De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants

Study on the role of calcium channel protein TRPV4 in the inflammatory pathway of type 2 diabetic adipose tissue based on gene databases

BACKGROUND

Chronic inflammation of adipose tissue may be one of the key factors contributing to the development of insulin resistance in T2DM adipose tissue. Transient receptor potential vanilloid type 4 (TRPV4) can be involved in a variety of cellular inflammatory responses. In this study, we evaluated the role of TRPV4 channelin in the T2DM adipose tissue inflammatory pathway.

METHODS

Based on the gene expression profiling data of the public database, bioinformatics methods were used to screen the target gene population of the TRPV4 channel protein involved in the regulation of T2DM fat cells. A mature adipocyte model was constructed to verify the expression level of target genes and to evaluate the regulatory effect of TRPV4 channel inhibition on target genes of inflammation-related pathways.

RESULTS

In shTRPV4 adipocytes, 144 genes with downregulation expression were screened, a PPI network was constructed and a core module containing 15 genes was screened out, and the core genes were mainly enriched in the Toll-like receptor signaling pathway through enrichment analysis. Constructing a mature adipocyte model found that the TRPV4 inhibitor HC067047 inhibited the effect of upregulation of the expression level of the relevant gene in the signaling pathway.

CONCLUSIONS

Our findings suggest that the expression of highly expressed pro-inflammatory cytokines and chemokines in T2DM adipose tissue decreases after inhibiting the expression of TRPV4 in adipocytes, suggesting that TRPV4 may become a potential drug target for the treatment of T2DM.

Transcriptome architecture reveals genetic networks of bolting regulation in spinach

BACKGROUND

Bolting refers to the early flowering stem production on agricultural and horticultural crops before harvesting. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components, which cause a large reduction in the quality and productivity of vegetable crops like spinach. However, little is known about the signaling pathways and molecular functions involved in bolting mechanisms in spinach. The genetic information regarding the transition from vegetative growth to the reproductive stage in spinach would represent an advantage to regulate bolting time and improvement of resistant cultivars to minimize performance loss.

RESULTS

To investigate the key genes and their genetic networks controlling spinach bolting, we performed RNA-seq analysis on early bolting accession Kashan and late-bolting accession Viroflay at both vegetative and reproductive stages and found a significant number of differentially expressed genes (DEGs) ranging from 195 to 1230 in different comparisons. These genes were mainly associated with the signaling pathways of vernalization, photoperiod/circadian clock, gibberellin, autonomous, and aging pathways. Gene ontology analysis uncovered terms associated with carbohydrate metabolism, and detailed analysis of expression patterns for genes of Fructose-1, 6-bisphosphate aldolase, TREHALOSE-6-PHOSPHATE SYNTHASE 1, FLOWERING PROMOTING FACTOR 1, EARLY FLOWERING, GIGANTEA, and MADS-box proteins revealed their potential roles in the initiating or delaying of bolting.

CONCLUSION

This study is the first report on identifying bolting and flowering-related genes based on transcriptome sequencing in spinach, which provides insight into bolting control and can be useful for molecular breeding programs and further study in the regulation of the genetic mechanisms related to bolting in other vegetable crops.

Overexpression of the Transcription Factor AtLEC1 Significantly Improved the Lipid Content of Chlorella ellipsoidea

Microalgae are considered to be a highly promising source for the production of biodiesel. However, the regulatory mechanism governing lipid biosynthesis has not been fully elucidated to date, and the improvement of lipid accumulation in microalgae is essential for the effective production of biodiesel. In this study, LEAFY COTYLEDON1 (LEC1) from Arabidopsis thaliana, a transcription factor (TF) that affects lipid content, was transferred into Chlorella ellipsoidea. Compared with wild-type (WT) strains, the total fatty acid content and total lipid content of AtLEC1 transgenic strains were significantly increased by 24.20–32.65 and 22.14–29.91%, respectively, under mixotrophic culture conditions and increased by 24.4–28.87 and 21.69–30.45%, respectively, under autotrophic conditions, while the protein content of the transgenic strains was significantly decreased by 18.23–21.44 and 12.28–18.66%, respectively, under mixotrophic and autotrophic conditions. Fortunately, the lipid and protein content variation did not affect the growth rate and biomass of transgenic strains under the two culture conditions. According to the transcriptomic data, the expression of 924 genes was significantly changed in the transgenic strain (LEC1-1). Of the 924 genes, 360 were upregulated, and 564 were downregulated. Based on qRT-PCR results, the expression profiles of key genes in the lipid synthesis pathway, such as ACCase, GPDH, PDAT1, and DGAT1, were significantly changed. By comparing the differentially expressed genes (DEGs) regulated by AtLEC1 in C. ellipsoidea and Arabidopsis, we observed that approximately 59% (95/160) of the genes related to lipid metabolism were upregulated in AtLEC1 transgenic Chlorella. Our research provides a means of increasing lipid content by introducing exogenous TF and presents a possible mechanism of AtLEC1 regulation of lipid accumulation in C. ellipsoidea.

Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana

Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.

Transcriptome landscape of Rafflesia cantleyi floral buds reveals insights into the roles of transcription factors and phytohormones in flower development

Rafflesia possesses unique biological features and known primarily for producing the world’s largest and existing as a single flower. However, to date, little is known about key regulators participating in Rafflesia flower development. In order to further understand the molecular mechanism that regulates Rafflesia cantleyi flower development, RNA-seq data from three developmental stages of floral bud, representing the floral organ primordia initiation, floral organ differentiation, and floral bud outgrowth, were analysed. A total of 89,890 transcripts were assembled of which up to 35% could be annotated based on homology search. Advanced transcriptome analysis using K-mean clustering on the differentially expressed genes (DEGs) was able to identify 12 expression clusters that reflect major trends and key transitional states, which correlate to specific developmental stages. Through this, comparative gene expression analysis of different floral bud stages identified various transcription factors related to flower development. The members of WRKY, NAC, bHLH, and MYB families are the most represented among the DEGs, suggesting their important function in flower development. Furthermore, pathway enrichment analysis also revealed DEGs that are involved in various phytohormone signal transduction events such as auxin and auxin transport, cytokinin and gibberellin biosynthesis. Results of this study imply that transcription factors and phytohormone signalling pathways play major role in Rafflesia floral bud development. This study provides an invaluable resource for molecular studies of the flower development process in Rafflesia and other plant species.

Functional network analysis of gene-phenotype connectivity based on pioglitazone

Pioglitazone, a type of insulin sensitizer, serves as an effective anti-hyperglycemic drug. The mechanism of action of pioglitazone is through the activation of the peroxisome proliferator-activated receptor (PPAR), which results in enhanced insulin sensitivity of peripheral tissues and the liver, causing a reduction in the production and output of liver sugar. It has been reported that pioglitazone increases the risk of bladder cancer, but the underlying mechanisms have remained elusive. It was hypothesized that modulation of pioglitazone activity may be predicted by systematically analyzing data published on drugs. This hypothesis was tested by querying the Drug-Target Interactome (DTome), a web-based tool that provides open-source data from three databases (DrugBank, PharmGSK and Protein Interaction Network analysis). A total of 4 direct target proteins (DTPs) and further DTP-associated genes were identified for pioglitazone. Subsequently, an enrichment analysis was performed for all DTP-associated genes using Cytoscape software. A total of 12 Kyoto Encyclopedia of Genes and Genomes pathways were identified, including the 'PPAR signaling pathway' as well as 'pathways in cancer' as relevant pathways. Functional network analysis was able to identify direct and indirect target genes of pioglitazone, resulting in a list of possible biological functions based on published databases. Furthermore, Kaplan-Meier analysis indicated that pioglitazone may affect the survival rate of patients with bladder cancer through genetic alterations (missense mutation, truncating mutation, amplification, deep deletion and fusion) of target genes. Therefore, it should be used with caution.

Comparative Transcriptome Analysis of Developing Seeds and Silique Wall Reveals Dynamic Transcription Networks for Effective Oil Production in Brassica napus L

Vegetable oil is an essential constituent of the human diet and renewable raw material for industrial applications. Enhancing oil production by increasing seed oil content in oil crops is the most viable, environmentally friendly, and sustainable approach to meet the continuous demand for the supply of vegetable oil globally. An in-depth understanding of the gene networks involved in oil biosynthesis during seed development is a prerequisite for breeding high-oil-content varieties. Rapeseed (Brassica napus) is one of the most important oil crops cultivated on multiple continents, contributing more than 15% of the world’s edible oil supply. To understand the phasic nature of oil biosynthesis and the dynamic regulation of key pathways for effective oil accumulation in B. napus, comparative transcriptomic profiling was performed with developing seeds and silique wall (SW) tissues of two contrasting inbred lines with ~13% difference in seed oil content. Differentially expressed genes (DEGs) between high- and low-oil content lines were identified across six key developmental stages, and gene enrichment analysis revealed that genes related to photosynthesis, metabolism, carbohydrates, lipids, phytohormones, transporters, and triacylglycerol and fatty acid synthesis tended to be upregulated in the high-oil-content line. Differentially regulated DEG patterns were revealed for the control of metabolite and photosynthate production in SW and oil biosynthesis and accumulation in seeds. Quantitative assays of carbohydrates and hormones during seed development together with gene expression profiling of relevant pathways revealed their fundamental effects on effective oil accumulation. Our results thus provide insights into the molecular basis of high seed oil content (SOC) and a new direction for developing high-SOC rapeseed and other oil crops.

Transcriptome analysis and identification of genes associated with flower development in Rhododendron pulchrum Sweet (Ericaceae)

Flowering process is essential for plant development. However, the molecular mechanisms driving flower development of ornamental woody Rhododendron pulchrum Sweet are difficult to elucidate due to the lack of genomic data. In this research, high-throughput sequencing and comparative transcriptome analyses of R. pulchrum flowers collected at three key stages were performed: floral bud stage, early flowering stage, and full-flowering stage. Furthermore, expression of genes involved in flower development was also validated with quantitative real-time PCR (qRT-PCR). RNA-seq yielded 96,350,697 bp of clean reads, which were assembled into 98,610 unigenes with an average length of 717 bp. 58,279 (59.10%) unigenes could be annotated, including 324 major unigenes associated with floral development. In addition, ten modules (20,443 mRNAs) were dissected in the co-expression network. Especially, Flowering Locus (FLC) and Flowering Locus T (FT) were co-expressed. 9493 differentially expressed genes (DEGs) were scanned among three stages, and most DEGs existed between flower bud stage and early flowering stage. In particular, 79 DGEs associated with flowering process were enriched in 28 GO terms. Moreover, the expression levels of MYC2, EIN3, and ARR-B were all lowest at early flowering stage, while transcripts of MYC2, TIR1, CYCD3, COL-1, and EIN3 were all peaked at flower bud stage. Transcriptome profile presented here will benefit deep insights into molecular mechanism underlying R. pulchrum flowering process.

Transcriptome analysis of abscisic acid induced 20E regulation in suspension Ajuga lobata cells

Ajuga lobata D. Don is a medicinal plant rich in 20-hydroxyecdysone (20E), alkaloids, and other active substances. In this study, the cell suspension was incubated for 7 days, followed by the analysis on the effects of abscisic acid (ABA) on the regulation of 20E synthesis. Then A. lobata suspension cells treated with 0.15 mg/l ABA were used as material, with the Illumina technology applied for transcriptome sequencing. Digital analysis on the gene expression profile was carried out on ABA treated and control samples, respectively. Finally, transcriptomics was applied to assess the molecular response of A. lobata induced by ABA through applying transcriptomics by evaluating differentially expressed genes. The results suggested that ABA promoted 20E accumulation, while longer processing time caused cell browning. A total of 154 genes were significantly regulated after ABA treatment, with 99 up-regulated and 55 down-regulated, respectively. In addition to 20E-related pathways, the genes belonged to the ko00900 (terpenoid backbone biosynthesis) pathway (six differentially expressed genes [DEGs]), ko00100 (steroid biosynthesis) pathway (four DEGs), and ko00140 (steroid hormone biosynthesis) pathway (six DEGs). Providing a better understanding of the 20E biosynthetic pathway and its regulation, in particular in plants, this study is necessary.

Revised Phylogeny of the Cellulose Synthase Gene Superfamily: Insights into Cell Wall Evolution

Cell walls are crucial for the integrity and function of all land plants and are of central importance in human health, livestock production, and as a source of renewable bioenergy. Many enzymes that mediate the biosynthesis of cell wall polysaccharides are encoded by members of the large cellulose synthase (CesA) gene superfamily. Here, we analyzed 29 sequenced genomes and 17 transcriptomes to revise the phylogeny of the CesA gene superfamily in angiosperms. Our results identify ancestral gene clusters that predate the monocot-eudicot divergence and reveal several novel evolutionary observations, including the expansion of the Poaceae-specific cellulose synthase-like CslF family to the graminids and restiids and the characterization of a previously unreported eudicot lineage, CslM, that forms a reciprocally monophyletic eudicot-monocot grouping with the CslJ clade. The CslM lineage is widely distributed in eudicots, and the CslJ clade, which was thought previously to be restricted to the Poales, is widely distributed in monocots. Our analyses show that some members of the CslJ lineage, but not the newly identified CslM genes, are capable of directing (1,3;1,4)-β-glucan biosynthesis, which, contrary to current dogma, is not restricted to Poaceae.

Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae)

BACKGROUND

Flower size varies dramatically across angiosperms, representing innovations over the course of >130 million years of evolution and contributing substantially to relationships with pollinators. However, the genetic underpinning of flower size is not well understood. Saltugilia (Polemoniaceae) provides an excellent non-model system for extending the genetic study of flower size to interspecific differences that coincide with variation in pollinators.

RESULTS

Using targeted gene capture methods, we infer phylogenetic relationships among all members of Saltugilia to provide a framework for investigating the genetic control of flower size differences via RNA-Seq de novo assembly. Nuclear concatenation and species tree inference methods provide congruent topologies. The inferred evolutionary trajectory of flower size is from small flowers to larger flowers. We identified 4 to 10,368 transcripts that are differentially expressed during flower development, with many unigenes associated with cell wall modification and components of the auxin and gibberellin pathways.

CONCLUSIONS

Saltugilia is an excellent model for investigating covarying floral and pollinator evolution. Four candidate genes from model systems (BIG BROTHER, BIG PETAL, GASA, and LONGIFOLIA) show differential expression during development of flowers in Saltugilia, and four other genes (FLOWERING-PROMOTING FACTOR 1, PECTINESTERASE, POLYGALACTURONASE, and SUCROSE SYNTHASE) fit into hypothesized organ size pathways. Together, these gene sets provide a strong foundation for future functional studies to determine their roles in specifying interspecific differences in flower size.

Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

BACKGROUND

Flowers have an amazingly diverse display of colors and shapes, and these characteristics often vary significantly among closely related species. The evolution of diverse floral form can be thought of as an adaptive response to pollination and reproduction, but it can also be seen through the lens of morphological and developmental constraints. To explore these interactions, we use RNA-seq across species and development to investigate gene expression and sequence evolution as they relate to the evolution of the diverse flowers in a group of Neotropical plants native to Mexico-magic flowers (Achimenes, Gesneriaceae).

RESULTS

The assembled transcriptomes contain between 29,000 and 42,000 genes expressed during development. We combine sequence orthology and coexpression clustering with analyses of protein evolution to identify candidate genes for roles in floral form evolution. Over 25% of transcripts captured were distinctive to Achimenes and overrepresented by genes involved in transcription factor activity. Using a model-based clustering approach we find dynamic, temporal patterns of gene expression among species. Selection tests provide evidence of positive selection in several genes with roles in pigment production, flowering time, and morphology. Combining these approaches to explore genes related to flower color and flower shape, we find distinct patterns that correspond to transitions of floral form among Achimenes species.

CONCLUSIONS

The floral transcriptomes developed from four species of Achimenes provide insight into the mechanisms involved in the evolution of diverse floral form among closely related species with different pollinators. We identified several candidate genes that will serve as an important and useful resource for future research. High conservation of sequence structure, patterns of gene coexpression, and detection of positive selection acting on few genes suggests that large phenotypic differences in floral form may be caused by genetic differences in a small set of genes. Our characterized floral transcriptomes provided here should facilitate further analyses into the genomics of flower development and the mechanisms underlying the evolution of diverse flowers in Achimenes and other Neotropical Gesneriaceae.

Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences

The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework. Here we compare ten de novo-assembled transcriptomes representing the major lineages of the angiosperm genus Cornus (dogwood) and relevant outgroups using a customized pipeline for analyses. Using three distinct approaches, molecular dating of orthologous genes, analyses of the distribution of synonymous substitutions between paralogous genes, and examination of substitution rates through time, we detected a shared WGD event in the late Cretaceous across all taxa sampled. The inferred doubling event coincides temporally with the paleoclimatic changes associated with the initial divergence of the genus into three major lineages. Analyses also showed an acceleration of rates of molecular evolution after WGD. The highest rates of molecular evolution were observed in the transcriptome of the herbaceous lineage, C. canadensis, a species commonly found at higher latitudes, including the Arctic. Our study demonstrates the value of transcriptome data for understanding genome evolution in closely related species. The results suggest dramatic increase in sea surface temperature in the late Cretaceous may have contributed to the evolution and diversification of flowering plants.

Transcriptome Analysis of Hamelia patens (Rubiaceae) Anthers Reveals Candidate Genes for Tapetum and Pollen Wall Development

Studies of the anther transcriptome on non-model plants without a known genome are surprisingly scarce. RNA-Seq and digital gene expression (DGE) profiling provides a comprehensive approach to identify candidate genes contributing to developmental processes in non-model species. Here we built a transcriptome library of developing anthers of Hamelia patens and analyzed DGE profiles from each stage to identify genes that regulate tapetum and pollen development. In total 7,720 putative differentially expressed genes across four anther stages were identified. The number of putative stage-specific genes was: 776 at microspore mother cell stage, 807 at tetrad stage, 322 at uninucleate microspore stage, and the highest number (1,864) at bicellular pollen stage. GO enrichment analysis revealed 243 differentially expressed and 108 stage-specific genes that are potentially related to tapetum development, sporopollenin synthesis, and pollen wall. The number of expressed genes, their function and expression profiles were all significantly correlated with anther developmental processes. Overall comparisons of anther and pollen transcriptomes with those of rice and Arabidopsis together with the expression profiles of homologs of known anther-expressed genes, revealed conserved patterns and also divergence. The divergence may reflect taxon-specific differences in gene expression, the use RNA-seq as a more sensitive methodology, variation in tissue composition and sampling strategies. Given the lack of genomic sequence, this study succeeded in assigning putative identity to a significant proportion of anther-expressed genes and genes relevant to tapetum and pollen development in H. patens. The anther transcriptome revealed a molecular distinction between developmental stages, serving as a resource to unravel the functions of genes involved in anther development in H. patens and informing the analysis of other members of the Rubiaceae.

De novo Sequencing and Comparative Transcriptomics of Floral Development of the Distylous Species Lithospermum multiflorum

Genes controlling the morphological, micromorphological, and physiological components of the breeding system distyly have been hypothesized, but many of the genes have not been investigated throughout development of the two floral morphs. To this end, the present study is an examination of comparative transcriptomes from three stages of development for the floral organs of the morphs of Lithospermum multiflorum. Transcriptomes of flowers of the two morphs, from various stages of development, were sequenced using an Illumina HiSeq 2000. The floral transcriptome of L. multiflorum was assembled, and differential gene expression (DE) was identified between morphs, throughout development. Additionally, Gene Ontology (GO) terms for DE genes were determined. Fewer genes were DE early in development compared to later in development, with more genes highly expressed in the gynoecium of the SS morph and the corolla and androecium of the LS morph. A reciprocal pattern was observed later in development, and many more genes were DE during this latter stage. During early development, DE genes appear to be involved in growth and floral development, and during later development, DE genes seem to affect physiological functions. Interestingly, many genes involved in response to stress were identified as DE between morphs.

De novo transcriptome sequencing in Monsonia burkeana revealed putative genes for key metabolic pathways involved in tea quality and medicinal value

Monsonia (Monsonia burkeana Planch. ex Harv) is one of the most valuable tea and traditional medicinal plants used in Southern Africa. In spite of this, there is no sequence information regarding this plant in literature. To provide understanding of the naturally occurring tea and drug-specific products and the key pathways for the biosynthesis of these molecules, we sequenced the leaf transcriptome using Illumina MiSeq platform and generated 2,590,652 paired-end reads that were assembled de novo into 45,450 high-quality transcripts. Annotation of these transcripts revealed best hits for homology to discover more than 17,800 functional genes and conserved domains. A total of 93 KEGG pathways and associated genes encoded by more than 90% of the coding transcripts are responsible for the biosynthesis of these life-saving metabolites. We validated and enriched the genes by GO annotation and linked this to enzyme-powered pathways through interactive network map. Caffeine metabolism, flavonoid, phenylpropanoid and terpenoids biosynthesis and xenobiotics degradation were typical in tea quality and drug therapy. The relatedness of more than 80 gene families encoding key enzymes was shown using unrooted phylogenetic tree. In conclusion, the M. burkeana leaf transcriptome gives insight into tea and drug-specific products, therefore representing basis in further investigation of the plant.

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.

De novo transcriptome analysis in radish (Raphanus sativus L.) and identification of critical genes involved in bolting and flowering

Background

The appropriate timing of bolting and flowering is pivotal for reproductive success in Brassicaceae crops including radish (Raphanus sativus L.). Although several flowering regulatory pathways had been described in some plant species, no study on genetic networks of bolting and flowering regulation was performed in radish. In this study, to generate dataset of radish unigene sequences for large-scale gene discovery and functional pathway identification, a cDNA library from mixed radish leaves at different developmental stages was subjected to high-throughput RNA sequencing (RNA-seq).

Results

A total of 54.64 million clean reads and 111,167 contigs representing 53,642 unigenes were obtained from the radish leaf transcriptome. Among these, 50,385 unigenes were successfully annotated by BLAST searching against the public protein databases. Functional classification and annotation indicated that 42,903 and 15,382 unique sequences were assigned to 55 GO terms and 25 COG categories, respectively. KEGG pathway analysis revealed that 25,973 unigenes were classified into 128 functional pathways, among which 24 candidate genes related to plant circadian rhythm were identified. Moreover, 142 potential bolting and flowering-related genes involved in various flowering pathways were identified. In addition, seven critical bolting and flowering-related genes were isolated and profiled by T-A cloning and RT-qPCR analysis. Finally, a schematic network model of bolting and flowering regulation and pathways was put forward in radish.

Conclusions

This study is the first report on systematic identification of bolting and flowering-related genes based on transcriptome sequencing and assembly in radish. These results could provide a foundation for further investigating bolting and flowering regulatory networks in radish, and facilitate dissecting molecular genetic mechanisms underlying bolting and flowering in Brassicaceae vegetable crops.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2633-2) contains supplementary material, which is available to authorized users.

Evolution of Selfing: Recurrent Patterns in Molecular Adaptation

Selfing has evolved in animals, fungi, and plants, and since Darwin's pioneering study, it is considered one of the most frequent evolutionary trends in flowering plants. Generally, the evolution of selfing is characterized by a loss of self-incompatibility, the selfing syndrome, and changes in genome-wide polymorphism patterns. Recent interdisciplinary studies involving molecular functional experiments, genome-wide data, experimental evolution, and evolutionary ecology using Arabidopsis thaliana, Caenorhabditis elegans, and other species show that the evolution of selfing is not merely a degradation of outcrossing traits but a model for studying the recurrent patterns underlying adaptive molecular evolution. For example, in wild Arabidopsis relatives, self-compatibility evolved from mutations in the male specificity gene, S-LOCUS CYSTEINE-RICH PROTEIN/S-LOCUS PROTEIN 11 (SCR/SP11), rather than the female specificity gene, S-LOCUS RECEPTOR KINASE (SRK), supporting the theoretical prediction of sexual asymmetry. Prevalence of dominant self-compatible mutations is consistent with Haldane's sieve, which acts against recessive adaptive mutations. Time estimates based on genome-wide polymorphisms and self-incompatibility genes generally support the recent origin of selfing.

Data set for transcriptome analysis of the Chinese giant salamander (Andrias davidianus )

The Chinese giant salamander (Andrias davidianus) occupies a seat at the phylogenetic and species evolution process, which makes it an invaluable model for genetics; however, the genetic information and gene sequences about the Chinese giant salamander in public databases are scanty. Hence, we aimed to perform transcriptome analysis with the help of high-throughput sequencing. In this data, 61,317,940 raw reads were acquired from Chinese giant salamander mRNA using Illumina paired-end sequencing platform. After de novo assembly, a total of 72,072 unigenes were gained, in which 33,834 (46.95%) and 29,479 (40.91%) transcripts exhibited homology to sequences in the Nr database and Swiss-Prot database, (E-value <10(-5)), respectively. In the obtained unigenes, 18,019 (25%) transcripts were assigned with at least one Gene Ontology term, of which 1218 (6.8%) transcripts were assigned to immune system processes. In addition, a total of 17,572 assembled sequences were assigned into 241 predicted KEGG metabolic pathways. Among these, 2552 (14.5%) transcripts were assigned to the immune system relevant pathway and 5 transcripts were identified as potential antimicrobial peptides (AMPs).

Transcriptome analysis of Brassica napus pod using RNA-Seq and identification of lipid-related candidate genes

Background

Brassica napus is an important oilseed crop. Dissection of the genetic architecture underlying oil-related biological processes will greatly facilitates the genetic improvement of rapeseed. The differential gene expression during pod development offers a snapshot on the genes responsible for oil accumulation in. To identify candidate genes in the linkage peaks reported previously, we used RNA sequencing (RNA-Seq) technology to analyze the pod transcriptomes of German cultivar Sollux and Chinese inbred line Gaoyou.

Methods

The RNA samples were collected for RNA-Seq at 5-7, 15-17 and 25-27 days after flowering (DAF). Bioinformatics analysis was performed to investigate differentially expressed genes (DEGs). Gene annotation analysis was integrated with QTL mapping and Brassica napus pod transcriptome profiling to detect potential candidate genes in oilseed.

Results

Four hundred sixty five and two thousand, one hundred fourteen candidate DEGs were identified, respectively, between two varieties at the same stages and across different periods of each variety. Then, 33 DEGs between Sollux and Gaoyou were identified as the candidate genes affecting seed oil content by combining those DEGs with the quantitative trait locus (QTL) mapping results, of which, one was found to be homologous to Arabidopsis thaliana lipid-related genes.

Discussion

Intervarietal DEGs of lipid pathways in QTL regions represent important candidate genes for oil-related traits. Integrated analysis of transcriptome profiling, QTL mapping and comparative genomics with other relative species leads to efficient identification of most plausible functional genes underlying oil-content related characters, offering valuable resources for bettering breeding program of Brassica napus.

Conclusions

This study provided a comprehensive overview on the pod transcriptomes of two varieties with different oil-contents at the three developmental stages.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2062-7) contains supplementary material, which is available to authorized users.

Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome

The advances in experimental methods and the development of high performance bioinformatic tools have substantially improved our understanding of microbial communities associated with human niches. Many studies have documented that changes in microbial abundance and composition of the human microbiome is associated with human health and diseased state. The majority of research on human microbiome is typically focused in the analysis of one level of biological information, i.e., metagenomics or metatranscriptomics. In this review, we describe some of the different experimental and bioinformatic strategies applied to analyze the 16S rRNA gene profiling and shotgun sequencing data of the human microbiome. We also discuss how some of the recent insights in the combination of metagenomics, metatranscriptomics and viromics can provide more detailed description on the interactions between microorganisms and viruses in oral and gut microbiomes. Recent studies on viromics have begun to gain importance due to the potential involvement of viruses in microbial dysbiosis. In addition, metatranscriptomic combined with metagenomic analysis have shown that a substantial fraction of microbial transcripts can be differentially regulated relative to their microbial genomic abundances. Thus, understanding the molecular interactions in the microbiome using the combination of metagenomics, metatranscriptomics and viromics is one of the main challenges towards a system level understanding of human microbiome.

De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification

Ipomoea nil is widely used as an ornamental plant due to its abundance of flower color, but the limited transcriptome and genomic data hinder research on it. Using illumina platform, transcriptome profiling of I. nil was performed through high-throughput sequencing, which was proven to be a rapid and cost-effective means to characterize gene content. Our goal is to use the resulting information to facilitate the relevant research on flowering and flower color formation in I. nil. In total, 268 million unique illumina RNA-Seq reads were produced and used in the transcriptome assembly. These reads were assembled into 220,117 contigs, of which 137,307 contigs were annotated using the GO and KEGG database. Based on the result of functional annotations, a total of 89,781 contigs were assigned 455,335 GO term annotations. Meanwhile, 17,418 contigs were identified with pathway annotation and they were functionally assigned to 144 KEGG pathways. Our transcriptome revealed at least 55 contigs as probably flowering-related genes in I. nil, and we also identified 25 contigs that encode key enzymes in the phenylpropanoid biosynthesis pathway. Based on the analysis relating to gene expression profiles, in the phenylpropanoid biosynthesis pathway of I. nil, the repression of lignin biosynthesis might lead to the redirection of the metabolic flux into anthocyanin biosynthesis. This may be the most likely reason that I. nil has high anthocyanins content, especially in its flowers. Additionally, 15,537 simple sequence repeats (SSRs) were detected using the MISA software, and these SSRs will undoubtedly benefit future breeding work. Moreover, the information uncovered in this study will also serve as a valuable resource for understanding the flowering and flower color formation mechanisms in I. nil.

Unfolding the secrets of coral-algal symbiosis

Dinoflagellates from the genus Symbiodinium form a mutualistic symbiotic relationship with reef-building corals. Here we applied massively parallel Illumina sequencing to assess genetic similarity and diversity among four phylogenetically diverse dinoflagellate clades (A, B, C and D) that are commonly associated with corals. We obtained more than 30,000 predicted genes for each Symbiodinium clade, with a majority of the aligned transcripts corresponding to sequence data sets of symbiotic dinoflagellates and <2% of sequences having bacterial or other foreign origin. We report 1053 genes, orthologous among four Symbiodinium clades, that share a high level of sequence identity to known proteins from the SwissProt (SP) database. Approximately 80% of the transcripts aligning to the 1053 SP genes were unique to Symbiodinium species and did not align to other dinoflagellates and unrelated eukaryotic transcriptomes/genomes. Six pathways were common to all four Symbiodinium clades including the phosphatidylinositol signaling system and inositol phosphate metabolism pathways. The list of Symbiodinium transcripts common to all four clades included conserved genes such as heat shock proteins (Hsp70 and Hsp90), calmodulin, actin and tubulin, several ribosomal, photosynthetic and cytochrome genes and chloroplast-based heme-containing cytochrome P450, involved in the biosynthesis of xanthophylls. Antioxidant genes, which are important in stress responses, were also preserved, as were a number of calcium-dependent and calcium/calmodulin-dependent protein kinases that may play a role in the establishment of symbiosis. Our findings disclose new knowledge about the genetic uniqueness of symbiotic dinoflagellates and provide a list of homologous genes important for the foundation of coral-algal symbiosis.

Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data

The narrow genetic base and limited genetic information on Arachis species have hindered the process of marker-assisted selection of peanut cultivars. However, recent developments in sequencing technologies have expanded opportunities to exploit genetic resources, and at lower cost. To use the genetic information for Arachis species available at the transcriptome level, it is important to have a good quality reference transcriptome. The available Tifrunner 454 FLEX transcriptome sequences have an assembly with 37,000 contigs and low N50 values of 500-751bp. Therefore, we generated de novo transcriptome assemblies, with about 38 million reads in the tetraploid cultivar OLin, and 16 million reads in each of the diploids, A. duranensis K38901 and A. ipaënsis KGBSPSc30076 using three different de novo assemblers, Trinity, SOAPdenovo-Trans and TransAByss. All these assemblers can use single kmer analysis, and the latter two also permit multiple kmer analysis. Assemblies generated for all three samples had N50 values ranging from 1278–1641 bp in Arachis hypogaea (AABB), 1401–1492 bp in Arachis duranensis (AA), and 1107–1342 bp in Arachis ipaënsis (BB). Comparison with legume ESTs and protein databases suggests that assemblies generated had more than 40% full length transcripts with good continuity. Also, on mapping the raw reads to each of the assemblies generated, Trinity had a high success rate in assembling sequences compared to both TransAByss and SOAPdenovo-Trans. De novo assembly of OLin had a greater number of contigs (67,098) and longer contig length (N50 = 1,641) compared to the Tifrunner TSA. Despite having shorter read length (2×50) than the Tifrunner 454FLEX TSA, de novo assembly of OLin proved superior in comparison. Assemblies generated to represent different genome combinations may serve as a valuable resource for the peanut research community.

The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations

The transition from outcrossing to selfing is predicted to reduce the genome-wide efficacy of selection because of the lower effective population size (Ne) that accompanies this change in mating system. However, strongly recessive deleterious mutations exposed in the homozygous backgrounds of selfers should be under strong purifying selection. Here, we examine estimates of the distribution of fitness effects (DFE) and changes in the magnitude of effective selection coefficients (Nes) acting on mutations during the transition from outcrossing to selfing. Using forward simulations, we investigated the ability of a DFE inference approach to detect the joint influence of mating system and the dominance of deleterious mutations on selection efficacy. We investigated predictions from our simulations in the annual plant Eichhornia paniculata, in which selfing has evolved from outcrossing on multiple occasions. We used range-wide sampling to generate population genomic datasets and identified nonsynonymous and synonymous polymorphisms segregating in outcrossing and selfing populations. We found that the transition to selfing was accompanied by a change in the DFE, with a larger fraction of effectively neutral sites (Nes < 1), a result consistent with the effects of reduced Ne in selfers. Moreover, an increased proportion of sites in selfers were under strong purifying selection (Nes > 100), and simulations suggest that this is due to the exposure of recessive deleterious mutations. We conclude that the transition to selfing has been accompanied by the genome-wide influences of reduced Ne and strong purifying selection against deleterious recessive mutations, an example of purging at the molecular level.

Transcriptome analysis reveals diversified adaptation of Stipa purpurea along a drought gradient on the Tibetan Plateau

Natural selection drives species adaptations to biotic and abiotic stresses. Species distributed along a moisture gradient, such as Stipa purpurea, a dominant grass in alpine arid and semi-arid meadows on the Tibetan Plateau, provide an opportunity to evaluate the effects of long-term adaptation to differing degrees of drought stress on gene expression. However, the genetic basis of this divergence remains largely unknown. Next-generation sequencing technologies have provided important genome-wide insights on the evolution of organisms for which genomic information is lacking. To understand how S. purpurea responds to drought stress, we selected five populations distributed along the degressive rainfall line on the northwestern Tibetan Plateau that currently present evolutionary acclimation to localized drought pressure at the physiological and biochemical levels and compared their transcriptome responses. In addition, we performed de novo assembly of the S. purpurea transcriptome using short read sequencing technology and successfully assembled 84,298 unigenes from approximately 51 million sequencing reads. We quantified gene expression level to compare their transcriptome responses using mRNA-Seq and identified differentially expressed transcripts that are involved in primary and secondary plant metabolism, plant hormone synthesis, defense responses, and cell wall synthesis. Furthermore, physiological and biochemical evidence supports that abscisic acid (ABA) accumulation and cell wall strengthening derived from the differential transcripts contribute to the tolerance of S. purpurea to drought stress. The mechanisms by which S. purpurea adapts to drought stress provide new insight into how plants ecologically adapt and evolve.

De novo transcriptome analysis of petal senescence in Gardenia jasminoides Ellis

BACKGROUND

The petal senescence of ethylene insensitive species has not been investigated thoroughly while little is known about the temporal and tissue specific expression patterns of transcription factors (TFs) in this developmental process. Even less is known on flower senescence of the ornamental pot plant Gardenia jasminoides, a non climacteric flower with significant commercial value.

RESULTS

We initiated a de novo transcriptome study to investigate the petal senescence in four developmental stages of cut gardenia flowers considering that the visible symptoms of senescence appear within 4 days of flower opening. De novo assembly of transcriptome sequencing resulted in 102,263 contigs with mean length of 360 nucleotides that generated 57,503 unigenes. These were further clustered into 20,970 clusters and 36,533 singletons. The comparison of the consecutive developmental stages resulted in 180 common, differentially expressed unigenes. A large number of Simple Sequence Repeats were also identified comprising a large number of dinucleotides and trinucleotides. The prevailing families of differentially expressed TFs comprise the AP2/EREBP, WRKY and the bHLH. There are 81 differentially expressed TFs when the symptoms of flower senescence become visible with the most prevailing being the WRKY family with 19 unigenes. No other WRKY TFs had been identified up to now in petal senescence of ethylene insensitive species. A large number of differentially expressed genes were identified at the initiation of visible symptoms of senescence compared to the open flower stage indicating a significant shift in the expression profiles which might be coordinated by up-regulated and/or down-regulated TFs. The expression of 16 genes that belong to the TF families of WRKY, bHLH and the ethylene sensing pathway was validated using qRT--PCR.

CONCLUSION

This de novo transcriptome analysis resulted in the identification of TFs with specific temporal expression patterns such as two WRKYs and one bHLH, which might play the role of senescence progression regulators. Further research is required to investigate their role in gardenia flowers in order to develop tools to delay petal senescence.

Comparison of the transcriptomes of ginger (Zingiber officinale Rosc.) and mango ginger (Curcuma amada Roxb.) in response to the bacterial wilt infection

Bacterial wilt in ginger (Zingiber officinale Rosc.) caused by Ralstonia solanacearum is one of the most important production constraints in tropical, sub-tropical and warm temperature regions of the world. Lack of resistant genotype adds constraints to the crop management. However, mango ginger (Curcuma amada Roxb.), which is resistant to R. solanacearum, is a potential donor, if the exact mechanism of resistance is understood. To identify genes involved in resistance to R. solanacearum, we have sequenced the transcriptome from wilt-sensitive ginger and wilt-resistant mango ginger using Illumina sequencing technology. A total of 26387032 and 22268804 paired-end reads were obtained after quality filtering for C. amada and Z. officinale, respectively. A total of 36359 and 32312 assembled transcript sequences were obtained from both the species. The functions of the unigenes cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. Large scale expression profiling showed that many of the disease resistance related genes were expressed more in C. amada. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either ginger or mango ginger. The identification of many defense related genes differentially expressed provides many insights to the resistance mechanism to R. solanacearum and for studying potential pathways involved in responses to pathogen. Also, several candidate genes that may underline the difference in resistance to R. solanacearum between ginger and mango ginger were identified. Finally, we have developed a web resource, ginger transcriptome database, which provides public access to the data. Our study is among the first to demonstrate the use of Illumina short read sequencing for de novo transcriptome assembly and comparison in non-model species of Zingiberaceae.

Limited genomic consequences of mixed mating in the recently derived sister species pair, Collinsia concolor and Collinsia parryi

Highly selfing species often show reduced effective population sizes and reduced selection efficacy. Whether mixed mating species, which produce both self and outcross progeny, show similar patterns of diversity and selection remains less clear. Examination of patterns of molecular evolution and levels of diversity in species with mixed mating systems can be particularly useful for investigating the relative importance of linked selection and demographic effects on diversity and the efficacy of selection, as the effects of linked selection should be minimal in mixed mating populations, although severe bottlenecks tied to founder events could still be frequent. To begin to address this gap, we assembled and analysed the transcriptomes of individuals from a recently diverged mixed mating sister species pair in the self-compatible genus, Collinsia. The de novo assembly of 52 and 37 Mbp C. concolor and C. parryi transcriptomes resulted in ~40 000 and ~55 000 contigs, respectively, both with an average contig size ~945. We observed a high ratio of shared polymorphisms to fixed differences in the species pair and minimal differences between species in the ratio of synonymous to replacement substitutions or codon usage bias implying comparable effective population sizes throughout species divergence. Our results suggest that differences in effective population size and selection efficacy in mixed mating taxa shortly after their divergence may be minimal and are likely influenced by fluctuating mating systems and population sizes.

De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers

BACKGROUND

The rubber tree, Hevea brasiliensis, is a species native to the Brazilian Amazon region and it supplies almost all the world's natural rubber, a strategic raw material for a variety of products. One of the major challenges for developing rubber tree plantations is adapting the plant to biotic and abiotic stress. Transcriptome analysis is one of the main approaches for identifying the complete set of active genes in a cell or tissue for a specific developmental stage or physiological condition.

RESULTS

Here, we report on the sequencing, assembling, annotation and screening for molecular markers from a pool of H. brasiliensis tissues. A total of 17,166 contigs were successfully annotated. Then, 2,191 Single Nucleotide Variation (SNV) and 1.397 Simple Sequence Repeat (SSR) loci were discriminated from the sequences. From 306 putative, mainly non-synonymous SNVs located in CDS sequences, 191 were checked for their ability to characterize 23 Hevea genotypes by an allele-specific amplification technology. For 172 (90%), the nucleotide variation at the predicted genomic location was confirmed, thus validating the different steps from sequencing to the in silico detection of the SNVs.

CONCLUSIONS

This is the first study of the H. brasiliensis transcriptome, covering a wide range of tissues and organs, leading to the production of the first developed SNP markers. This process could be amplified to a larger set of in silico detected SNVs in expressed genes in order to increase the marker density in available and future genetic maps. The results obtained in this study will contribute to the H. brasiliensis genetic breeding program focused on improving of disease resistance and latex yield.

Genome-wide transcriptome analysis of Chinese pollination-constant nonastringent persimmon fruit treated with ethanol

Background

The persimmon Diospyros kaki Thunb. is an important commercial and deciduous fruit tree. The fruits have proanthocyanidin (PA) content of >25% of the dry weight and are astringent. PAs cause astringency that is often undesirable for human consumption; thus, the removal of astringency is an important practice in the persimmon industry. Soluble PAs can be converted to insoluble PAs by enclosing the fruit in a polyethylene bag containing diluted ethanol. The genomic resource development of the persimmon is delayed because of its large and complex genome. Second-generation sequencing is an efficient technique for generating huge sequences that can represent a large number of genes and their expression levels.

Results

We used 454 sequencing for the de novo transcriptome assembly of persimmon fruit treated with 5% ethanol (Tr library) and without treatment as the control (Co library) to investigate the genes and pathways that control PA biosynthesis and other secondary metabolites. We obtained 374.6 Mb in clean nucleotides comprising 624,690 and 626,203 clean sequencing reads from the Tr and Co libraries, respectively. We also identified 83,898 unigenes; 54,719 (~65.2%) unigenes were annotated based on similarity searches with known proteins. Up to 14,954 of the unigenes were assigned to the protein database Clusters of Orthologous Groups (COG), 24,337 were assigned to the term annotation database of Gene Ontology (GO), and 45,506 were assigned to 200 pathways in the database of Kyoto Encyclopedia of Genes and Genomes (KEGG). The two libraries were compared to identify the differentially expressed unigenes. The expression levels of genes involved in PA biosynthesis and tannin coagulation were analysed, and some of them were verified using quantitative real time PCR (qRT-PCR).

Conclusions

This study provides abundant genomic data for persimmon and offers comprehensive sequence resources for persimmon research. The transcriptome dataset will improve our understanding of the molecular mechanisms of tannin coagulation and other biochemical processes in persimmons.

Comparative de novo transcriptome analysis and metabolic pathway studies of Citrus paradisi flavedo from naive stage to ripened stage

Grapefruit (Citrus pardisi) is a popular citrus fruit that is a cross between a sweet orange and pummelo. This research article focuses on an in silico approach for comparative analysis of C. paradisi green flavedo (GF) and ethylene treated flavedo (ETF) transcriptome data. Our pathway analysis provides comprehensive information of genes playing significant role in different stages of ripening in fruit. De novo assembly was carried out using six different assemblers namely GS assembler, SeqMan NGEN, Velvet/Oases, CLC, iAssembler and Cortex followed by subsequent meta-assembly, annotation and pathway analysis. We conclude that de novo transcriptome assembly using meta-assembly approach is used to increase assembly quality in comparison to single assembler.

Insights into hepatopancreatic functions for nutrition metabolism and ovarian development in the crab Portunus trituberculatus: gene discovery in the comparative transcriptome of different hepatopancreas stages

The crustacean hepatopancreas has different functions including absorption, storage of nutrients and vitellogenesis during growth, and ovarian development. However, genetic information on the biological functions of the crustacean hepatopancreas during such processes is limited. The swimming crab, Portunus trituberculatus, is a commercially important species for both aquaculture and fisheries in the Asia-Pacific region. This study compared the transcriptome in the hepatopancreas of female P. trituberculatus during the growth and ovarian maturation stages by 454 high-throughput pyrosequencing and bioinformatics. The goal was to discover genes in the hepatopancreas involved in food digestion, nutrition metabolism and ovarian development, and to identify patterns of gene expression during growth and ovarian maturation. Our transcriptome produced 303,450 reads with an average length of 351 bp, and the high quality reads were assembled into 21,635 contigs and 31,844 singlets. Based on BLASTP searches of the deduced protein sequences, there were 7,762 contigs and 4,098 singlets with functional annotation. Further analysis revealed 33,427 unigenes with ORFs, including 17,388 contigs and 16,039 singlets in the hepatopancreas, while only 7,954 unigenes (5,691 contigs and 2,263 singlets) with the predicted protein sequences were annotated with biological functions. The deduced protein sequences were assigned to 3,734 GO terms, 25 COG categories and 294 specific pathways. Furthermore, there were 14, 534, and 22 identified unigenes involved in food digestion, nutrition metabolism and ovarian development, respectively. 212 differentially expressed genes (DEGs) were found between the growth and endogenous stage of the hepatopancreas, while there were 382 DEGs between the endogenous and exogenous stage hepatopancreas. Our results not only enhance the understanding of crustacean hepatopancreatic functions during growth and ovarian development, but also represent a basis for further research on new genes and functional genomics of P. trituberculatus or closely related species.

Identifying the genes underlying quantitative traits: a rationale for the QTN programme

The goal of identifying the genes or even nucleotides underlying quantitative and adaptive traits has been characterized as the 'QTN programme' and has recently come under severe criticism. Part of the reason for this criticism is that much of the QTN programme has asserted that finding the genes and nucleotides for adaptive and quantitative traits is a fundamental goal, without explaining why it is such a hallowed goal. Here we outline motivations for the QTN programme that offer general insight, regardless of whether QTNs are of large or small effect, and that aid our understanding of the mechanistic dynamics of adaptive evolution. We focus on five areas: (i) vertical integration of insight across different levels of biological organization, (ii) genetic parallelism and the role of pleiotropy in shaping evolutionary dynamics, (iii) understanding the forces maintaining genetic variation in populations, (iv) distinguishing between adaptation from standing variation and new mutation, and (v) the role of genomic architecture in facilitating adaptation. We argue that rather than abandoning the QTN programme, we should refocus our efforts on topics where molecular data will be the most effective for testing hypotheses about phenotypic evolution.

De novo sequencing, characterization, and comparison of inflorescence transcriptomes of Cornus canadensis and C. florida (Cornaceae)

BACKGROUND

Transcriptome sequencing analysis is a powerful tool in molecular genetics and evolutionary biology. Here we report the results of de novo 454 sequencing, characterization, and comparison of inflorescence transcriptomes of two closely related dogwood species, Cornus canadensis and C. florida (Cornaceae). Our goals were to build a preliminary source of genome sequence data, and to identify genes potentially expressed differentially between the inflorescence transcriptomes for these important horticultural species.

RESULTS

The sequencing of cDNAs from inflorescence buds of C. canadensis (cc) and C. florida (cf), and normalized cDNAs from leaves of C. canadensis resulted in 251799 (ccBud), 96245 (ccLeaf) and 114648 (cfBud) raw reads, respectively. The de novo assembly of the high quality (HQ) reads resulted in 36088, 17802 and 21210 unigenes for ccBud, ccLeaf and cfBud. A reference transcriptome for C. canadensis was built by assembling HQ reads of ccBud and ccLeaf, containing 40884 unigenes. Reference mapping and comparative analyses found 10926 sequences were putatively specific to ccBud, and 6979 putatively specific to cfBud. Putative differentially expressed genes between ccBud and cfBud that are related to flower development and/or stress response were identified among 7718 shared sequences by ccBud and cfBud. Bi-directional BLAST found 87 (41.83% of 208) of Arabidopsis genes related to inflorescence development had putative orthologs in the dogwood transcriptomes. Comparisons of the shared sequences by ccBud and cfBud yielded 65931 high quality SNPs between two species. The twenty unigenes with the most SNPs are listed as potential genetic markers for evolutionary studies.

CONCLUSIONS

The data provide an important, although preliminary, information platform for functional genomics and evolutionary developmental biology in Cornus. The study identified putative candidates potentially involved in the genetic regulation of inflorescence evolution and/or disease resistance in dogwoods for future analyses. Results of the study also provide markers useful for dogwood phylogenomic studies.

Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola

Background

Five-needle pines are important forest species that have been devastated by white pine blister rust (WPBR, caused by Cronartium ribicola) across North America. Currently little transcriptomic and genomic data are available to understand molecular interactions in the WPBR pathosystem.

Results

We report here RNA-seq analysis results using Illumina deep sequencing of primary needles of western white pine (Pinus monticola) infected with WPBR. De novo gene assembly was used to generate the first P. monticola consensus transcriptome, which contained 39,439 unique transcripts with an average length of 1,303 bp and a total length of 51.4 Mb. About 23,000 P. monticola unigenes produced orthologous hits in the Pinus gene index (PGI) database (BLASTn with E values < e-100) and 6,300 genes were expressed actively (at RPKM ≥ 10) in the healthy tissues. Comparison of transcriptomes from WPBR-susceptible and -resistant genotypes revealed a total of 979 differentially expressed genes (DEGs) with a significant fold change > 1.5 during P. monticola- C. ribicola interactions. Three hundred and ten DEGs were regulated similarly in both susceptible and resistant seedlings and 275 DEGs showed regulatory differences between susceptible and resistant seedlings post infection by C. ribicola. The DEGs up-regulated in resistant seedlings included a set of putative signal receptor genes encoding disease resistance protein homologs, calcineurin B-like (CBL)-interacting protein kinases (CIPK), F-box family proteins (FBP), and abscisic acid (ABA) receptor; transcriptional factor (TF) genes of multiple families; genes homologous to apoptosis-inducing factor (AIF), flowering locus T-like protein (FT), and subtilisin-like protease. DEGs up-regulated in resistant seedlings also included a wide diversity of down-stream genes (encoding enzymes involved in different metabolic pathways, pathogenesis-related -PR proteins of multiple families, and anti-microbial proteins). A large proportion of the down-regulated DEGs were related to photosystems, the metabolic pathways of carbon fixation and flavonoid biosynthesis.

Conclusions

The novel P. monticola transcriptome data provide a basis for future studies of genetic resistance in a non-model, coniferous species. Our global gene expression profiling presents a comprehensive view of transcriptomic regulation in the WPBR pathosystem and yields novel insights on molecular and biochemical mechanisms of disease resistance in conifers.

Evaluation of assembly strategies using RNA-seq data associated with grain development of wheat (Triticum aestivum L.)

Wheat (Triticum aestivum L.) is one of the most important crops cultivated worldwide. Identifying the complete transcriptome of wheat grain could serve as foundation for further study of wheat seed development. However, the relatively large size and the polyploid complexity of the genome have been substantial barriers to molecular genetics and transcriptome analysis of wheat. Alternatively, RNA sequencing has provided some useful information about wheat genes. However, because of the large number of short reads generated by RNA sequencing, factors that are crucial to transcriptome assembly, including software, candidate parameters and assembly strategies, need to be optimized and evaluated for wheat data. In the present study, four cDNA libraries associated with wheat grain development were constructed and sequenced. A total of 14.17 Gb of high-quality reads were obtained and used to assess different assembly strategies. The most successful approach was to filter the reads with Q30 prior to de novo assembly using Trinity, merge the assembled contigs with genes available in wheat cDNA reference data sets, and combine the resulting assembly with an assembly from a reference-based strategy. Using this approach, a relatively accurate and nearly complete transcriptome associated with wheat grain development was obtained, suggesting that this is an effective strategy for generation of a high-quality transcriptome from RNA sequencing data.

Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing

Raphanus sativus is not only a popular edible vegetable but also an important source of medicinal compounds. However, the paucity of knowledge about the transcriptome of R. sativus greatly impedes better understanding of the functional genomics and medicinal potential of R. sativus. In this study, the transcriptome sequencing of leaf tissues in R. sativus was performed for the first time. Approximately 22 million clean reads were generated and used for transcriptome assembly. The generated unigenes were subsequently annotated against gene ontology (GO) database. KEGG analysis further revealed two important pathways in the bolting stage of R.sativus including spliceosome assembly and alkaloid synthesis. In addition, a total of 6,295 simple sequence repeats (SSRs) with various motifs were identified in the unigene library of R. sativus. Finally, four unigenes of R. sativus were selected for alignment with their homologs from other plants, and phylogenetic trees for each of the genes were constructed. Taken together, this study will provide a platform to facilitate gene discovery and advance functional genomic research of R. sativus.

Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella

The shift from outcrossing to self-fertilization is among the most common evolutionary transitions in flowering plants. Until recently, however, a genome-wide view of this transition has been obscured by both a dearth of appropriate data and the lack of appropriate population genomic methods to interpret such data. Here, we present a novel population genomic analysis detailing the origin of the selfing species, Capsella rubella, which recently split from its outcrossing sister, Capsella grandiflora. Due to the recency of the split, much of the variation within C. rubella is also found within C. grandiflora. We can therefore identify genomic regions where two C. rubella individuals have inherited the same or different segments of ancestral diversity (i.e. founding haplotypes) present in C. rubella's founder(s). Based on this analysis, we show that C. rubella was founded by multiple individuals drawn from a diverse ancestral population closely related to extant C. grandiflora, that drift and selection have rapidly homogenized most of this ancestral variation since C. rubella's founding, and that little novel variation has accumulated within this time. Despite the extensive loss of ancestral variation, the approximately 25% of the genome for which two C. rubella individuals have inherited different founding haplotypes makes up roughly 90% of the genetic variation between them. To extend these findings, we develop a coalescent model that utilizes the inferred frequency of founding haplotypes and variation within founding haplotypes to estimate that C. rubella was founded by a potentially large number of individuals between 50 and 100 kya, and has subsequently experienced a twenty-fold reduction in its effective population size. As population genomic data from an increasing number of outcrossing/selfing pairs are generated, analyses like the one developed here will facilitate a fine-scaled view of the evolutionary and demographic impact of the transition to self-fertilization.

While many plants require pollen from another individual to set seed, in some species self-pollination is the norm. This evolutionary shift from outcrossing to self-fertilization is among the most common transitions in flowering plants. Here, we use dense genome sequence data to identify where in the genome two individuals have inherited the same or different segments of ancestral diversity present in the founders of the selfing species, Capsella rubella to obtain a genome-wide view of this transition. This identification of founding haplotypes allows us to partition mutations into those that occurred before and after C. rubella separated from its outcrossing progenitor, C. grandiflora. With this partitioning, we estimate that C. rubella split from C. grandiflora between 50 and 100 kya. In this relatively short time frame, an extreme reduction in C. rubella's population size is associated with a massive loss of genetic variation and an increase in the relative proportion of putatively deleterious polymorphisms.

Development of an expressed gene catalogue and molecular markers from the de novo assembly of short sequence reads of the lentil (Lens culinaris Medik.) transcriptome

Genomic resources such as ESTs, molecular markers and linkage maps are essential for crop improvement. However, these resources are still limited in important legumes such as lentil (Lens culinaris Medik.), which is valued world wide as a rich source of dietary protein. In this study, the de novo transcriptome assembly of 119,855,798 short reads, generated by Illumina paired-end sequencing, was performed using various assembly programs. This resulted in 42,196 nonredundant high-quality transcripts of average length 810 bases, N50 value of 1,432 and an average expression per transcript of 26.21 rpkm reads per kilobase per million(RPKM). Similarity search with the unigenes and protein sequences of other plants resulted in maximum similarity with soybean. A total of 20,009 nonredundant transcripts showed similarity with the UniProtKB database and of these, 18,064 transcripts were grouped into three main GO categories, that is, biological process (15,126), molecular function (15,505) and cellular component (9,434). Annotated transcripts were mapped to 289 predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 8,893 transcripts were classified into 24 functional categories based on Cluster of Orthologous Groups (COG) of proteins. Mining the data set for the presence of SSRs resulted in 8,722 SSRs with a frequency occurrence of one SSR per 3.92 kb. From these, 5,673 SSR primer pairs were designed, and a subset of these were utilized for diversity analysis. This study, which provides a large data set of annotated transcripts and gene-based SSR markers, would serve as a foundation for various applications in lentil breeding and genetics.

Transcriptome sequencing and de novo analysis of a cytoplasmic male sterile line and its near-isogenic restorer line in chili pepper (Capsicum annuum L.)

BACKGROUND

The use of cytoplasmic male sterility (CMS) in F1 hybrid seed production of chili pepper is increasingly popular. However, the molecular mechanisms of cytoplasmic male sterility and fertility restoration remain poorly understood due to limited transcriptomic and genomic data. Therefore, we analyzed the difference between a CMS line 121A and its near-isogenic restorer line 121C in transcriptome level using next generation sequencing technology (NGS), aiming to find out critical genes and pathways associated with the male sterility.

RESULTS

We generated approximately 53 million sequencing reads and assembled de novo, yielding 85,144 high quality unigenes with an average length of 643 bp. Among these unigenes, 27,191 were identified as putative homologs of annotated sequences in the public protein databases, 4,326 and 7,061 unigenes were found to be highly abundant in lines 121A and 121C, respectively. Many of the differentially expressed unigenes represent a set of potential candidate genes associated with the formation or abortion of pollen.

CONCLUSIONS

Our study profiled anther transcriptomes of a chili pepper CMS line and its restorer line. The results shed the lights on the occurrence and recovery of the disturbances in nuclear-mitochondrial interaction and provide clues for further investigations.

Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid Erycina pusilla

The high chromosome numbers, polyploid genomes, and long juvenile phases of most ornamental orchid species render functional genomics difficult and limit the discovery of genes influencing horticultural traits. The orchid Erycina pusilla has a low chromosome number (2n = 12) and flowers in vitro within 1 year, making it a standout candidate for use as a model orchid. However, transcriptomic and genomic information from E. pusilla remains limited. In this study, next-generation sequencing (NGS) technology was used to identify 90,668 unigenes by de novo assembly. These unigenes were annotated functionally and analyzed with regard to their gene ontology (GO), clusters of orthologous groups (COG), and KEGG pathways. To validate the discovery methods, a homolog of CONSTANS (CO), one of the key genes in the flowering pathway, was further analyzed. The Arabidopsis CO-Like (COL) amino acid sequences were used to screen for homologs in the E. pusilla transcriptome database. Specific primers to the homologous unigenes were then used to isolate BAC clones, which were sequenced to identify 12 E. pusilla CO-like (EpCOL) full-length genes. Based on sequence homology, domain structure, and phylogenetic analysis, these EpCOL genes were divided into four groups. Four EpCOLs fused with GFP were localized in the nucleus. Some EpCOL genes were regulated by light. These results demonstrate that nascent E. pusilla resources (transcriptome and BAC library) can be used to investigate the E. pusilla photoperiod-dependent flowering genes. In future, this strategy can be applied to other biological processes, marketable traits, and molecular breeding in this model orchid.

Comparative population genomics in Collinsia sister species reveals evidence for reduced effective population size, relaxed selection, and evolution of biased gene conversion with an ongoing mating system shift

Selfing species experience reduced effective recombination rates and effective population size, which can lead to reductions in polymorphism and the efficacy of natural selection. Here, we use illumina transcriptome sequencing and population resequencing to test for changes in polymorphism, base composition, and selection in the selfing angiosperm Collinsia rattanii (Plantaginaceae) compared with its more outcrossing sister species Collinsia linearis. Coalescent analysis indicates intermediate species divergence (500,000-1 million years) with no ongoing gene flow, but also evidence that the C. rattanii clade remains polymorphic for floral morphology and mating system, suggesting either an ongoing shift to selfing or a potential reversal from selfing to outcrossing. We identify a significant reduction in polymorphism in C. rattanii, particularly within populations. Analysis of polymorphisms suggests an elevated ratio of unique nonsynonymous to synonymous polymorphism in C. rattanii, consistent with relaxed selection in selfing lineages. We additionally find higher linkage disequilibrium and differentiation, lower GC content at variable sites, and reduced expression of genes important in pollen production and pollinator attraction in C. rattanii compared with C. linearis. Together, our results highlight the potential for rapid shifts in the efficacy of selection, gene expression and base composition associated with ongoing evolution of selfing.

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

INTRODUCTION

Traditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. Here we provide a comparative analysis of de novo assembled transcriptomic data for ten non-model species of previously understudied animal taxa.

RESULTS

cDNA libraries of ten species belonging to five animal phyla (2 Annelida [including Sipuncula], 2 Arthropoda, 2 Mollusca, 2 Nemertea, and 2 Porifera) were sequenced in different batches with an Illumina Genome Analyzer II (read length 100 or 150 bp), rendering between ca. 25 and 52 million reads per species. Read thinning, trimming, and de novo assembly were performed under different parameters to optimize output. Between 67,423 and 207,559 contigs were obtained across the ten species, post-optimization. Of those, 9,069 to 25,681 contigs retrieved blast hits against the NCBI non-redundant database, and approximately 50% of these were assigned with Gene Ontology terms, covering all major categories, and with similar percentages in all species. Local blasts against our datasets, using selected genes from major signaling pathways and housekeeping genes, revealed high efficiency in gene recovery compared to available genomes of closely related species. Intriguingly, our transcriptomic datasets detected multiple paralogues in all phyla and in nearly all gene pathways, including housekeeping genes that are traditionally used in phylogenetic applications for their purported single-copy nature.

CONCLUSIONS

We generated the first study of comparative transcriptomics across multiple animal phyla (comparing two species per phylum in most cases), established the first Illumina-based transcriptomic datasets for sponge, nemertean, and sipunculan species, and generated a tractable catalogue of annotated genes (or gene fragments) and protein families for ten newly sequenced non-model organisms, some of commercial importance (i.e., Octopus vulgaris). These comprehensive sets of genes can be readily used for phylogenetic analysis, gene expression profiling, developmental analysis, and can also be a powerful resource for gene discovery. The characterization of the transcriptomes of such a diverse array of animal species permitted the comparison of sequencing depth, functional annotation, and efficiency of genomic sampling using the same pipelines, which proved to be similar for all considered species. In addition, the datasets revealed their potential as a resource for paralogue detection, a recurrent concern in various aspects of biological inquiry, including phylogenetics, molecular evolution, development, and cellular biochemistry.

Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes

Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ≥1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers.

Genomic consequences of transitions from cross- to self-fertilization on the efficacy of selection in three independently derived selfing plants

Background

Transitions from cross- to self-fertilization are associated with increased genetic drift rendering weakly selected mutations effectively neutral. The effect of drift is predicted to reduce selective constraints on amino acid sequences of proteins and relax biased codon usage. We investigated patterns of nucleotide variation to assess the effect of inbreeding on the accumulation of deleterious mutations in three independently evolved selfing plants. Using high-throughput sequencing, we assembled the floral transcriptomes of four individuals of Eichhornia (Pontederiaceae); these included one outcrosser and two independently derived selfers of E. paniculata, and E. paradoxa, a selfing outgroup. The dataset included ~8000 loci totalling ~3.5 Mb of coding DNA.

Results

Tests of selection were consistent with purifying selection constraining evolution of the transcriptome. However, we found an elevation in the proportion of non-synonymous sites that were potentially deleterious in the E. paniculata selfers relative to the outcrosser. Measurements of codon usage in high versus low expression genes demonstrated reduced bias in both E. paniculata selfers.

Conclusions

Our findings are consistent with a small reduction in the efficacy of selection on protein sequences associated with transitions to selfing, and reduced selection in selfers on synonymous changes that influence codon usage.

De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing

Garlic is widely used as a spice throughout the world for the culinary value of its flavor and aroma, which are created by the chemical transformation of a series of organic sulfur compounds. To analyze the transcriptome of Allium sativum and discover the genes involved in sulfur metabolism, cDNAs derived from the total RNA of Allium sativum buds were analyzed by Illumina sequencing. Approximately 26.67 million 90 bp paired-end clean reads were achieved in two libraries. A total of 127,933 unigenes were generated by de novo assembly and were compared with the sequences in public databases. Of these, 45,286 unigenes had significant hits to the sequences in the Nr database, 29,514 showed significant similarity to known proteins in the Swiss-Prot database and, 20,706 and 21,952 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Moreover, genes involved in organic sulfur biosynthesis were identified. These unigenes data will provide the foundation for research on gene expression, genomics and functional genomics in Allium sativum. Key message The obtained unigenes will provide the foundation for research on functional genomics in Allium sativum and its closely related species, and fill the gap of the existing plant EST database.