulmus gene expression, population genomics and association genetics studies, especially taking into account the scarce molecular information available for this genus and the great impact that DED has on elm populations.

Transcriptomic analysis of the primary roots of Alhagi sparsifolia in response to water stress

BACKGROUND

Alhagi sparsifolia is a typical desert phreatophyte and has evolved to withstand extreme dry, cold and hot weather. While A. sparsifolia represents an ideal model to study the molecular mechanism of plant adaption to abiotic stress, no research has been done in this aspect to date. Here we took advantage of Illumina platform to survey transcriptome in primary roots of A. sparsifolia under water stress conditions in aim to facilitate the exploration of its genetic basis for drought tolerance.

METHODOLOGY AND PRINCIPAL FINDINGS

We sequenced four primary roots samples individually collected at 0, 6, 24 and 30h from the A. sparsifolia seedlings in the course of 24h of water stress following 6h of rehydration. The resulting 38,763,230, 67,511,150, 49,259,804 and 54,744,906 clean reads were pooled and assembled into 33,255 unigenes with an average length of 1,057 bp. All-unigenes were subjected to functional annotation by searching against the public databases. Based on the established transcriptome database, we further evaluated the gene expression profiles in the four different primary roots samples, and identified numbers of differently expressed genes (DEGs) reflecting the early response to water stress (6h vs. 0h), the late response to water stress (24h vs. 0h) and the response to post water stress rehydration (30h vs. 24h). Moreover, the DEGs specifically regulated at 6, 24 and 30h were captured in order to depict the dynamic changes of gene expression during water stress and subsequent rehydration. Functional categorization of the DEGs indicated the activation of oxidoreductase system, and particularly emphasized the significance of the 'Glutathione metabolism pathway' in response to water stress.

CONCLUSIONS

This is the first description of the genetic makeup of A. sparsifolia, thus providing a substantial contribution to the sequence resources for this species. The identified DEGs offer a deep insight into the molecular mechanism of A. sparsifolia in response to water stress, and merit further investigation.

Transcriptome sequencing and comparative analysis reveal long-term flowing mechanisms in Hevea brasiliensis latex

BACKGROUND

The rubber tree, Hevea brasiliensis, is a major commercial source of natural rubber. Increasing the rubber yield of rubber trees is a very serious problem since the demands for high quality rubber materials are great. Establishment of a tapping system is based on an estimate of tapping intensity from the rubber tree. Latex flowing time is one of the most critical factors that determine the rubber yield. Long-term flow is a type of phenomenon of the rubber tree latex with longer flowing time than normal latex flow, and is always caused by intensive tapping. Thus, transcriptome and expression profiling data for long-term flowing latex (LFL) are needed as an important resource to identify genes and to better understand the biological mechanisms of latex flow in rubber trees.

RESULTS

The transcripts were sequenced using the Illumina sequencing platform. After cleaning, quality checks and sequencing, 98,697 transcripts and 38,584 unigenes were assembled with the mean size of 1437.31bp and 923.86bp, respectively. In BLAST searches of our database against public databases, 65.17% (25,147) of the unigenes were annotated with gene descriptions, conserved protein domains, or gene ontology terms. Functional categorization further revealed 853 individual unigenes related to long-term flow. According to KEGG classification, the clusters for "cysteine and methionine metabolism", "energy", "oxidative phosphorylation", "terpenoid backbone biosynthesis", "plant hormone signal transduction" and "copper, potassium transporter" were significantly enriched metabolic pathways.

CONCLUSIONS

We conducted high-resolution transcriptome profiling related to LFL in H. brasiliensis. The research facilitates further studies on gene discovery and on the molecular mechanisms related to the estimation of tapping intensity and prolonging latex flowing time. We concluded that it was necessary to improve energy supplies for intensive tapping and the copper ion content of rubber tree latex could be considered as a standard to estimate tapping intensity.

Legume genomics: understanding biology through DNA and RNA sequencing

BACKGROUND

The legume family (Leguminosae) consists of approx. 17 000 species. A few of these species, including, but not limited to, Phaseolus vulgaris, Cicer arietinum and Cajanus cajan, are important dietary components, providing protein for approx. 300 million people worldwide. Additional species, including soybean (Glycine max) and alfalfa (Medicago sativa), are important crops utilized mainly in animal feed. In addition, legumes are important contributors to biological nitrogen, forming symbiotic relationships with rhizobia to fix atmospheric N2 and providing up to 30 % of available nitrogen for the next season of crops. The application of high-throughput genomic technologies including genome sequencing projects, genome re-sequencing (DNA-seq) and transcriptome sequencing (RNA-seq) by the legume research community has provided major insights into genome evolution, genomic architecture and domestication.

SCOPE AND CONCLUSIONS

This review presents an overview of the current state of legume genomics and explores the role that next-generation sequencing technologies play in advancing legume genomics. The adoption of next-generation sequencing and implementation of associated bioinformatic tools has allowed researchers to turn each species of interest into their own model organism. To illustrate the power of next-generation sequencing, an in-depth overview of the transcriptomes of both soybean and white lupin (Lupinus albus) is provided. The soybean transcriptome focuses on analysing seed development in two near-isogenic lines, examining the role of transporters, oil biosynthesis and nitrogen utilization. The white lupin transcriptome analysis examines how phosphate deficiency alters gene expression patterns, inducing the formation of cluster roots. Such studies illustrate the power of next-generation sequencing and bioinformatic analyses in elucidating the gene networks underlying biological processes.

Integrating de novo transcriptome assembly and cloning to obtain chicken Ovocleidin-17 full-length cDNA

Efficiently obtaining full-length cDNA for a target gene is the key step for functional studies and probing genetic variations. However, almost all sequenced domestic animal genomes are not ‘finished’. Many functionally important genes are located in these gapped regions. It can be difficult to obtain full-length cDNA for which only partial amino acid/EST sequences exist. In this study we report a general pipeline to obtain full-length cDNA, and illustrate this approach for one important gene (Ovocleidin-17, OC-17) that is associated with chicken eggshell biomineralization. Chicken OC-17 is one of the best candidates to control and regulate the deposition of calcium carbonate in the calcified eggshell layer. OC-17 protein has been purified, sequenced, and has had its three-dimensional structure solved. However, researchers still cannot conduct OC-17 mRNA related studies because the mRNA sequence is unknown and the gene is absent from the current chicken genome. We used RNA-Seq to obtain the entire transcriptome of the adult hen uterus, and then conducted de novo transcriptome assembling with bioinformatics analysis to obtain candidate OC-17 transcripts. Based on this sequence, we used RACE and PCR cloning methods to successfully obtain the full-length OC-17 cDNA. Temporal and spatial OC-17 mRNA expression analyses were also performed to demonstrate that OC-17 is predominantly expressed in the adult hen uterus during the laying cycle and barely at immature developmental stages. Differential uterine expression of OC-17 was observed in hens laying eggs with weak versus strong eggshell, confirming its important role in the regulation of eggshell mineralization and providing a new tool for genetic selection for eggshell quality parameters. This study is the first one to report the full-length OC-17 cDNA sequence, and builds a foundation for OC-17 mRNA related studies. We provide a general method for biologists experiencing difficulty in obtaining candidate gene full-length cDNA sequences.