Comparison of next generation sequencing technologies for transcriptome characterization

The isolation and identification of Bacillus velezensis ZN-S10 from vanilla (V. planifolia), and the microbial distribution after the curing process

The market value of vanilla beans (Vanilla planifolia) is constantly increasing due to their natural aroma and flavor properties that improve after a curing process, where bacteria colonization plays a critical role. However, a few publications suggest that bacteria play a role in the curing process. Hence, this study aimed to isolate Bacillus sp. that could be used for fermenting V. planifolia while analyzing their role in the curing process. Bacillus velezensis ZN-S10 identified with 16S rRNA sequencing was isolated from conventionally cured V. planifolia beans. A bacteria culture solution of B. velezensis ZN-S10 (1 mL of 1 × 107 CFU mL-1) was then coated on 1 kg of non-cured vanilla pods that was found to ferment and colonize vanilla. PCA results revealed distinguished bacterial communities of fermented vanilla and the control group, suggesting colonization of vanilla. Phylogenetic analysis showed that ZN-S10 was the dominant Bacillus genus member and narrowly correlated to B. velezensis EM-1 and B. velezensis PMC206-1, with 78% and 73% similarity, respectively. The bacterial taxonomic profiling of cured V. planifolia had a significant relative abundance of Firmicutes, Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes phyla according to the predominance. Firmicutes accounted for 55% of the total bacterial sequences, suggesting their colonization and effective fermentation roles in curing vanilla.

Next-Generation Sequencing Data-Based Association Testing of a Group of Genetic Markers for Complex Responses Using a Generalized Linear Model Framework

Association testing has been widely used to study the relationship between genetic variants and phenotypes. Most association testing methods are genotype-based, i.e. first estimate genotype and then regress phenotype on estimated genotype and other variables. Directly testing methods based on next generation sequencing (NGS) data without genotype calling have been proposed and shown advantage over genotype-based methods in the scenarios when genotype calling is not accurate. NGS data-based single-variant testing have been proposed including our previously proposed single-variant testing method, i.e. UNC combo method [1]. NGS data-based group testing methods for continuous phenotype have also been proposed by us using a linear model framework which can handle continuous responses [2]. In this paper, we extend our linear model-based framework to a generalized linear model-based framework so that the methods can handle other types of responses especially binary responses which is commonly-faced in association studies. We have conducted extensive simulation studies to evaluate the performance of different estimators and compare our estimators with their corresponding genotype-based methods. We found that all methods have Type I errors controlled, and our NGS data-based testing methods have better performance than their corresponding genotype-based methods in the literature for other types of responses including binary responses (logistic regression) and count responses (Poisson regression especially when sequencing depth is low. In conclusion, we have extended our previous linear model (LM) framework to a generalized linear model (GLM) framework and derived NGS data-based testing methods for a group of genetic variants. Compared with our previously proposed LM-based methods [2], the new GLM-based methods can handle more complex responses (for example, binary responses and count responses) in addition to continuous responses. Our methods have filled the literature gap and shown advantage over their corresponding genotype-based methods in the literature.

Transcriptome analysis of mulberry (Morus alba L.) leaves to identify differentially expressed genes associated with post-harvest shelf-life elongation

Present study deals with molecular expression patterns responsible for post-harvest shelf-life extension of mulberry leaves. Quantitative profiling showed retention of primary metabolite and accumulation of stress markers in NS7 and CO7 respectively. The leaf mRNA profiles was sequenced using the Illumina platform to identify DEGs. A total of 3413 DEGs were identified between the treatments. Annotation with Arabidopsis database has identified 1022 DEGs unigenes. STRING generated protein-protein interaction, identified 1013 DEGs nodes with p < 1.0e-16. KEGG classifier has identified genes and their participating biological processes. MCODE and BiNGO detected sub-networking and ontological enrichment, respectively at p ≤ 0.05. Genes associated with chloroplast architecture, photosynthesis, detoxifying ROS and RCS, and innate-immune response were significantly up-regulated, responsible for extending shelf-life in NS7. Loss of storage sucrose, enhanced activity of senescence-related hormones, accumulation of xenobiotics, and development of osmotic stress inside tissue system was the probable reason for tissue deterioration in CO7. qPCR validation of DEGs was in good agreement with RNA sequencing results, indicating the reliability of the sequencing platform. Present outcome provides a molecular insight regarding involvement of genes in self-life extension, which might help the sericulture industry to overcome their pre-existing problems related to landless farmers and larval feeding during monsoon.

The Full-Length Transcriptome Sequencing and Identification of Na+/H+ Antiporter Genes in Halophyte Nitraria tangutorum Bobrov

Nitraria tangutorum Bobrov is a halophyte that is resistant to salt and alkali and is widely distributed in northwestern China. However, its genome has not been sequenced, thereby limiting studies on this particular species. For species without a reference genome, the full-length transcriptome is a convenient and rapid way to obtain reference gene information. To better study N. tangutorum, we used PacBio single-molecule real-time technology to perform full-length transcriptome analysis of this halophyte. In this study, a total of 21.83 Gb of data were obtained, and 198,300 transcripts, 51,875 SSRs (simple sequence repeats), 55,574 CDS (coding sequence), and 74,913 lncRNAs (long non-coding RNA) were identified. In addition, using this full-length transcriptome, we identified the key Na⁺/H⁺ antiporter (NHX) genes that maintain ion balance in plants and found that these are induced to express under salt stress. The results indicate that the full-length transcriptome of N. tangutorum can be used as a database and be utilized in elucidating the salt tolerance mechanism of N. tangutorum.

Reanalysis and Revision of the Complete Mitochondrial Genome of Artemia urmiana Günther, 1899 (Crustacea: Anostraca)

In the previously published mitochondrial genome sequence of Artemia urmiana (NC_021382 [JQ975176]), the taxonomic status of the examined Artemia had not been determined, due to parthenogenetic populations coexisting with A. urmiana in Urmia Lake. Additionally, NC_021382 [JQ975176] has been obtained with pooled cysts of Artemia (0.25 g cysts consists of 20,000–25,000 cysts), not a single specimen. With regard to coexisting populations in Urmia Lake, and intra- and inter-specific variations in the pooled samples, NC_021382 [JQ975176] cannot be recommended as a valid sequence and any attempt to attribute it to A. urmiana or a parthenogenetic population is unreasonable. With the aid of next-generation sequencing methods, we characterized and assembled a complete mitochondrial genome of A. urmiana with defined taxonomic status. Our results reveal that in the previously published mitogenome (NC_021382 [JQ975176]), tRNA-Phe has been erroneously attributed to the heavy strand but it is encoded in the light strand. There was a major problem in the position of the ND5. It was extended over the tRNA-Phe, which is biologically incorrect. We have also identified a partial nucleotide sequence of 311 bp that was probably erroneously duplicated in the assembly of the control region of NC_021382 [JQ975176], which enlarges the control region length by 16%. This partial sequence could not be recognized in our assembled mitogenome as well as in 48 further examined specimens of A. urmiana. Although, only COX1 and 16S genes have been widely used for phylogenetic studies in Artemia, our findings reveal substantial differences in the nucleotide composition of some other genes (including ATP8, ATP6, ND3, ND6, ND1 and COX3) among Artemia species. It is suggested that these markers should be included in future phylogenetic studies.

Using Apache Spark on genome assembly for scalable overlap-graph reduction

Background

De novo genome assembly is a technique that builds the genome of a specimen using overlaps of genomic fragments without additional work with reference sequence. Sequence fragments (called reads) are assembled as contigs and scaffolds by the overlaps. The quality of the de novo assembly depends on the length and continuity of the assembly. To enable faster and more accurate assembly of species, existing sequencing techniques have been proposed, for example, high-throughput next-generation sequencing and long-reads-producing third-generation sequencing. However, these techniques require a large amounts of computer memory when very huge-size overlap graphs are resolved. Also, it is challenging for parallel computation.

Results

To address the limitations, we propose an innovative algorithmic approach, called Scalable Overlap-graph Reduction Algorithms (SORA). SORA is an algorithm package that performs string graph reduction algorithms by Apache Spark. The SORA’s implementations are designed to execute de novo genome assembly on either a single machine or a distributed computing platform. SORA efficiently compacts the number of edges on enormous graphing paths by adapting scalable features of graph processing libraries provided by Apache Spark, GraphX and GraphFrames.

Conclusions

We shared the algorithms and the experimental results at our project website, https://github.com/BioHPC/SORA. We evaluated SORA with the human genome samples. First, it processed a nearly one billion edge graph on a distributed cloud cluster. Second, it processed mid-to-small size graphs on a single workstation within a short time frame. Overall, SORA achieved the linear-scaling simulations for the increased computing instances.

Functional annotation of mulberry (Morus spp.) transcriptome, differential expression of genes related to growth and identification of putative genic SSRs, SNPs and InDels

Growth is a complex trait associated with mulberry leaf yield and controlled by several genes. In this study, we have explored the molecular basis underlying growth using Transcriptome profiling of contrasting genotypes. A total of 66.6 Mbp of primary transcriptomes from high growth (HGG)-Jalalgarah-3 and M. laevigata (H) and, low growth genotypes (LGG)-Harmutty and Vadagaraparai-2; resulting in 24210, 27998, 28085 and 28764 final transcripts respectively. Out of the 34096 pooled transcripts, 20249 transcripts matched with at least one sequence of the non-redundant database. Functional annotation resulted in the categorization of 18970 transcripts into 3 gene ontology (GO) terms and 7440 were assigned to 23 Kyoto encyclopaedia of genes and genomes (KEGG) pathway. Based on the differentially expressed genes and gene enrichment analysis, over expression of photosynthetic related transcripts in HGG and defence related transcripts in LGG were noted. Simple sequence repeats were mined from unique transcripts and the most abundant motifs were tri- (1883) followed by di- (1710), tetra- (192), penta- (68) and hexa- (40) repeats. Further, a total of 390897 high quality SNPs and 8081 InDels were identified by mapping onto Morus notabilis reference genome. The study provides an insight into the expression of genes involved in growth and further research on utilization in gentic improvement of the crop.

Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism

Parasitic plants in the genus Striga, commonly known as witchweeds, cause major crop losses in sub-Saharan Africa and pose a threat to agriculture worldwide. An understanding of Striga parasite biology, which could lead to agricultural solutions, has been hampered by the lack of genome information. Here, we report the draft genome sequence of Striga asiatica with 34,577 predicted protein-coding genes, which reflects gene family contractions and expansions that are consistent with a three-phase model of parasitic plant genome evolution. Striga seeds germinate in response to host-derived strigolactones (SLs) and then develop a specialized penetration structure, the haustorium, to invade the host root. A family of SL receptors has undergone a striking expansion, suggesting a molecular basis for the evolution of broad host range among Striga spp. We found that genes involved in lateral root development in non-parasitic model species are coordinately induced during haustorium development in Striga, suggesting a pathway that was partly co-opted during the evolution of the haustorium. In addition, we found evidence for horizontal transfer of host genes as well as retrotransposons, indicating gene flow to S. asiatica from hosts. Our results provide valuable insights into the evolution of parasitism and a key resource for the future development of Striga control strategies.

Entomology in the 21st Century: Tackling Insect Invasions, Promoting Advancements in Technology, and Using Effective Science Communication-2018 Student Debates

The 2018 student debates of the Entomological Society of America were held at the Joint Annual Meeting for the Entomological Societies of America, Canada, and British Columbia in Vancouver, BC. Three unbiased introductory speakers and six debate teams discussed and debated topics under the theme 'Entomology in the 21st Century: Tackling Insect Invasions, Promoting Advancements in Technology, and Using Effective Science Communication'. This year's debate topics included: 1) What is the most harmful invasive insect species in the world? 2) How can scientists diffuse the stigma or scare factor surrounding issues that become controversial such as genetically modified organisms, agricultural biotechnological developments, or pesticide chemicals? 3) What new/emerging technologies have the potential to revolutionize entomology (other than Clustered Regularly Interspaced Short Palindromic Repeats)? Introductory speakers and debate teams spent approximately 9 mo preparing their statements and arguments and had the opportunity to share this at the Joint Annual Meeting with an engaged audience.

Transcriptome profiling uncovers β-galactosidases of diverse domain classes influencing hypocotyl development in jute (Corchorus capsularis L.)

Enzyme β-galactosidase (EC 3.2.1.23) is known to influence vascular differentiation during early vegetative growth of plants, but its role in hypocotyl development is not yet fully understood. We generated the hypocotyl transcriptome data of a hypocotyl-defect jute (Corchorus capsularis L.) mutant (52,393 unigenes) and its wild-type (WT) cv. JRC-212 (44,720 unigenes) by paired-end RNA-seq and identified 11 isoforms of β-galactosidase, using a combination of sequence annotation, domain identification and structural-homology modeling. Phylogenetic analysis classified the jute β-galactosidases into six subfamilies of glycoside hydrolase-35 family, which are closely related to homologs from Malvaceous species. We also report here the expression of a β-galactosidase of glycoside hydrolase-2 family that was earlier considered to be absent in higher plants. Comparative analysis of domain structure allowed us to propose a domain-centric evolution of the five classes of plant β-galactosidases. Further, we observed 1.8-12.2-fold higher expression of nine β-galactosidase isoforms in the mutant hypocotyl, which was characterized by slower growth, undulated shape and deformed cell wall. In vitro and in vivo β-galactosidase activities were also higher in the mutant hypocotyl. Phenotypic analysis supported a significant (P ≤ 0.01) positive correlation between enzyme activity and undulated hypocotyl. Taken together, our study identifies the complete set of β-galactosidases expressed in the jute hypocotyl, and provides compelling evidence that they may be involved in cell wall degradation during hypocotyl development.

Complete mitochondrial genome of a kind of snakehead fish Channa siamensis and its phylogenetic consideration

The snakehead fish, Channa siamensis, belongs to the genus of Channa (perciformes: Channidae) and was first reported by Günther in 1861. Despite it has been described approximately for 15 decades, the genetic information is limited and the taxon status of this kind of fish is still unclear. The primary objective of this study is to get more genomic data and calculate the taxon location of this kind of fish. The next generation sequencing method was used to obtain the whole mitochondrial DNA information, and bioinformatic analysis was performed to investigate the evolutionary status and taxon location of C. siamensis. The circular mitochondrial DNA was 16,570 bp in length, and which showed typical piscine structure and arrangement. The overall nucleotide composition was 29.28% A, 24.72% T, 30.71% C, 15.29% G, with 54.1% AT, respectively. Phylogenetic analyses using concatenated amino acid and nucleotide sequences of the 13 protein-coding genes with two different methods (Maximum likelihood and Bayesian analysis) both highly supported C. siamensis belongs to the genus Channa and shows a close relationship with C. micropeltes. These data will provide more useful information for a better understanding of the mitochondrial genomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.

Comparative Analysis of Impatiens Leaf Transcriptomes Reveal Candidate Genes for Resistance to Downy Mildew Caused by Plasmopara obducens

Impatiens downy mildew (IDM) is a devastating disease to garden impatiens. A good understanding of IDM resistance in New Guinea impatiens is essential for improving garden impatiens resistance to this disease. The present study was conducted to sequence, assemble, annotate and compare the leaf transcriptomes of two impatiens cultivars differing in resistance to IDM, reveal sequence polymorphisms and identify candidate genes for IDM resistance. RNA-Seq was performed on cultivars Super Elfin® XP Pink (SEP) and SunPatiens® Compact Royal Magenta (SPR). De novo assembly of obtained sequence reads resulted in 121,497 unigenes with an average length of 1156 nucleotides and N50 length of 1778 nucleotides. Searching the non-redundant protein and non-redundant nucleotide, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups and Gene Ontology databases, resulted in annotation of 57.7% to 73.6% of the unigenes. Fifteen unigenes were highly similar to disease resistance genes and more abundant in the IDM-resistant cultivar than in the susceptible cultivar. A total of 22,484 simple sequence repeats (SSRs) and 245,936 and 120,073 single nucleotide polymorphisms (SNPs) were identified from SPR and SEP respectively. The assembled transcripts and unigenes, identified disease resistance genes and SSRs and SNPs sites will be a valuable resource for improving impatiens and its IDM resistance.

Comparative De Novo Transcriptome Assembly of Notophthalmus viridescens RNA-seq Data using Two Commercial Software Programs

Background and Purpose

The reduction of cost and ease of using core laboratories or commercial sequencing companies have allowed biomedical and health researchers alike to employ reference-based genomic or transcriptomic sequencing (RNA-seq) projects to expand their work. Non-reference based data analysis, in cases of inexperienced researchers, become more challenging despite the availability of many open source and commercial software programs.

Methods

We performed de novo assembly of RNA-seq data obtained from a non-model organism (Eastern Newt skin) to compare data output of two commercially available software workflows.

Results

Our results show that the software packages performed satisfactorily albeit with differences in how the annotated and novel transcripts were identified and listed.

Conclusion

Overall, we conclude that the use of commercial software platforms has a clear advantage to that of open source programs because of convenience with data analysis workflows. One caveat is that users need to know the software's basic algorithm and technical approach, in order to determine the precision and validity of the data output. Thus, it is imperative that researchers fully evaluate the software according to their needs to determine their suitability.

Transcriptome analysis of mud crab (Scylla paramamosain) gills in response to Mud crab reovirus (MCRV)

Mud crab (Scylla paramamosain) is an economically important marine cultured species in China's coastal area. Mud crab reovirus (MCRV) is the most important pathogen of mud crab, resulting in large economic losses in crab farming. In this paper, next-generation sequencing technology and bioinformatics analysis are used to study transcriptome differences between MCRV-infected mud crab and normal control. A total of 104.3 million clean reads were obtained, including 52.7 million and 51.6 million clean reads from MCRV-infected (CA) and controlled (HA) mud crabs respectively. 81,901, 70,059 and 67,279 unigenes were gained respectively from HA reads, CA reads and HA&CA reads. A total of 32,547 unigenes from HA&CA reads called All-Unigenes were matched to at least one database among Nr, Nt, Swiss-prot, COG, GO and KEGG databases. Among these, 13,039, 20,260 and 11,866 unigenes belonged to the 3, 258 and 25 categories of GO, KEGG pathway, and COG databases, respectively. Solexa/Illumina's DGE platform was also used, and about 13,856 differentially expressed genes (DEGs), including 4444 significantly upregulated and 9412 downregulated DEGs were detected in diseased crabs compared with the control. KEGG pathway analysis revealed that DEGs were obviously enriched in the pathways related to different diseases or infections. This transcriptome analysis provided valuable information on gene functions associated with the response to MCRV in mud crab, as well as detail information for identifying novel genes in the absence of the mud crab genome database.

Microbial Ecology: Where are we now?

Conventional microbiological methods have been readily taken over by newer molecular techniques due to the ease of use, reproducibility, sensitivity and speed of working with nucleic acids. These tools allow high throughput analysis of complex and diverse microbial communities, such as those in soil, freshwater, saltwater, or the microbiota living in collaboration with a host organism (plant, mouse, human, etc). For instance, these methods have been robustly used for characterizing the plant (rhizosphere), animal and human microbiome specifically the complex intestinal microbiota. The human body has been referred to as the Superorganism since microbial genes are more numerous than the number of human genes and are essential to the health of the host. In this review we provide an overview of the Next Generation tools currently available to study microbial ecology, along with their limitations and advantages.

Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit

BACKGROUND

Symplocos paniculata, asiatic sweetleaf or sapphire berry, is a widespread shrub or small tree from Symplocaceae with high oil content and excellent fatty acid composition in fruit. It has been used as feedstocks for biodiesel and cooking oil production in China. Little transcriptome information is available on the regulatory molecular mechanism of oil accumulation at different fruit development stages.

RESULTS

The transcriptome at four different stages of fruit development (10, 80,140, and 170 days after flowering) of S. paniculata were analyzed. Approximately 28 million high quality clean reads were generated. These reads were trimmed and assembled into 182,904 non-redundant putative transcripts with a mean length of 592.91 bp and N50 length of 785 bp, respectively. Based on the functional annotation through Basic Local Alignment Search Tool (BLAST) with public protein database, the key enzymes involved in lipid metabolism were identified, and a schematic diagram of the pathway and temporal expression patterns of lipid metabolism was established. About 13,939 differentially expressed unigenes (DEGs) were screened out using differentially expressed sequencing (DESeq) method. The transcriptional regulatory patterns of the identified enzymes were highly related to the dynamic oil accumulation along with the fruit development of S. paniculata. In addition, quantitative real-time PCR (qRT-PCR) of six vital genes was significantly correlated with DESeq data.

CONCLUSIONS

The transcriptome sequences obtained and deposited in NCBI would enrich the public database and provide an unprecedented resource for the discovery of the genes associated with lipid metabolism pathway in S. paniculata. Results in this study will lay the foundation for exploring transcriptional regulatory profiles, elucidating molecular regulatory mechanisms, and accelerating genetic engineering process to improve the yield and quality of seed oil of S. paniculata.

RNA-seq analysis of Paris polyphylla var. yunnanensis roots identified candidate genes for saponin synthesis

Paris polyphylla Smith var. yunnanensis (Franch.) Hand.-Mazz. is a rhizomatous, herbaceous, perennial plant that has been used for more than a thousand years in traditional Chinese medicine. It is facing extinction due to overharvesting. Steroids are the major therapeutic components in Paris roots, the commercial value of which increases with age. To date, no genomic data on the species have been available. In this study, transcriptome analysis of an 8-year-old root and a 4-year-old root provided insight into the metabolic pathways that generate the steroids. Using Illumina sequencing technology, we generated a high-quality sequence and demonstrated de novo assembly and annotation of genes in the absence of prior genome information. Approximately 87,577 unique sequences, with an average length of 614 bases, were obtained from the root cells. Using bioinformatics methods, we annotated approximately 65.51% of the unique sequences by conducting a similarity search with known genes in the National Center for Biotechnology Information's non-redundant database. The unique transcripts were functionally classified using the Gene Ontology hierarchy and the Kyoto Encyclopedia of Genes and Genomes database. Of 3082 genes that were identified as significantly differentially expressed between roots of different ages, 1518 (49.25%) were upregulated and 1564 (50.75%) were downregulated in the older root. Metabolic pathway analysis predicted that 25 unigenes were responsible for the biosynthesis of the saponins steroids. These data represent a valuable resource for future genomic studies on this endangered species and will be valuable for efforts to genetically engineer P. polyphylla and facilitate saponin-rich plant development.

De novo transcriptome sequencing and gene expression profiling of spinach (Spinacia oleracea L.) leaves under heat stress

Spinach (Spinacia oleracea) has cold tolerant but heat sensitive characteristics. The spinach variety ‘Island,’ is suitable for summer periods. There is lack molecular information available for spinach in response to heat stress. In this study, high throughput de novo transcriptome sequencing and gene expression analyses were carried out at different spinach variety ‘Island’ leaves (grown at 24 °C (control), exposed to 35 °C for 30 min (S1), and 5 h (S2)). A total of 133,200,898 clean reads were assembled into 59,413 unigenes (average size 1259.55 bp). 33,573 unigenes could match to public databases. The DEG of controls vs S1 was 986, the DEG of control vs S2 was 1741 and the DEG of S1 vs S2 was 1587. Gene Ontology (GO) and pathway enrichment analysis indicated that a great deal of heat-responsive genes and other stress-responsive genes were identified in these DEGs, suggesting that the heat stress may have induced an extensive abiotic stress effect. Comparative transcriptome analysis found 896 unique genes in spinach heat response transcript. The expression patterns of 13 selected genes were verified by RT-qPCR (quantitative real-time PCR). Our study found a series of candidate genes and pathways that may be related to heat resistance in spinach.

Study Design for Sequencing Studies

Once a biochemical method has been devised to sample RNA or DNA of interest, sequencing can be used to identify the sampled molecules with high fidelity and low bias. High-throughput sequencing has therefore become the primary data acquisition method for many genomics studies and is being used more and more to address molecular biology questions. By applying principles of statistical experimental design, sequencing experiments can be made more sensitive to the effects under study as well as more biologically sound, hence more replicable.

Physiological Characterization and Comparative Transcriptome Analysis of a Slow-Growing Reduced-Thylakoid Mutant of Chinese Cabbage (Brassica campestris ssp. pekinensis)

Mutants are ideal for studying physiological processes. The leaves of Chinese cabbage are a major place for photosynthesis, and the mutation of these leaves may directly affect the rate of plant growth and development, thus influencing the formation of its leafy head. We characterized a slow-growing mutant, which was designated as drm. The drm exhibited slow growth and development at the seedling and heading stages, leading to the production of a tiny, leafy head, and chlorophyll-deficient leaves, especially in seedlings. Genetic analysis indicated that the phenotype of drm was controlled by a single recessive nuclear gene. Compared with the wild-type "FT" line, the drm's chlorophyll content was significantly reduced and its chloroplast structure was abnormal. Moreover, its photosynthetic efficiency and chlorophyll fluorescence parameters were significantly decreased. The changes in leaf color, combined with these altered physiological characters, may influence the growth and development of plant, ultimately resulting in the slow-growing phenotype. To further understand the molecular regulation mechanisms of phenotypic differences between "FT" and drm, comparative transcriptome analyses were performed using RNA-Seq; a total of 338 differentially expressed genes (DEGs) were detected between "FT" and drm. According to GO and KEGG pathway analysis, a number of DEGs involved in chlorophyll degradation and photosynthesis were identified, such as chlorophyllase and ribulose-1,5-bisphosphate carboxylase/oxygenase. In addition, the expression patterns of 12 DEGs, including three chlorophyll degradation- and photosynthesis-related genes and nine randomly-selected genes, were confirmed by qRT-PCR. Numerous single nucleotide polymorphisms were also identified, providing a valuable resource for research and molecular marker-assistant breeding in Chinese cabbage. These results contribute to our understanding of the molecular regulation mechanisms underlying growth and development and lay the foundation for future genetic and functional genomics in Chinese cabbage.

Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.)

Wheat is a staple food worldwide and provides 40% of the calories in the diet. Climate change and global warming pose a threat to wheat production, however, and demand a deeper understanding of how heat stress might impact wheat production and wheat biology. However, it is difficult to identify novel heat stress associated genes when the genomic information is not available. Wheat has a very large and complex genome that is about 37 times the size of the rice genome. The present study sequenced the whole transcriptome of the wheat cv. HD2329 at the flowering stage, under control (22°±3°C) and heat stress (42°C, 2 h) conditions using Illumina HiSeq and Roche GS-FLX 454 platforms. We assembled more than 26.3 and 25.6 million high-quality reads from the control and HS-treated tissues transcriptome sequences respectively. About 76,556 (control) and 54,033 (HS-treated) contigs were assembled and annotated de novo using different assemblers and a total of 21,529 unigenes were obtained. Gene expression profile showed significant differential expression of 1525 transcripts under heat stress, of which 27 transcripts showed very high (>10) fold upregulation. Cellular processes such as metabolic processes, protein phosphorylation, oxidations-reductions, among others were highly influenced by heat stress. In summary, these observations significantly enrich the transcript dataset of wheat available on public domain and show a de novo approach to discover the heat-responsive transcripts of wheat, which can accelerate the progress of wheat stress-genomics as well as the course of wheat breeding programs in the era of climate change.

Do Molecular Markers Inform About Pleiotropy?

The availability of dense panels of common single-nucleotide polymorphisms and sequence variants has facilitated the study of statistical features of the genetic architecture of complex traits and diseases via whole-genome regressions (WGRs). At the onset, traits were analyzed trait by trait, but recently, WGRs have been extended for analysis of several traits jointly. The expectation is that such an approach would offer insight into mechanisms that cause trait associations, such as pleiotropy. We demonstrate that correlation parameters inferred using markers can give a distorted picture of the genetic correlation between traits. In the absence of knowledge of linkage disequilibrium relationships between quantitative or disease trait loci and markers, speculating about genetic correlation and its causes (e.g., pleiotropy) using genomic data is conjectural.

Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids

BACKGROUND

Avocado (Persea americana) is an economically important tropical fruit considered to be a good source of fatty acids. Despite its importance, the molecular and cellular characterization of biochemical and developmental processes in avocado is limited due to the lack of transcriptome and genomic information.

RESULTS

The transcriptomes of seeds, roots, stems, leaves, aerial buds and flowers were determined using different sequencing platforms. Additionally, the transcriptomes of three different stages of fruit ripening (pre-climacteric, climacteric and post-climacteric) were also analyzed. The analysis of the RNAseqatlas presented here reveals strong differences in gene expression patterns between different organs, especially between root and flower, but also reveals similarities among the gene expression patterns in other organs, such as stem, leaves and aerial buds (vegetative organs) or seed and fruit (storage organs). Important regulators, functional categories, and differentially expressed genes involved in avocado fruit ripening were identified. Additionally, to demonstrate the utility of the avocado gene expression atlas, we investigated the expression patterns of genes implicated in fatty acid metabolism and fruit ripening.

CONCLUSIONS

A description of transcriptomic changes occurring during fruit ripening was obtained in Mexican avocado, contributing to a dynamic view of the expression patterns of genes involved in fatty acid biosynthesis and the fruit ripening process.

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.

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies

The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.

The effect on the transcriptome of Anemone coronaria following infection with rust (Tranzschelia discolor)

In order to understand plant/pathogen interaction, the transcriptome of uninfected (1S) and infected (2I) plant was sequenced at 3'end by the GS FLX 454 platform. De novo assembly of high-quality reads generated 27,231 contigs leaving 37,191 singletons in the 1S and 38,393 in the 2I libraries. ESTcalc tool suggested that 71% of the transcriptome had been captured, with 99% of the genes present being represented by at least one read. Unigene annotation showed that 50.5% of the predicted translation products shared significant homology with protein sequences in GenBank. In all 253 differential transcript abundance (DTAs) were in higher abundance and 52 in lower abundance in the 2I library. 128 higher abundance DTA genes were of fungal origin and 49 were clearly plant sequences. A tBLASTn-based search of the sequences using as query the full length predicted polypeptide product of 50 R genes identified 16 R gene products. Only one R gene (PGIP) was up-regulated. The response of the plant to fungal invasion included the up-regulation of several pathogenesis related protein (PR) genes involved in JA signaling and other genes associated with defense response and down regulation of cell wall associated genes, non-race-specific disease resistance1 (NDR1) and other genes like myb, presqualene diphosphate phosphatase (PSDPase), a UDP-glycosyltransferase 74E2-like (UGT). The DTA genes identified here should provide a basis for understanding the A. coronaria/T. discolor interaction and leads for biotechnology-based disease resistance breeding.

Pathways associated with lignin biosynthesis in lignomaniac jute fibres

We generated the bast transcriptomes of a deficient lignified phloem fibre mutant and its wild-type jute (Corchorus capsularis) using Illumina paired-end sequencing. A total of 34,163 wild-type and 29,463 mutant unigenes, with average lengths of 1442 and 1136 bp, respectively, were assembled de novo, ~77-79 % of which were functionally annotated. These annotated unigenes were assigned to COG (~37-40 %) and GO (~22-28 %) classifications and mapped to 189 KEGG pathways (~19-21 %). We discovered 38 and 43 isoforms of 16 and 10 genes of the upstream shikimate-aromatic amino acid and downstream monolignol biosynthetic pathways, respectively, rendered their sequence similarities, confirmed the identities of 22 of these candidate gene families by phylogenetic analyses and reconstructed the pathway leading to lignin biosynthesis in jute fibres. We also identified major genes and bast-related transcription factors involved in secondary cell wall (SCW) formation. The quantitative RT-PCRs revealed that phenylalanine ammonia-lyase 1 (CcPAL1) was co-down-regulated with several genes of the upstream shikimate pathway in mutant bast tissues at an early growth stage, although its expression relapsed to the normal level at the later growth stage. However, cinnamyl alcohol dehydrogenase 7 (CcCAD7) was strongly down-regulated in mutant bast tissues irrespective of growth stages. CcCAD7 disruption at an early growth stage was accompanied by co-up-regulation of SCW-specific genes cellulose synthase A7 (CcCesA7) and fasciclin-like arabinogalactan 6 (CcFLA6), which was predicted to be involved in coordinating the S-layers' deposition in the xylan-type jute fibres. Our results identified CAD as a promising target for developing low-lignin jute fibres using genomics-assisted molecular approaches.

A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia)

BACKGROUND

Pods of the vanilla orchid (Vanilla planifolia) accumulate large amounts of the flavor compound vanillin (3-methoxy, 4-hydroxy-benzaldehyde) as a glucoside during the later stages of their development. At earlier stages, the developing seeds within the pod synthesize a novel lignin polymer, catechyl (C) lignin, in their coats. Genomic resources for determining the biosynthetic routes to these compounds and other flavor components in V. planifolia are currently limited.

RESULTS

Using next-generation sequencing technologies, we have generated very large gene sequence datasets from vanilla pods at different times of development, and representing different tissue types, including the seeds, hairs, placental and mesocarp tissues. This developmental series was chosen as being the most informative for interrogation of pathways of vanillin and C-lignin biosynthesis in the pod and seed, respectively. The combined 454/Illumina RNA-seq platforms provide both deep sequence coverage and high quality de novo transcriptome assembly for this non-model crop species.

CONCLUSIONS

The annotated sequence data provide a foundation for understanding multiple aspects of the biochemistry and development of the vanilla bean, as exemplified by the identification of candidate genes involved in lignin biosynthesis. Our transcriptome data indicate that C-lignin formation in the seed coat involves coordinate expression of monolignol biosynthetic genes with the exception of those encoding the caffeoyl coenzyme A 3-O-methyltransferase for conversion of caffeoyl to feruloyl moieties. This database provides a general resource for further studies on this important flavor species.

Transcriptome sequencing and profiling of expressed genes in phloem and xylem of ramie (Boehmeria nivea L. Gaud)

Ramie (Boehmeria nivea L. Gaud) is a highly versatile herbaceous plant which is widely cropped in southern China. The success of this herbaceous plant relies on wide use in modern industry. Understanding the profiling of expressed genes in phloem and xylem of ramie is crucial for improving its industrial performance. Herein, we uncover the transcriptome profile in phloem and xylem in present study. Using Illumina paired-end sequencing technology, 57 million high quality reads were generated. De novo assembly yielded 87,144 unigenes with an average length of 635 bp. By sequence similarity searching for public databases, a total of 32,541 (41.77%) unigenes were annotated for their function. Among these genes, 57,873 (66.4%) and 28,678 (32.9%) unigenes were assigned to categories of Gene Ontology and Orthologous Groups database, respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 18,331 (21.0%) unigenes were mapped to 125 pathways. The metabolic pathways were assigned the most unigene (4,793, 26.2%). Furthermore, Pol II and Pol III subunits as well as the genes of Galactose metabolism pathway had higher expression in phloem compared to xylem. In addition, fatty acid metabolism pathway genes showed more abundant in xylem than phloem. These results suggest that high activities of RNA synthesis and Galactose metabolism pathway promises fiber synthesis in phloem. The present study is the initial exploration to uncover the fiber biosynthesis difference between phloem and xylem in ramie through the analysis of deep sequencing data.

A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird

De novo assembled transcriptomes, in combination with RNA-Seq, are powerful tools to explore gene sequence and expression level in organisms without reference genomes. Investigators must first choose which high throughput sequencing platforms will provide data most suitable for their experimental goals. In this study, we explore the utility of 454 and Illumina sequences for de novo transcriptome assembly and downstream RNA-Seq applications in a reproductive gland from a non-model bird species, the Japanese quail (Coturnix japonica). Four transcriptomes composed of either pure 454 or Illumina reads or mixtures of read types were assembled and evaluated for the same cost. Illumina assemblies performed best for de novo transcriptome characterization in terms of contig length, transcriptome coverage, and complete assembly of gene transcripts. Improvements over the Hybrid assembly were marginal, with the exception that the addition of 454 data significantly increased the number of genes annotated. The Illumina assembly provided the best reference to align an independent set of RNA-Seq data as ∼84% of reads mapped to single genes in the transcriptome. Contigs constructed solely from 454 data may impose problems for RNA-Seq as our 454 transcriptome revealed a high number of indels and many ambiguously mapped reads. Correcting the 454 transcriptome with Illumina reads was an effective strategy to deal with indel and frameshift errors inherent to the 454 transcriptome, but at the cost of transcriptome coverage. In the absence of a reference genome, we find that Illumina reads alone produced a high quality transcriptome appropriate for RNA-Seq gene expression analyses.

Future of portable devices for plant pathogen diagnosis

The demand for rapid and accurate diagnosis of plant diseases has risen in the last decade. On-site diagnosis of single or multiple pathogens using portable devices is the first step in this endeavour. Despite extensive attempts to develop portable devices for pathogen detection, current technologies are still restricted to detecting known pathogens with limited detection accuracy. Developing new detection techniques for rapid and accurate detection of multiple plant pathogens and their associated variants is essential. Recent single DNA sequencing technologies are a promising new avenue for developing future portable devices for plant pathogen detection. In this review, we detail the current progress in portable devices and technologies used for detecting plant pathogens, the current position of emerging sequencing technologies for analysis of plant genomics, and the future of portable devices for rapid pathogen diagnosis.

Transcriptome analysis of the oil-rich tea plant, Camellia oleifera, reveals candidate genes related to lipid metabolism

Background

Rapidly driven by the need for developing sustainable sources of nutritionally important fatty acids and the rising concerns about environmental impacts after using fossil oil, oil-plants have received increasing awareness nowadays. As an important oil-rich plant in China, Camellia oleifera has played a vital role in providing nutritional applications, biofuel productions and chemical feedstocks. However, the lack of C. oleifera genome sequences and little genetic information have largely hampered the urgent needs for efficient utilization of the abundant germplasms towards modern breeding efforts of this woody oil-plant.

Results

Here, using the 454 GS-FLX sequencing platform, we generated approximately 600,000 RNA-Seq reads from four tissues of C. oleifera. These reads were trimmed and assembled into 104,842 non-redundant putative transcripts with a total length of ∼38.9 Mb, representing more than 218-fold of all the C. oleifera sequences currently deposited in the GenBank (as of March 2014). Based on the BLAST similarity searches, nearly 42.6% transcripts could be annotated with known genes, conserved domains, or Gene Ontology (GO) terms. Comparisons with the cultivated tea tree, C. sinensis, identified 3,022 pairs of orthologs, of which 211 exhibited the evidence under positive selection. Pathway analysis detected the majority of genes potentially related to lipid metabolism. Evolutionary analysis of omega-6 fatty acid desaturase (FAD2) genes among 20 oil-plants unexpectedly suggests that a parallel evolution may occur between C. oleifera and Olea oleifera. Additionally, more than 2,300 simple sequence repeats (SSRs) and 20,200 single-nucleotide polymorphisms (SNPs) were detected in the C. oleifera transcriptome.

Conclusions

The generated transcriptome represents a considerable increase in the number of sequences deposited in the public databases, providing an unprecedented opportunity to discover all related-genes associated with lipid metabolic pathway in C. oleifera. It will greatly enhance the generation of new varieties of C. oleifera with increased yields and high quality.

Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca×Picea engelmannii)

Species respond to environmental stress through a combination of genetic adaptation and phenotypic plasticity, both of which may be important for survival in the face of climatic change. By characterizing the molecular basis of plastic responses and comparing patterns among species, it is possible to identify how such traits evolve. Here, we used de novo transcriptome assembly and RNAseq to explore how patterns of gene expression differ in response to temperature, moisture, and light regime treatments in lodgepole pine (Pinus contorta) and interior spruce (a natural hybrid population of Picea glauca and Picea engelmannii). We found wide evidence for an effect of treatment on expression within each species, with 6413 and 11,658 differentially expressed genes identified in spruce and pine, respectively. Comparing patterns of expression among these species, we found that 74% of all orthologs with differential expression had a pattern that was conserved in both species, despite 140 million yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression. We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species.

The first set of expressed sequence tags (EST) from the medicinal mushroom Agaricus subrufescens delivers resource for gene discovery and marker development

Agaricus subrufescens is one of the most important culinary-medicinal cultivable mushrooms with potentially high-added-value products and extended agronomical valorization. The development of A. subrufescens-related technologies is hampered by, among others, the lack of suitable molecular tools. Thus, this mushroom is considered as a genomic orphan species with a very limited number of available molecular markers or sequences. To fill this gap, this study reports the generation and analysis of the first set of expressed sequence tags (EST) for A. subrufescens. cDNA fragments obtained from young sporophores (SP) and vegetative mycelium in liquid culture (CL) were sequenced using 454 pyrosequencing technology. After assembly process, 4,989 and 5,125 sequences were obtained in SP and CL libraries, respectively. About 87% of the EST had significant similarity with Agaricus bisporus-predicted proteins, and 79% correspond to known proteins. Functional categorization according to Gene Ontology could be assigned to 49% of the sequences. Some gene families potentially involved in bioactive compound biosynthesis could be identified. A total of 232 simple sequence repeats (SSRs) were identified, and a set of 40 EST-SSR polymorphic markers were successfully developed. This EST dataset provides a new resource for gene discovery and molecular marker development. It constitutes a solid basis for further genetic and genomic studies in A. subrufescens.

The mitochondrial genome of the leaf-cutter ant Atta laevigata: a mitogenome with a large number of intergenic spacers

In this paper we describe the nearly complete mitochondrial genome of the leaf-cutter ant Atta laevigata, assembled using transcriptomic libraries from Sanger and Illumina next generation sequencing (NGS), and PCR products. This mitogenome was found to be very large (18,729 bp), given the presence of 30 non-coding intergenic spacers (IGS) spanning 3,808 bp. A portion of the putative control region remained unsequenced. The gene content and organization correspond to that inferred for the ancestral pancrustacea, except for two tRNA gene rearrangements that have been described previously in other ants. The IGS were highly variable in length and dispersed through the mitogenome. This pattern was also found for the other hymenopterans in particular for the monophyletic Apocrita. These spacers with unknown function may be valuable for characterizing genome evolution and distinguishing closely related species and individuals. NGS provided better coverage than Sanger sequencing, especially for tRNA and ribosomal subunit genes, thus facilitating efforts to fill in sequence gaps. The results obtained showed that data from transcriptomic libraries contain valuable information for assembling mitogenomes. The present data also provide a source of molecular markers that will be very important for improving our understanding of genomic evolutionary processes and phylogenetic relationships among hymenopterans.

Mining Gene Expression Data Focusing Cancer Therapeutics: A Digest

An understanding towards genetics and epigenetics is essential to cope up with the paradigm shift which is underway. Personalized medicine and gene therapy will confluence the days to come. This review highlights traditional approaches as well as current advancements in the analysis of the gene expression data from cancer perspective. Due to improvements in biometric instrumentation and automation, it has become easier to collect a lot of experimental data in molecular biology. Analysis of such data is extremely important as it leads to knowledge discovery that can be validated by experiments. Previously, the diagnosis of complex genetic diseases has conventionally been done based on the non-molecular characteristics like kind of tumor tissue, pathological characteristics, and clinical phase. The microarray data can be well accounted for high dimensional space and noise. Same were the reasons for ineffective and imprecise results. Several machine learning and data mining techniques are presently applied for identifying cancer using gene expression data. While differences in efficiency do exist, none of the well-established approaches is uniformly superior to others. The quality of algorithm is important, but is not in itself a guarantee of the quality of a specific data analysis.

Transcriptomic analysis of Asiatic lily in the process of vernalization via RNA-seq

The new transcriptomes provided comprehensive sequence profiling data of transcriptomic variation during vernalization in Lily Asiatic Hybrids 'Tiny ghost'. A number of 52,277,184 sequencing raw reads totaling 5.11 Gbp of the chilling treatment (4 °C) sample and 39,466,176 sequencing raw reads totaling 3.85 Gbp of room temperature control (25 °C) sample were assembled de novo into 68,718 unigenes with a mean length of 984 bp, and a total of 33,208 (45.6%) unigenes were annotated by using public protein databases with a cut-off E value about 10(-5). There are 6,153 unigenes of which were assigned to specific metabolic pathways by the Kyoto encyclopedia of genes and genomes. Gene Ontology analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with signal transduction mechanisms, posttranslational modification, protein turnover and chaperones. In addition, the genes expression levels were compared just after vernalization completion between the cold treatment and room temperature control. There are 68,116 unigenes were differentially expressed, and hierarchical clustering analysis arranged 7,301 significantly differentially-expressed unigenes into 56 groups. Six genes related to the vernalization were selected to confirm their expression levels by using quantitative real-time polymerase chain reaction. Furthermore, typical vernalization unigenes VRN1 and VRN2 were identified, and also some vernalization-associated unigenes, such as CBF, SOC, TaAGL, AP2, LEA, LIM et al. were also annotated in the present study. As for VRN1 and VRN2, their expressions were consistent with some previous related studies. Also, this was the first time the vernalization genes VRN1 and VRN2 were founded in lily. According to the results of the present studies, we predicted that they would play an important role during vernalization in Lily Asiatic Hybrids; these data provided the foundation for the future studies of metabolism during vernalization of Asiatic lily.

Gene discovery and molecular marker development, based on high-throughput transcript sequencing of Paspalum dilatatum Poir

Background

Paspalum dilatatum Poir. (common name dallisgrass) is a native grass species of South America, with special relevance to dairy and red meat production. P. dilatatum exhibits higher forage quality than other C4 forage grasses and is tolerant to frost and water stress. This species is predominantly cultivated in an apomictic monoculture, with an inherent high risk that biotic and abiotic stresses could potentially devastate productivity. Therefore, advanced breeding strategies that characterise and use available genetic diversity, or assess germplasm collections effectively are required to deliver advanced cultivars for production systems. However, there are limited genomic resources available for this forage grass species.

Results

Transcriptome sequencing using second-generation sequencing platforms has been employed using pooled RNA from different tissues (stems, roots, leaves and inflorescences) at the final reproductive stage of P. dilatatum cultivar Primo. A total of 324,695 sequence reads were obtained, corresponding to c. 102 Mbp. The sequences were assembled, generating 20,169 contigs of a combined length of 9,336,138 nucleotides. The contigs were BLAST analysed against the fully sequenced grass species of Oryza sativa subsp. japonica, Brachypodium distachyon, the closely related Sorghum bicolor and foxtail millet (Setaria italica) genomes as well as against the UniRef 90 protein database allowing a comprehensive gene ontology analysis to be performed. The contigs generated from the transcript sequencing were also analysed for the presence of simple sequence repeats (SSRs). A total of 2,339 SSR motifs were identified within 1,989 contigs and corresponding primer pairs were designed. Empirical validation of a cohort of 96 SSRs was performed, with 34% being polymorphic between sexual and apomictic biotypes.

Conclusions

The development of genetic and genomic resources for P. dilatatum will contribute to gene discovery and expression studies. Association of gene function with agronomic traits will significantly enable molecular breeding and advance germplasm enhancement.

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 analyses of two Geraniaceae transcriptomes using next-generation sequencing

BACKGROUND

Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum.

RESULTS

Normalized cDNA libraries of G. maderense and P. x hortorum were used for transcriptome sequencing. Five assemblers (MIRA, Newbler, SOAPdenovo, SOAPdenovo-trans [SOAPtrans], Trinity) and two next-generation technologies (454 and Illumina) were compared to determine the optimal transcriptome sequencing approach. Trinity provided the highest quality assembly of Illumina data with the deepest transcriptome coverage. An analysis to determine the amount of sequencing needed for de novo assembly revealed diminishing returns of coverage and quality with data sets larger than sixty million Illumina paired end reads for both species. The G. maderense and P. x hortorum transcriptomes contained fewer transcripts encoding the PLS subclass of PPR proteins relative to other angiosperms, consistent with reduced mitochondrial RNA editing activity in Geraniaceae. In addition, transcripts for all six plastid targeted sigma factors were identified in both transcriptomes, suggesting that one of the highly divergent rpoA-like ORFs in the P. x hortorum plastid genome is functional.

CONCLUSIONS

The findings support the use of the Illumina platform and assemblers optimized for transcriptome assembly, such as Trinity or SOAPtrans, to generate high-quality de novo transcriptomes with broad coverage. In addition, results indicated no major improvements in breadth of coverage with data sets larger than six billion nucleotides or when sampling RNA from four tissue types rather than from a single tissue. Finally, this work demonstrates the power of cross-compartmental genomic analyses to deepen our understanding of the correlated evolution of the nuclear, plastid, and mitochondrial genomes in plants.

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system. TRAPID is freely available at http://bioinformatics.psb.ugent.be/webtools/trapid/.

Transcriptome of Atlantic cod (Gadus morhua L.) early embryos from farmed and wild broodstocks

Significant efforts have been made to elucidate factors affecting egg quality in fish. Recently, we have shown that eggs originating from wild broodstock (WB) of Atlantic cod (Gadus morhua L.) are of superior quality to those derived from farmed broodstock (FB), and this is associated with differences in the chemical composition of egg yolk. However, maternal transcripts, accumulated during oogenesis, have not been studied extensively in fish. The aim of the present study was to characterize putative maternal mRNA transcriptome in fertilized eggs of Atlantic cod and to compare transcript pools between WB and FB in order to investigate the relation between egg developmental potential and putative maternal mRNA deposits. We performed high-throughput 454 pyrosequencing. For each WB and FB group, five cDNA libraries were individually tagged and sequenced, resulting in 98,687 (WB) and 119,333 (FB) average reads per library. Sequencing reads were de novo assembled, annotated, and mapped. Out of 13,726 identified isotigs, 238 were differentially expressed between WB and FB, with 155 isotigs significantly upregulated in WB. The sequence reads were mapped to 11,340 different Atlantic cod transcripts and 158 sequences were differentially expressed between the 2 groups. Important transcripts involved in fructose metabolism, fatty acid metabolism, glycerophospholipid metabolism, and oxidative phosphorylation were differentially represented between the two broodstock groups, showing potential as biomarkers of egg quality in teleosts. Our findings contribute to the hypothesis that maternal mRNAs affect egg quality and, consequently, the early development of fish.

Next-generation sequencing-based transcriptome analysis of Helicoverpa armigera Larvae immune-primed with Photorhabdus luminescens TT01

Although invertebrates are incapable of adaptive immunity, immunal reactions which are functionally similar to the adaptive immunity of vertebrates have been described in many studies of invertebrates including insects. The phenomenon was termed immune priming. In order to understand the molecular mechanism of immune priming, we employed Illumina/Solexa platform to investigate the transcriptional changes of the hemocytes and fat body of Helicoverpa armigera larvae immune-primed with the pathogenic bacteria Photorhabdus luminescens TT01. A total of 43.6 and 65.1 million clean reads with 4.4 and 6.5 gigabase sequence data were obtained from the TT01 (the immune-primed) and PBS (non-primed) cDNA libraries and assembled into 35,707 all-unigenes (non-redundant transcripts), which has a length varied from 201 to 16,947 bp and a N50 length of 1,997 bp. For 35,707 all-unigenes, 20,438 were functionally annotated and 2,494 were differentially expressed after immune priming. The differentially expressed genes (DEGs) are mainly related to immunity, detoxification, development and metabolism of the host insect. Analysis on the annotated immune related DEGs supported a hypothesis that we proposed previously: the immune priming phenomenon observed in H. armigera larvae was achieved by regulation of key innate immune elements. The transcriptome profiling data sets (especially the sequences of 1,022 unannotated DEGs) and the clues (such as those on immune-related signal and regulatory pathways) obtained from this study will facilitate immune-related novel gene discovery and provide valuable information for further exploring the molecular mechanism of immune priming of invertebrates. All these will increase our understanding of invertebrate immunity which may provide new approaches to control insect pests or prevent epidemic of infectious diseases in economic invertebrates in the future.

De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress

Background

Anthurium andraeanum is one of the most popular tropical flowers. In temperate and cold zones, a much greater risk of cold stress occurs in the supply of Anthurium plants. Unlike the freeze-tolerant model plants, Anthurium plants are particularly sensitive to low temperatures. Improvement of chilling tolerance in Anthurium may significantly increase its production and extend its shelf-life. To date, no previous genomic information has been reported in Anthurium plants.

Results

Using Illumina sequencing technology, we generated over two billion base of high-quality sequence in Anthurium, and demonstrated de novo assembly and annotation of genes without prior genome information. These reads were assembled into 44,382 unigenes (mean length = 560 bp). Based on similarity search with known protein in the non-redundant (nr) protein database, 27396 unigenes (62%) were functionally annotated with a cut-off E-value of 10^-5. Further, DGE tags were mapped to the assembled transcriptome for gene expression analysis under cold stress. In total, 4363 differentially expressed genes were identified. Among these genes, 292, 805 and 708 genes were up-regulated after 1-h, 5-h and 24-h cold treatment, respectively. Then we mapped these cold-induced genes to the KEGG database. Specific enrichment was observed in photosynthesis pathway, metabolic pathways and oxidative phosphorylation pathway in 1-h cold-treated plants. After a 5-h cold treatment, the metabolic pathways and oxidative phosphorylation pathway were significantly identified as the top two pathways. After 24-h cold treatment, mRNA surveillance pathway, RNA transport pathway and plant-pathogen interaction pathway were significantly enriched. Together, a total of 39 cold-inducible transcription factors were identified, including subsets of AP2/ERF, Zinc figure, NAC, MYB and bZIP family members.

Conclusion

Our study is the first to provide the transcriptome sequence resource for Anthurium plants, and demonstrate its digital gene expression profiling under cold conditions using the assembled transcriptome data for reference. These data provides a valuable resource for genetic and genomic studies under abiotic conditions for Anthurium plants.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-827) contains supplementary material, which is available to authorized users.

LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance

In contrast to orthodox seeds that acquire desiccation tolerance during maturation, recalcitrant seeds are unable to survive drying. These desiccation-sensitive seeds constitute an interesting model for comparative analysis with phylogenetically close species that are desiccation tolerant. Considering the importance of LEA (late embryogenesis abundant) proteins as protective molecules both in drought and in desiccation tolerance, the heat-stable proteome was characterized in cotyledons of the legume Castanospermum australe and it was compared with that of the orthodox model legume Medicago truncatula. RNA sequencing identified transcripts of 16 homologues out of 17 LEA genes for which polypeptides are detected in M. truncatula seeds. It is shown that for 12 LEA genes, polypeptides were either absent or strongly reduced in C. australe cotyledons compared with M. truncatula seeds. Instead, osmotically responsive, non-seed-specific dehydrins accumulated to high levels in the recalcitrant cotyledons compared with orthodox seeds. Next, M. truncatula mutants of the abscisic acid insensitive3 (ABI3) gene were characterized. Mature Mtabi3 seeds were found to be desiccation sensitive when dried below a critical water content of 0.4 g H2O g DW(-1). Characterization of the LEA proteome of the Mtabi3 seeds revealed a subset of LEA proteins with severely reduced abundance that were also found to be reduced or absent in C. australe cotyledons. Transcripts of these genes were indeed shown to be ABI3 responsive. The results highlight those LEA proteins that are critical to desiccation tolerance and suggest that comparable regulatory pathways responsible for their accumulation are missing in both desiccation-sensitive genotypes, revealing new insights into the mechanistic basis of the recalcitrant trait in seeds.

Transcriptome profile analysis of sugarcane responses to Sporisorium scitaminea infection using Solexa sequencing technology

To understand the molecular basis of sugarcane-smut interaction, it is important to identify sugarcane genes that respond to the pathogen attack. High-throughput tag-sequencing (tag-seq) analysis by Solexa technology was performed on sugarcane infected with Sporisorium scitaminea, which should have massively increased the amount of data available for transcriptome profile analysis. After mapping to sugarcane EST databases in NCBI, we obtained 2015 differentially expressed genes, of which 1125 were upregulated and 890 downregulated by infection. Gene ontology (GO) analysis revealed that the differentially expressed genes involve in many cellular processes. Pathway analysis revealed that metabolic pathways and ribosome function are significantly affected, where upregulation of expression dominates over downregulation. Differential expression of three candidate genes involved in MAP kinase signaling pathway, ScBAK1 (GenBank Accession number: KC857629), ScMapkk (GenBank Accession number: KC857627), and ScGloI (GenBank Accession number: KC857628), was confirmed by reverse transcription polymerase chain reaction (RT-PCR). Real-time quantitative PCR (qRT-PCR) analysis concluded that the expression of these genes were all up-regulated after the infection of S. scitaminea and may play a role in pathogen response in sugarcane. The present study provides insights into the molecular mechanism of sugarcane defense to S. scitaminea infection, leading to a more comprehensive understanding of sugarcane-smut interaction.

Comprehensive transcriptional profiling of NaHCO3-stressed Tamarix hispida roots reveals networks of responsive genes

Root tissue is the primary site of perception for stress from soil, and is the main tissue involved in stress response. Tamarix hispida is a woody halophyte that is highly tolerant to salt and drought stress, but little information available about gene expression in roots in response to abiotic stress. In this study, eight transcriptomes from roots of T. hispida treated with NaHCO3 for 0, 12, 24 and 48 h (two biological replicates were set at each time point) were built. In total, 47,324 unigenes were generated, and 6,267 differentially expressed genes (DEGs) were identified. There were 2,510, 3,690, and 2,636 genes significantly differentially expressed after stress for 12, 24 and 48 h, respectively. Co-expressed DEGs were clustered into ten classes (P < 0.001). Gene ontology enrichment analysis showed that 13 pathways were highly enriched, such as signal transduction, cell wall, phosphatase activity, and lipid kinase activity, suggesting that these pathways play important roles in the saline-alkaline response. Furthermore, the genes involved in lignin metabolic processes and biosynthesis of proline and trehalose are found closely involved in NaHCO3 stress response. This systematic analysis may provide an in-depth view of stress tolerance mechanisms in T. hispida.

The detection of microRNA associated with Alzheimer's disease in biological fluids using next-generation sequencing technologies

Diagnostic tools for neurodegenerative diseases such as Alzheimer's disease (AD) currently involve subjective neuropsychological testing and specialized brain imaging techniques. While definitive diagnosis requires a pathological brain evaluation at autopsy, neurodegenerative changes are believed to begin years before the clinical presentation of cognitive decline. Therefore, there is an essential need for reliable biomarkers to aid in the early detection of disease in order to implement preventative strategies. microRNAs (miRNA) are small non-coding RNA species that are involved in post-transcriptional gene regulation. Expression levels of miRNAs have potential as diagnostic biomarkers as they are known to circulate and tissue specific profiles can be identified in a number of bodily fluids such as plasma, CSF and urine. Recent developments in deep sequencing technology present a viable approach to develop biomarker discovery pipelines in order to profile miRNA signatures in bodily fluids specific to neurodegenerative diseases. Here we review the potential use of miRNA deep sequencing in biomarker identification from biological fluids and its translation into clinical practice.