Analysis of leaf and root transcriptomes of soil-grown Avena barbata plants

Transcriptome analysis of Curcuma wenyujin from Haikou and Wenzhou, and a comparison of the main constituents and related genes of Rhizoma Curcumae

For more than a thousand years, Rhizoma Curcumae (known as E zhu), a Chinese herbal medicine, has been used to eradicate blood stasis and relieve aches. The plant Curcuma wenyujin, which is grown primarily in Wenzhou, China, is considered the best source of Rhizoma Curcumae. In this study, we sought to ascertain differences in transcript profiles of C. wenyujin grown in traditional (Wenzhou) and recently established (Haikou) production areas based on Illumina and RNA (RNA-seq) sequencing. We also examined differences in the main components of the volatile oil terpene; curcumin, polysaccharide, and starch constituents and related genes in the corresponding pathways, in C. wenyujin cultivated in the two production areas. We accordingly found that the essential oil (2.05%), curcumin (1.46%), and polysaccharide (8.90%) content in Wenzhou rhizomes was higher than that in the rhizomes of plants from Haikou (1.60%, 0.91%, and 6.15%, respectively). In contrast, the starch content of Wenzhou rhizomes (17.0%) was lower than that of Haikou rhizomes (23.8%). Furthermore, we detected significant differences in the oil components of Haikou and Wenzhou rhizomes, with curzerene (32.34%), curdione (21.35%), and germacrene B (9.39%) being the primary components of the essential oil derived from Wenzhou rhizomes, and curzerene (20.13%), curdione (14.73%), and cineole (9.76%) being the main constituents in Haikou rhizomes. Transcriptome and qPCR analyses revealed considerable differences in gene expression between Wenzhou and Haikou rhizomes. The expression of terpene, curcumin, and polysaccharide pathway-related genes in Wenzhou rhizomes was significantly up-regulated, whereas the expression of starch-associated genes was significantly down-regulated, compared with those in Haikou rhizomes. Difference in the content of terpene, curcumin, polysaccharides, and starch in rhizomes from the two production areas could be explained in terms of differences in expression of the related genes.

Pathogen-induced AdDjSKI of the wild peanut, Arachis diogoi, potentiates tolerance of multiple stresses in E. coli and tobacco

A gene encoding a serine-rich DnaJIII protein called AdDjSKI that has a 4Fe-4S cluster domain was found to be differentially upregulated in the wild peanut, Arachis diogoi in its resistance responses against the late leaf spot causing fungal pathogen Phaeoisariopsis personata when compared with the cultivated peanut, Arachis hypogaea. AdDjSKI is induced in multiple stress conditions in A. diogoi. Recombinant E. coli cells expressing AdDjSKI showed better growth kinetics when compared with vector control cells under salinity, osmotic, acidic and alkaline stress conditions. Overexpression of this type three J-protein potentiates not only abiotic stress tolerance in Nicotiana tabacum var. Samsun, but also enhances its disease resistance against the phytopathogenic fungi Phytophthora parasitica pv nicotianae and Sclerotinia sclerotiorum. In the present study we show transcriptional upregulation of APX, Mn-SOD and HSP70 under heat stress and increased transcripts of PR genes in response to fungal infection. This transmembrane-domain-containing J protein displays punctate localization in chloroplasts. AdDjSKI appears to ensure proper folding of proteins associated with the photosynthetic machinery under stress.

De novo transcriptome analyses reveals putative pathway genes involved in biosynthesis and regulation of camptothecin in Nothapodytes nimmoniana (Graham) Mabb

Comprehensive transcriptome analysis of leaf and root tissues of Nothapodytes nimmoniana unravels several putative pathway genes, transcription factors and CYPs related to camptothecin (CPT) biosynthesis. Additionally, post-transcriptional suppression by artificial microRNA (aMIR) of NnCYP76B6 (geraniol 10-hydroxylase) suggests its role in CPT biosynthesis. Tissue-specific LC-MS/MS analysis revealed the presence of secologanin as the central intermediate of MIA pathway in N. nimmoniana. Nothapodytes nimmoniana is a rich source of potent anticancer drug camptothecin (CPT) whose biosynthetic pathway is unresolved due to the lack of genomic and transcriptomic information. Present investigation entails deep transcriptome analysis of N. nimmoniana which led to identification of putative pathway genes and regulatory components involved in CPT biosynthesis. Using Illumina HiSeq 2500 sequencing platform a total of 31,172,889 (6.23 Gb) and 31,218,626 (6.24 Gb) raw reads were generated from leaf and root wood, respectively. These were assembled de novo into 138,183 unique contigs. Additionally, 16 cytochrome P450 transcripts related to secondary metabolism were also identified. Further, transcriptome data pool presented 1683 putative transcription factors of which transcripts corresponding to WRKY TFs were the most abundant (14.14%). A total of 2741 transcripts were differentially expressed out of which 478 contigs showed downregulation in root wood and 2263 contigs were up-regulated. Further, comparative analyses of 17 genes involved in CPT biosynthetic pathway were validated by qRT-PCR. On basis of intermediates, two distinct seco-iridoid pathways are involved in the biosynthesis of monoterpene indole alkaloids either through multiple isomers of strictosidinic acid or strictosidine. Tissue-specific LC-MS/MS analysis revealed the presence of secologanin as the central intermediate of MIA pathway in N. nimmoniana. Geraniol-10 hydroxylase (NnCYP76B6) an important enzyme in CPT biosynthesis which specifically shunts geraniol into the secologanin pathway was also cloned from the trancriptome resource. In planta transient expression of NnCYP76B6 showed a significant enhancement in mRNA transcript levels coincident with enhanced CPT accumulation. Further, artificial microRNA (aMIR) mediated downregulation of NnCYP76B6 resulted in reduction of mRNA transcript levels as well as CPT content in comparison to control. These empirical results suggest a plausible regulatory role for NnCYP76B6 in CPT biosynthesis and also establish a valuable repository for deciphering various structural, rate limiting and regulatory genes of CPT biosynthetic pathway.

Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity

BACKGROUND

Soil salinity affects growth and yield of crop plants. Plants respond to salinity by physiological and biochemical adjustments through a coordinated regulation and expression of a cascade of genes. Recently, halophytes have attracted attention of the biologists to understand their salt adaptation mechanisms. Spartina alterniflora (smooth cordgrass) is a Louisiana native monocot halophyte that can withstand salinity up to double the strength of sea water. To dissect the molecular mechanisms underlying its salinity adaptation, leaf and root transcriptome of S. alterniflora was sequenced using 454/GS-FLX.

RESULTS

Altogether, 770,690 high quality reads with an average length 324-bp were assembled de novo into 73,131 contigs (average 577-bp long) with 5.9X sequence coverage. Most unigenes (95 %) annotated to proteins with known functions, and had more than 90 % similarity to rice genes. About 28 % unigenes were considered specific to S. alterniflora. Digital expression profiles revealed significant enrichment (P < 0.01) of transporters, vacuolar proton pump members and transcription factors under salt stress, which suggested the role of ion homeostasis and transcriptional regulation in the salinity adaptation of this grass. Also, 10,805 SSRs markers from 9457 unigenes were generated and validated through genetic diversity analysis among 13 accessions of S. alterniflora.

CONCLUSIONS

The present study explores the transcriptome of S. alterniflora to understand the gene regulation under salt stress in halophytes. The sequenced transcriptome (control and salt-regulated) of S. alterniflora provides a platform for further gene finding studies in grasses. This study and our previously published studies suggested that S. alterniflora is a rich reservoir of salt tolerance genes that can be used to develop salt tolerant cereal crops, especially rice, a major food crop of global importance.

Genomics of crop wild relatives: expanding the gene pool for crop improvement

Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production.

Transcriptome Analysis of Differentially Expressed Genes Involved in Proanthocyanidin Accumulation in the Rhizomes of Fagopyrum dibotrys and an Irradiation-Induced Mutant

The rhizome of Fagopyrum dibotrys is a traditional Chinese medicine that has recently gained attention due to substantial findings regarding its bioactive proanthocyanidin (PA) compounds. However, the molecular mechanism underlying PA accumulation in F. dibotrys remains elusive. We previously obtained an irradiation-induced mutant (RM_R) of F. dibotrys that had a higher PA content compared to that of the wild-type (CK_R). The present study aimed to elucidate the molecular mechanism underlying PA accumulation in F. dibotrys by comparing the rhizome transcriptomes of the irradiation-induced mutant and wild-type using RNA-seq analysis. A total of 53,540 unigenes were obtained, of which 29,901 (55.84%) were annotated based on BLAST searches against public databases, and 501 unique sequences were differentially expressed between the two samples, which consisted of 204 up-regulated and 297 down-regulated unigenes. Further analysis showed that the expression patterns of some unigenes encoding enzymes involved in PAs biosynthesis in F. dibotrys rhizomes differed between RM_R and CK_R. In addition, we identified transcription factor families and several cytochrome P450s that may be involved in PA regulation in F. dibotrys. Finally, 12 unigenes that encode PA biosynthetic enzymes were confirmed by qRT-PCR analysis. This study sheds light on the molecular mechanism underlying radiation-mediated flavonoid accumulation and regulation in F. dibotrys rhizomes. These results will also provide a platform for further functional genomic research on this particular species.

Integrating transcriptomics and metabolomics to characterise the response of Astragalus membranaceus Bge. var. mongolicus (Bge.) to progressive drought stress

BACKGROUND

Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao (A. mongolicus) is an important traditional Chinese herb that is cultivated on a large scale in northwestern China. Understanding plant responses to drought has important effects on ecological environment recovery and local economic development. Here, we combined transcriptomics (Illumina Hiseq 2000) and metabolomics ((1)H-NMR) to investigate how the roots of two-year-old A. mongolicus responded to 14 days of progressive drought stress.

RESULTS

The dried soil reduced the relative water content (RWC) of the leaves and biomass, induced the differential expression of a large fraction of the transcriptome and significantly altered the metabolic processes. PCA analysis demonstrated that the sucrose, proline, and malate metabolites contributed greatly to the separation. Strikingly, proline was increased by almost 60-fold under severe stress compared to the control. Some backbone pathways, including glycolysis, tricarboxylic acid (TCA) cycle, glutamate-mediated proline biosynthesis, aspartate family metabolism and starch and sucrose metabolism, were significantly affected by drought. An integrated analysis of the interaction between key genes and the altered metabolites involved in these pathways was performed.

CONCLUSIONS

Our findings demonstrated that the expression of drought-responsive genes showed a strong stress-dose dependency. Analysis of backbone pathways of the transcriptome and metabolome revealed specific genotypic responses to different levels of drought. The variation in molecular strategies to the drought may play an important role in how A. mongolicus and other legume crops adapt to drought stress.

Comparison of root transcriptomes and expressions of genes involved in main medicinal secondary metabolites from Bupleurum chinense and Bupleurum scorzonerifolium, the two Chinese official Radix bupleuri source species

Radix bupleuri, roots of Bupleurum species, is a widely used traditional Chinese medicine. Here, we compared the root transcriptomes of both Bupleurum chinense DC. and Bupleurum scorzonerifolium Willd. A total of 313 483 and 342 263 high quality expressed sequence tags were obtained, respectively. In addition, 17 117 (59.2%) and 19 416 (62.8%) unigenes for B. chinense and B. scorzonerifolium had homologous genes in the opposite dataset. For B. chinense, Kyoto Encyclopedia of Genes and Genomes database (KEGG) annotation identified carbohydrate metabolism, energy metabolism and amino acid metabolism as the three highest groups in the metabolism category. For B. scorzonerifolium, the lipid metabolism group had the most unigenes. Genes that may participate in the biosynthesis of terpenoid, triterpenoid, sterol, lignan and flavonoids were identified according to their annotations. (Tri)terpenoid-related genes were predominantly found in B. chinense. The expressions of certain genes were analyzed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) in the roots of the two species. A total of 558 putative transcription factors (TFs) and 137 transcriptional regulators (TRs) among 1364 TFs and 327 TRs, and 610 TFs and 129 TRs among 1600 TFs and 323 TRs were specific for B. chinense and B. scorzonerifolium, respectively. Our transcriptome comparison reflects the different types and proportions of metabolites synthesized by the two species. The data, especially, those genes involved in the biosynthesis of particular types of metabolites, will provide the basis for further investigations of the secondary metabolite repertoire of the two Bupleurum species, as well as other species from the genus of Bupleurum.

"The usual suspects"- analysis of transcriptome sequences reveals deviating B gene activity in C. vulgaris bud bloomers

BACKGROUND

The production of heather (Calluna vulgaris) in Germany is highly dependent on cultivars with mutated flower morphology, the so-called diplocalyx bud bloomers. So far, this unique flower type of C. vulgaris has not been reported in any other plant species. The flowers are characterised by an extremely extended flower attractiveness, since the flower buds remain closed throughout the complete flowering season. The flowers of C. vulgaris bud bloomers are male sterile, because the stamens are absent. Furthermore, petals are converted into sepals. Therefore the diplocalyx bud bloomer flowers consist of two whorls of sepals directly followed by the gynoecium.

RESULTS

A broad comparison was undertaken to identify genes differentially expressed in the bud flowering phenotype and in the wild type of C. vulgaris. Transcriptome sequence reads were generated using 454 sequencing of two flower type specific cDNA libraries. In total, 360,000 sequence reads were obtained, assembled to 12,200 contigs, functionally mapped, and annotated. Transcript abundances were compared and 365 differentially expressed genes detected. Among these differentially expressed genes, Calluna vulgaris PISTILLATA (CvPI) which is the orthologue of the Arabidopsis B gene PISTILLATA (PI) was considered as the most promising candidate gene. Quantitative Reverse Transcription Polymerase Chain Reaction (qRT PCR) was performed to analyse the gene expression levels of two C. vulgaris B genes CvPI and Calluna vulgaris APETALA 3 (CvAP3) in both flower types. CvAP3 which is the orthologue of the Arabidopsis B gene APETALA 3 (AP3) turned out to be ectopically expressed in sepals of wild type and bud bloomer flowers. CvPI expression was proven to be reduced in the bud blooming flowers.

CONCLUSIONS

Differential expression patterns of the B-class genes CvAP3 and CvPI were identified to cause the characteristic morphology of C. vulgaris flowers leading to the following hypotheses: ectopic expression of CvAP3 is a convincing explanation for the formation of a completely petaloid perianth in both flower types. In C. vulgaris, CvPI is essential for determination of petal and stamen identity. The characteristic transition of petals into sepals potentially depends on the observed deficiency of CvPI and CvAP3 expression in bud blooming flowers.

Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)

BACKGROUND

In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light: dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions.

RESULTS

Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence.

CONCLUSIONS

Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses.

Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)

BACKGROUND

In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light: dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions.

RESULTS

Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence.

CONCLUSIONS

Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses.

Generation and analysis of expressed sequence tags (ESTs) from halophyte Atriplex canescens to explore salt-responsive related genes

Little information is available on gene expression profiling of halophyte A. canescens. To elucidate the molecular mechanism for stress tolerance in A. canescens, a full-length complementary DNA library was generated from A. canescens exposed to 400 mM NaCl, and provided 343 high-quality ESTs. In an evaluation of 343 valid EST sequences in the cDNA library, 197 unigenes were assembled, among which 190 unigenes (83.1% ESTs) were identified according to their significant similarities with proteins of known functions. All the 343 EST sequences have been deposited in the dbEST GenBank under accession numbers JZ535802 to JZ536144. According to Arabidopsis MIPS functional category and GO classifications, we identified 193 unigenes of the 311 annotations EST, representing 72 non-redundant unigenes sharing similarities with genes related to the defense response. The sets of ESTs obtained provide a rich genetic resource and 17 up-regulated genes related to salt stress resistance were identified by qRT-PCR. Six of these genes may contribute crucially to earlier and later stage salt stress resistance. Additionally, among the 343 unigenes sequences, 22 simple sequence repeats (SSRs) were also identified contributing to the study of A. canescens resources.

Unlocking Triticeae genomics to sustainably feed the future

The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species-barley, wheat, Tausch's goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)-have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.

Transcriptional profiling of sweetpotato (Ipomoea batatas) roots indicates down-regulation of lignin biosynthesis and up-regulation of starch biosynthesis at an early stage of storage root formation

Background

The number of fibrous roots that develop into storage roots determines sweetpotato yield. The aim of the present study was to identify the molecular mechanisms involved in the initiation of storage root formation, by performing a detailed transcriptomic analysis of initiating storage roots using next-generation sequencing platforms. A two-step approach was undertaken: (1) generating a database for the sweetpotato root transcriptome using 454-Roche sequencing of a cDNA library created from pooled samples of two root types: fibrous and initiating storage roots; (2) comparing the expression profiles of initiating storage roots and fibrous roots, using the Illumina Genome Analyzer to sequence cDNA libraries of the two root types and map the data onto the root transcriptome database.

Results

Use of the 454-Roche platform generated a total of 524,607 reads, 85.6% of which were clustered into 55,296 contigs that matched 40,278 known genes. The reads, generated by the Illumina Genome Analyzer, were found to map to 31,284 contigs out of the 55,296 contigs serving as the database. A total of 8,353 contigs were found to exhibit differential expression between the two root types (at least 2.5-fold change). The Illumina-based differential expression results were validated for nine putative genes using quantitative real-time PCR. The differential expression profiles indicated down-regulation of classical root functions, such as transport, as well as down-regulation of lignin biosynthesis in initiating storage roots, and up-regulation of carbohydrate metabolism and starch biosynthesis. In addition, data indicated delicate control of regulators of meristematic tissue identity and maintenance, associated with the initiation of storage root formation.

Conclusions

This study adds a valuable resource of sweetpotato root transcript sequences to available data, facilitating the identification of genes of interest. This resource enabled us to identify genes that are involved in the earliest stage of storage root formation, highlighting the reduction in carbon flow toward phenylpropanoid biosynthesis and its delivery into carbohydrate metabolism and starch biosynthesis, as major events involved in storage root initiation. The novel transcripts related to storage root initiation identified in this study provide a starting point for further investigation into the molecular mechanisms underlying this process.

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)

Spartina species have a critical ecological role in salt marshes and represent an excellent system to investigate recurrent polyploid speciation. Using the 454 GS-FLX pyrosequencer, we assembled and annotated the first reference transcriptome (from roots and leaves) for two related hexaploid Spartina species that hybridize in Western Europe, the East American invasive Spartina alterniflora and the Euro-African S. maritima. The de novo read assembly generated 38 478 consensus sequences and 99% found an annotation using Poaceae databases, representing a total of 16 753 non-redundant genes. Spartina expressed sequence tags were mapped onto the Sorghum bicolor genome, where they were distributed among the subtelomeric arms of the 10 S. bicolor chromosomes, with high gene density correlation. Normalization of the complementary DNA library improved the number of annotated genes. Ecologically relevant genes were identified among GO biological function categories in salt and heavy metal stress response, C4 photosynthesis and in lignin and cellulose metabolism. Expression of some of these genes had been found to be altered by hybridization and genome duplication in a previous microarray-based study in Spartina. As these species are hexaploid, up to three duplicated homoeologs may be expected per locus. When analyzing sequence polymorphism at four different loci in S. maritima and S. alterniflora, we found up to four haplotypes per locus, suggesting the presence of two expressed homoeologous sequences with one or two allelic variants each. This reference transcriptome will allow analysis of specific Spartina genes of ecological or evolutionary interest, estimation of homoeologous gene expression variation using RNA-seq and further gene expression evolution analyses in natural populations.

Designing a transcriptome next-generation sequencing project for a nonmodel plant species

The application of next-generation sequencing (NGS) to transcriptomics, commonly called RNA-seq, allows the nearly complete characterization of transcriptomic events occurring in a specific tissue. It has proven particularly useful in nonmodel species, which often lack the resources available for sequenced organisms. Mainly, RNA-seq does not require a reference genome to gain useful transcriptomic information. In this review, the application of RNA-seq to nonmodel plant species will be addressed. Important experimental considerations from presequencing issues to postsequencing analysis, including sample and platform selection, and useful bioinformatics tools for assembly and data analysis, are covered. Methods of assembling RNA-seq data and analyses commonly performed with RNA-seq data, including single nucleotide polymorphism detection and analysis of differential expression, are explored. In addition, studies that have used RNA-seq to elucidate nonmodel plant transcriptomics are highlighted.

Molecular genetics, physiology and biology of self-incompatibility in Brassicaceae

Self-incompatibility (SI) is defined as the inability to produce zygotes after self-pollination in a fertile hermaphrodite plant, which has stamens and pistils in the same flower. This structural organization of the hermaphrodite flower increases the risk of self-pollination, leading to low genetic diversity. To avoid this problem plants have established several pollination systems, among which the most elegant system is surely SI. The SI trait can be observed in Brassica crops, including cabbage, broccoli, turnip and radish. To produce hybrid seed of these crops efficiently, the SI trait has been employed in an agricultural context. From another point of view, the recognition reaction of SI during pollen-stigma interaction is an excellent model system for cell-cell communication and signal transduction in higher plants. In this review, we describe the molecular mechanisms of SI in Brassicaceae, which have been dissected by genetic, physiological, and biological approaches, and we discuss the future prospects in relation to associated scientific fields and new technologies.

Transcriptome analysis of Bupleurum chinense focusing on genes involved in the biosynthesis of saikosaponins

BACKGROUND

Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. The 454 pyrosequencing technology provides a promising opportunity for finding novel genes that participate in plant metabolism. Consequently, this technology may help to identify the candidate genes involved in the saikosaponin biosynthetic pathway.

RESULTS

One-quarter of the 454 pyrosequencing runs produced a total of 195, 088 high-quality reads, with an average read length of 356 bases (NCBI SRA accession SRA039388). A de novo assembly generated 24, 037 unique sequences (22, 748 contigs and 1, 289 singletons), 12, 649 (52.6%) of which were annotated against three public protein databases using a basic local alignment search tool (E-value ≤1e-10). All unique sequences were compared with NCBI expressed sequence tags (ESTs) (237) and encoding sequences (44) from the Bupleurum genus, and with a Sanger-sequenced EST dataset (3, 111). The 23, 173 (96.4%) unique sequences obtained in the present study represent novel Bupleurum genes. The ESTs of genes related to saikosaponin biosynthesis were found to encode known enzymes that catalyze the formation of the saikosaponin backbone; 246 cytochrome P450 (P450s) and 102 glycosyltransferases (GTs) unique sequences were also found in the 454 dataset. Full length cDNAs of 7 P450s and 7 uridine diphosphate GTs (UGTs) were verified by reverse transcriptase polymerase chain reaction or by cloning using 5' and/or 3' rapid amplification of cDNA ends. Two P450s and three UGTs were identified as the most likely candidates involved in saikosaponin biosynthesis. This finding was based on the coordinate up-regulation of their expression with β-AS in methyl jasmonate-treated adventitious roots and on their similar expression patterns with β-AS in various B. chinense tissues.

CONCLUSIONS

A collection of high-quality ESTs for B. chinense obtained by 454 pyrosequencing is provided here for the first time. These data should aid further research on the functional genomics of B. chinense and other Bupleurum species. The candidate genes for enzymes involved in saikosaponin biosynthesis, especially the P450s and UGTs, that were revealed provide a substantial foundation for follow-up research on the metabolism and regulation of the saikosaponins.

De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae)

Members of the angiosperm genus Silene are widely used in studies of ecology and evolution, but available genomic and population genetic resources within Silene remain limited. Deep transcriptome (i.e. expressed sequence tag or EST) sequencing has proven to be a rapid and cost-effective means to characterize gene content and identify polymorphic markers in non-model organisms. In this study, we report the results of 454 GS-FLX Titanium sequencing of a polyA-selected and normalized cDNA library from Silene vulgaris. The library was generated from a single pool of transcripts, combining RNA from leaf, root and floral tissue from three genetically divergent European subpopulations of S. vulgaris. A single full-plate 454 run produced 959,520 reads totalling 363.6 Mb of sequence data with an average read length of 379.0 bp after quality trimming and removal of custom library adaptors. We assembled 832,251 (86.7%) of these reads into 40,964 contigs, which have a total length of 25.4 Mb and can be organized into 18,178 graph-based clusters or 'isogroups'. Assembled sequences were annotated based on homology to genes in multiple public databases. Analysis of sequence variants identified 13,432 putative single-nucleotide polymorphisms (SNPs) and 1320 simple sequence repeats (SSRs) that are candidates for microsatellite analysis. Estimates of nucleotide diversity from 1577 contigs were used to generate genome-wide distributions that revealed several outliers with high diversity. All of these resources are publicly available through NCBI and/or our website (http://silenegenomics.biology.virginia.edu) and should provide valuable genomic and population genetic tools for the Silene research community.

Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma

A large region of suppressed recombination surrounds the sex-determining locus of the self-fertile fungus Neurospora tetrasperma. This region encompasses nearly one-fifth of the N. tetrasperma genome and suppression of recombination is necessary for self-fertility. The similarity of the N. tetrasperma mating chromosome to plant and animal sex chromosomes and its recent origin (<5 MYA), combined with a long history of genetic and cytological research, make this fungus an ideal model for studying the evolutionary consequences of suppressed recombination. Here we compare genome sequences from two N. tetrasperma strains of opposite mating type to determine whether structural rearrangements are associated with the nonrecombining region and to examine the effect of suppressed recombination for the evolution of the genes within it. We find a series of three inversions encompassing the majority of the region of suppressed recombination and provide evidence for two different types of rearrangement mechanisms: the recently proposed mechanism of inversion via staggered single-strand breaks as well as ectopic recombination between transposable elements. In addition, we show that the N. tetrasperma mat a mating-type region appears to be accumulating deleterious substitutions at a faster rate than the other mating type (mat A) and thus may be in the early stages of degeneration.