Comprehensive Gene Expression Information Research Articles

De novo transcriptome revealed genes involved in anthocyanin biosynthesis, transport, and regulation in a mutant of Acer pseudosieboldianum

BackgroundAcer pseudosieboldianum is a kind of excellent color-leafed plants, and well known for its red leaves in autumn. At the same time, A. pseudosieboldianum is one of the native tree species in the northeast of China, and it plays an important role in improving the lack of color-leafed plants in the north. In previous study, we found a mutant of the A. pseudosieboldianum that leaves intersect red and green in spring and summer. However, it is unclear which genes cause the color change of mutant leaves.ResultsIn order to study the molecular mechanism of leaf color formation, we analyzed the leaves of the mutant group and the control group from A. pseudosieboldianum by RNA deep sequencing in this study. Using an Illumina sequencing platform, we obtained approximately 276,071,634 clean reads. After the sequences were filtered and assembled, the transcriptome data generated a total of 70,014 transcripts and 54,776 unigenes, of which 34,486 (62.96%) were successfully annotated in seven public databases. There were 8,609 significant DEGs identified between the control and mutant groups, including 4,897 upregulated and 3,712 downregulated genes. We identified 13 genes of DEGs for leaf color synthesis that was involved in the flavonoid pathway, 26 genes that encoded transcription factors, and eight genes associated with flavonoid transport.ConclusionOur results provided comprehensive gene expression information about A. pseudosieboldianum transcriptome, and directed the further study of accumulation of anthocyanin in A. pseudosieboldianum, aiming to provide insights into leaf coloring of it through transcriptome sequencing and analysis.

Determinants of correlated expression of transcription factors and their target genes

While transcription factors (TFs) are known to regulate the expression of their target genes (TGs), only a weak correlation of expression between TFs and their TGs has generally been observed. As lack of correlation could be caused by additional layers of regulation, the overall correlation distribution may hide the presence of a subset of regulatory TF–TG pairs with tight expression coupling. Using reported regulatory pairs in the plant Arabidopsis thaliana along with comprehensive gene expression information and testing a wide array of molecular features, we aimed to discern the molecular determinants of high expression correlation of TFs and their TGs. TF-family assignment, stress-response process involvement, short genomic distances of the TF-binding sites to the transcription start site of their TGs, few required protein-protein-interaction connections to establish physical interactions between the TF and polymerase-II, unambiguous TF-binding motifs, increased numbers of miRNA target-sites in TF-mRNAs, and a young evolutionary age of TGs were found particularly indicative of high TF–TG correlation. The modulating roles of post-transcriptional, post-translational processes, and epigenetic factors have been characterized as well. Our study reveals that regulatory pairs with high expression coupling are associated with specific molecular determinants.

Transcriptomics of Chinese Sapium Sebiferum (L.) Roxb seed to reveal key enzymes involved in oil accumulation

Chinese Sapium sebiferum (L.) Roxb has great potential to emerge as a promising biodiesel resource plant due to abundant oil content in seed. However, the unavailability of transcriptomic and genomic data impedes the progress of application in biodiesel production. Transcriptome analysis will help to further exploit tallow and kernel oil utilization in industry and facilitate molecular-breeding-based genetic improvement of S. sebiferum. Illumina hiseq 2000 sequencing platform was used to perform de novo transcriptome assembly and gene expression analyses of seeds from three strains in three developmental stages. A total of 188,254 unigenes over 200 bp were assembled with average length of 699 bp. These transcriptic unigenes were functionally assigned by GO and KEGG pathways. RPKM was used to identify differentially expressed unigenes of five cDNA libraries. Transcriptic genes endcoding enzymes related to fatty acid metabolism were evaluated. qRT-PCR was employed to confirm five key enzymes involved in fatty acid and triacylglycerol biosynthesis. This study provided comprehensive gene expression information of Chinese S. sebiferum seed at transcriptional level. These transcriptome data will facilitate high-oil-content genetic cultivation of S. sebiferum, which will further exploit tallow and kernel oil utilization in biodiesel industry.

Differential gene expression profiling of the goose pineal gland

ABSTRACT1. The present study was conducted to obtain a better understanding of the molecular mechanisms underlying broodiness in a commercial breed, Tianfu geese, as little is known about the role of the pineal gland in this period. The aim was to identify genes which are differentially expressed in the pineal gland between the laying and broodiness periods by performing a transcriptome screen.2. After sequencing cDNA derived from the pineal gland and annotation of the results, a sequencing depth of 14.82 and 18.17 million mapped tags was obtained during the laying and broodiness periods, respectively, and a total of 120 differentially expressed genes were identified. Of these, 32 genes showing up-regulated expression and 88 genes showing down-regulated expression were identified in broodiness period vs. laying period libraries.3. Gene ontology (GO) analyses showed that these genes were related to the visual process, phototransduction, and lipoprotein metabolism. Kyoto Encyclopaedia of Genes and Genome (KEGG) analyses showed that phototransduction and tryptophan metabolism pathways exhibited the largest enrichment factors. The reliability of the RNA sequence data was confirmed by quantitative real-time PCR analysis of five genes, and the results were mostly consistent with those from the high-throughput RNA sequencing.4. The goose transcriptome and the identification of differentially expressed genes provided comprehensive gene expression information that enables a better understanding of the molecular mechanisms underlying the broodiness period of geese.

Cytological and Molecular Characteristics of Pollen Abortion in Lily with Dysplastic Tapetum

Lily was grown worldwide as a fresh cutting flower because of its colorful petals, but its anther contained a large number of pollen grains that cause serious pollen contamination, however, pollen abortion can effectively reduce the level of pollen pollution. Our analysis aims to use cytological observation to detect the critical stage when pollen abortion occurs and to provide comprehensive gene expression information at the transcriptional level. The result showed that pollen abortion in ‘Little Kiss’ began at the mononuclear stage and the callose that covers the microspores failed to degenerate when young pollens were released from the tetrads. In addition, compared with the normally developed one, the tapetum of ‘Little Kiss’ degraded in advance while the degradation of callose was delayed. Furthermore, 103 differentially expressed genes (DEGs) related to the advance degeneration of tapetum cells and callose were found in the expression levels, including 22 transcription factors (TFs). In particular, two β-glucanase genes (endo-1,3(4)-β-glucanase, exo-β-glucanase) responsible for callose degeneration were significantly down-regulated. These results suggested that pollen abortion may occur at mononuclear stage and that early degeneration of tapetum cells resulted in a significant down-regulation of β-glucanase genes. As a result, the callose to cover microspores impedes the formation of pollen walls, which may possibly lead to pollen abortion.

RNA sequencing analysis of Cymbidium goeringii identifies floral scent biosynthesis related genes

BackgroundCymbidium goeringii belongs to the Orchidaceae, which is one of the most abundant angiosperm families. Cymbidium goeringii consist with high economic value and characteristics include fragrance and multiple flower colors. Floral scent is one of the important strategies for ensuring fertilization. However, limited genetic data is available in this non-model plant, and little known about the molecular mechanism responsible for floral scent in this orchid. Transcriptome and expression profiling data are needed to identify genes and better understand the biological mechanisms of floral scents in this species. Present transcriptomic data provides basic information on the genes and enzymes related to and pathways involved in flower secondary metabolism in this plant.ResultsIn this study, RNA sequencing analyses were performed to identify changes in gene expression and biological pathways related scent metabolism. Three cDNA libraries were obtained from three developmental floral stages: closed bud, half flowering stage and full flowering stage. Using Illumina technique 159,616,374 clean reads were obtained and were assembled into 85,868 final unigenes (average length 1194 nt), 33.85% of which were annotated in the NCBI non redundant protein database. Among this unigenes 36,082 were assigned to gene ontology and 23,164 were combined with COG groups. Total 33,417 unigenes were assigned in 127 pathways according to the Kyoto Encyclopedia of Genes and Genomes pathway database. According these transcriptomic data we identified number of candidates genes which differentially expressed in different developmental stages of flower related to fragrance biosynthesis. In q-RT-PCR most of the fragrance related genes highly expressed in half flowering stage.ConclusionsRNA-seq and DEG data provided comprehensive gene expression information at the transcriptional level that could be facilitate the molecular mechanisms of floral biosynthesis pathways in three developmental phase’s flowers in Cymbidium goeringii, moreover providing useful information for further analysis on C. goeringii, and other plants of genus Cymbidium.

Identification of candidate genes involved in anthocyanin accumulation using Illmuina-based RNA-seq in peach skin

Peach (Prunus persica) is one of the most economically important crops, its fruit quality is defined by various criteria, including external quality and fruit taste. Peach contain anthocyanins as the main pigment with important nutritional and medical usages. Therefore, increasing the anthocyanin content in peach skin can make the fruit appearance of bright and attractive. This study investigated the formation mechanism of the external quality of peach fruit and utilized RNA-seq technology to analyze the molecular mechanisms of anthocyanin biosynthesis regulation in P. persica fruit skin. Approximately 333,899,176 clean reads were obtained, 25,694 unigenes were annotated in five public databases. After the different expression genes of the compared sequences were quantitated by RPKM method and sifted by a limited term, in total, 1665, 3214, and 639 differentially expressed genes were screened among 120 DAF (days after flowering) vs 105 DAF, 135 DAF vs 105 DAF, and 135 DAF vs 120 DAF, respectively. We identified 15 structural genes, 16 transcription factors, and 17 transferase genes that may be involved in the anthocyanin biosynthesis from P. persica and analyzed their expression patterns by using real-time PCR. Our results presented comprehensive gene expression information about peach skin transcriptome; and enhanced our understanding of key genes regulating the biological pathways of anthocyanin biosynthesis. This study could help us understand the molecular mechanism of anthocyanin metabolism in peach skin and provide important technical support for regulating peach skin coloration.

De novo transcriptome analysis revealed genes involved in flavonoid biosynthesis, transport and regulation in Ginkgo biloba

Ginkgo biloba breeding commonly concentrates on the selection of superior trees that have high flavonoid contents. The flavonoids present in Ginkgo leaves have strong medicinal implications, including anti-dengue, anti-HIV, anticancer, antioxidant and anti-inflammatory properties. Flavonoids play important roles in plant immune responses; however, the molecular mechanisms underlying these interesting responses remain unclear. To obtain a comprehensive understanding, we performed the transcriptome sequencing of Ginkgo with different flavonoid contents. Using an Illumina sequencing platform, we obtained approximately 533,952,528 clean reads. After the sequences were filtered and assembled, the transcriptome data generated 37,625 unigenes, of which 21,472 (57.07%) were successfully annotated in five public databases. Among those genes, many candidates were involved in flavonoid biosynthesis, transport and regulation. Expression profiles were generated, and 457 genes were found to be significantly differentially expressed between the Sample_GB_FH1/2/3 (FH) and Sample_GB_FL1/2/3 (FL) libraries; 246 (53.83%) genes were up-regulated, and 211 (46.17%) were down-regulated. These genes included 14 genes that were enriched in flavonoid transport, 1 MYB gene that encoded a putative transcription factor (TF), and 1 dihydroflavonol reductase (DFR) gene that was involved in the flavonoid pathway. Our results provide comprehensive gene expression information about the Ginkgo transcriptome and can facilitate our understanding of the molecular mechanisms of flavonoid development in Ginkgo. Furthermore, our results markedly expand both the available Ginkgo genetic library and analyses of the species and provide valuable information to the Ginkgo-related pharmaceutical industry.

Transcriptomic analysis reveals differentially expressed genes associated with wool length in rabbit

Rabbit fur characteristics are primarily genetically determined traits. We used Illumina high-throughput sequencing technology to assess gene expression in the skin tissues of rabbits derived from a cross between Wanxi Angora rabbits and Rex rabbits, which exhibit differential characteristics of short and long wool respectively, to investigate molecular mechanisms related to wool length determination. To identify key regulatory genes involved in rabbit wool length, genes that were differentially expressed between the long- and short-wool rabbits based on a P-value < 0.05 and log2 |fold change|>1 were characterized. A total of 798 genes were up-regulated and 523 were down-regulated in the long-wool group compared to expression levels in the short-wool group, and these genes were annotated with GO terms and KEGG pathways, revealing wool-development-related biological functions. The Wnt, Hedgehog and TGF-β signaling pathways, which are related to cell proliferation, fibroblast proliferation and hair follicle regulation respectively, were identified. The expression levels of eight genes were validated by RT-qPCR. In addition, an interaction network was constructed to show the regulatory relationships among the differentially expressed genes. In this study, we found that FGF5, WNT5A, BMP4 and BMP7 showed significant differential expression between the two groups. These transcriptomic profiling results provide comprehensive gene expression information for improving understanding of the molecular mechanisms involved in the growth and development of rabbit wool.

Transcriptome profiling to identify key mediators of granulosa cell proliferation upon FSH stimulation in the goose (Anser cygnoides)

ABSTRACT1. The low reproductive performance of geese has seriously hampered the development of the industry. Reproductive performance, particularly the egg laying rate mainly depends on the development of the follicle. Previous studies have shown that follicle-stimulating hormone (FSH) plays an important role in the process of follicular development, but the exact underlying mechanism remains unclear.2. This study showed that FSH stimulated granulosa cell proliferation in a dose-dependent manner. The effect of FSH treatment on granulosa cell proliferation was greatest at a dose of 100 mIU/ml FSH for 24 h.3. Secondly, the effect of different concentrations of FSH on goose granulosa cell proliferation was investigated, and de novo transcriptome assembly and gene expression analysis performed using short-read sequencing technology (Illumina). High-throughput sequencing results yielded 62.61 M reads and 7.8 G base pairs from granulosa cells treated with 100 mIU/ml FSH. These reads were assembled into 65,757 unigenes (mean length: 705 bp) with an N50 of 903 bp. A total of 110 upregulated and 510 downregulated differentially expressed genes (DEGs) were identified by RNA-seq.4. Functional analysis by gene ontology (GO) and KEGG pathway annotation indicated that hormone biosynthesis (GO:0042446), positive regulation of hormone secretion (GO:0046887), steroid biosynthesis, oxidative phosphorylation and carbon metabolism pathways were involved in FSH-mediated proliferation of goose granulosa cells.5. After screening, a group of key responsive genes including superoxide dismutase 1, fatty acyl-CoA reductase 1, transforming growth factor-beta receptor-associated protein 1 and follistatin were tested by real-time reverse transcription PCR to confirm differential expression in granulosa cells stimulated by FSH.6. FSH-stimulated goose granulosa cells and DEG profiling data provided comprehensive gene expression information at the transcriptional level that could promote better understanding of the molecular mechanisms underlying follicle development in response to FSH stimulation.

Gene expression profiling analysis reveals fur development in rex rabbits (Oryctolagus cuniculus).

Fur is an important economic trait in rabbits. The identification of genes that influence fur development and knowledge regarding the actions of these genes provides useful tools for improving fur quality. However, the mechanism of fur development is unclear. To obtain candidate genes related to fur development, the transcriptomes of tissues from backs and bellies of Chinchilla rex rabbits were compared. Of the genes analyzed, 336 showed altered expression in the two groups (285 upregulated and 51 downregulated, P ≤ 0.05, fold-change ≥2 or ≤0.5). Using GO and KEGG to obtain gene classes that were differentially enriched, we found several genes to be involved in many important biological processes. In addition, we identified several signaling pathways involved in fur development, including the Wnt and MAPK signaling pathways, revealing mechanisms of skin and hair follicle development, and epidermal cell and keratinocytes differentiation. The obtained rabbit transcriptome and differentially expressed gene profiling data provided comprehensive gene expression information for SFRP2, FRZB, CACNG1, SLC25A4, and SLC16A3. To validate the RNA-seq data, the expression levels of eight differentially expressed genes involved in fur development were confirmed by qRT-PCR. The results of rabbit transcriptomic profiling provide a basis for understanding the molecular mechanisms of fur development.

Differential gene expression profile of Buyanghuanwu decoction in rats with ventricular remodeling post-myocardial infarction

ObjectiveTo investigate the effect of Buyanghuanwu decoction (BYHWD) on gene expression in ventricular remodeling post-myocardial infarction in rats. MethodsAnimal models of myocardial infarction were established by permanent ligation of the left anterior descending coronary artery. Echocardiography measurements were performed after the treatment of BYHWD (18 g·kg−1·dΔ1) for 90 days. Myocardial collagen was observed by mallory trichrome staining. Capillary density was quantified by using Factor VIII immunohistochemical staining. Differentially expressed genes were explored by a short-read sequencing technology combined with a tag-based digital gene expression profiling (DGE) system. Real-time quantitative polymerase chain reaction detecting system (qPCR) was used to validate the sequencing results. After assembling the gene information from Sham, model and BYHWD groups, we constructed three DGE libraries based on each group. The sequencing of three libraries generated 66 000-73 000 unique tags, which were mapped to reference sequences for annotation of expressed genes. ResultsAmong them, 511 and 352 differentially expressed genes were found in comparison with sham/model and model/BYHWD, respectively. Fifty-five genes exhibited reversed direction of gene expression differences between Sham/Model and Model/BYHWD groups. We found that transforming growth factor beta receptor-1, junctophilin-2, monocyte chemotactic protein 1, neuropeptide Y, arachidonate 5-Lipoxygenase, arachidonate 15-Lipoxygenase were significantly modulated, which suggested the involvement of these genes in BYHWD treatment. ConclusionThe DGE profiling data provide comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the pharmacological mechanisms of BYHWD in ventricular remodeling post-myocardial infarction.

Integrated mRNA and microRNA transcriptome variations in the multi-tepal mutant provide insights into the floral patterning of the orchid Cymbidium goeringii

BackgroundCymbidium goeringii is a very famous traditional orchid plant in China, which is well known for its spectacular and diverse flower morphology. In particular, the multi-tepal mutants have considerable ecological and cultural value. However, the current understanding of the molecular mechanisms of floral patterning and multi-tepal development is limited. In this study, we performed expression profiling of both microRNA (miRNA) and mRNA from wild-type and typical multi-tepal-mutant flowers of C. goeringii for the first time, to identify the genes and pathways regulating floral morphogenesis in C. goeringii.ResultsTotal clean reads of 98,988,774 and 100,188,534 bp were obtained from the wild-type and mutant library, respectively, and de novo assembled into 98,446 unigenes, with an average length of 989 bp. Among them, 18,489 were identified as differentially expressed genes between the two libraries according to comparative transcript profiling. The majority of the gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathway enrichment responses were for membrane-building and ploidy-related processes, consistent with the excessive floral organs and altered cell size observed in the mutant. There were 29 MADS-box genes, as well as a large number of floral-related regulators and hormone-responsive genes, considered as candidates regulating floral patterning of C. goeringii. Small RNA sequencing revealed 132 conserved miRNA families expressed in flowers of C. goeringii, and 11 miRNAs corresponding to 455 putative target genes were considered to be responsible for multi-tepal development. Importantly, integrated analysis of mRNA and miRNA sequencing data showed two transcription factor/microRNA-based genetic pathways contributing to the multi-tepal trait: well-known floral-related miR156/SPL and miR167/ARF regulatory modes involved in reproductive organ development; and the miR319/TCP4–miR396/GRF regulatory cascade probably regulating cell proliferation of the multi-tepal development.ConclusionsIntegrated mRNA and miRNA profiling data provided comprehensive gene expression information on the wild-type and multi-tepal mutant at the transcriptional level that could facilitate our understanding of the molecular mechanisms of floral patterning of C. goeringii. These data could also be used as an important resource for investigating the genetics of floral morphogenesis and various biological mechanisms of orchid plants.

Transcriptome Analysis of the Chrysanthemum Foliar Nematode, Aphelenchoides ritzemabosi (Aphelenchida: Aphelenchoididae).

The chrysanthemum foliar nematode (CFN), Aphelenchoides ritzemabosi, is a plant parasitic nematode that attacks many plants. In this study, a transcriptomes of mixed-stage population of CFN was sequenced on the Illumina HiSeq 2000 platform. 68.10 million Illumina high quality paired end reads were obtained which generated 26,817 transcripts with a mean length of 1,032 bp and an N50 of 1,672 bp, of which 16,467 transcripts were annotated against six databases. In total, 20,311 coding region sequences (CDS), 495 simple sequence repeats (SSRs) and 8,353 single-nucleotide polymorphisms (SNPs) were predicted, respectively. The CFN with the most shared sequences was B. xylophilus with 16,846 (62.82%) common transcripts and 10,543 (39.31%) CFN transcripts matched sequences of all of four plant parasitic nematodes compared. A total of 111 CFN transcripts were predicted as homologues of 7 types of carbohydrate-active enzymes (CAZymes) with plant/fungal cell wall-degrading activities, fewer transcripts were predicted as homologues of plant cell wall-degrading enzymes than fungal cell wall-degrading enzymes. The phylogenetic analysis of GH5, GH16, GH43 and GH45 proteins between CFN and other organisms showed CFN and other nematodes have a closer phylogenetic relationship. In the CFN transcriptome, sixteen types of genes orthologues with seven classes of protein families involved in the RNAi pathway in C. elegans were predicted. This research provides comprehensive gene expression information at the transcriptional level, which will facilitate the elucidation of the molecular mechanisms of CFN and the distribution of gene functions at the macro level, potentially revealing improved methods for controlling CFN.

Transcriptome Analysis of Capsicum Chlorosis Virus-Induced Hypersensitive Resistance Response in Bell Capsicum.

BackgroundCapsicum chlorosis virus (CaCV) is an emerging pathogen of capsicum, tomato and peanut crops in Australia and South-East Asia. Commercial capsicum cultivars with CaCV resistance are not yet available, but CaCV resistance identified in Capsicum chinense is being introgressed into commercial Bell capsicum. However, our knowledge of the molecular mechanisms leading to the resistance response to CaCV infection is limited. Therefore, transcriptome and expression profiling data provide an important resource to better understand CaCV resistance mechanisms.Methodology/Principal FindingsWe assembled capsicum transcriptomes and analysed gene expression using Illumina HiSeq platform combined with a tag-based digital gene expression system. Total RNA extracted from CaCV/mock inoculated CaCV resistant (R) and susceptible (S) capsicum at the time point when R line showed a strong hypersensitive response to CaCV infection was used in transcriptome assembly. Gene expression profiles of R and S capsicum in CaCV- and buffer-inoculated conditions were compared. None of the genes were differentially expressed (DE) between R and S cultivars when mock-inoculated, while 2484 genes were DE when inoculated with CaCV. Functional classification revealed that the most highly up-regulated DE genes in R capsicum included pathogenesis-related genes, cell death-associated genes, genes associated with hormone-mediated signalling pathways and genes encoding enzymes involved in synthesis of defense-related secondary metabolites. We selected 15 genes to confirm DE expression levels by real-time quantitative PCR.Conclusion/SignificanceDE transcript profiling data provided comprehensive gene expression information to gain an understanding of the underlying CaCV resistance mechanisms. Further, we identified candidate CaCV resistance genes in the CaCV-resistant C. annuum x C. chinense breeding line. This knowledge will be useful in future for fine mapping of the CaCV resistance locus and potential genetic engineering of resistance into CaCV-susceptible crops.

Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies.

Somatic embryogenesis is a unique process in plants and has considerable interest for biotechnological application. Compare to japonica, indica rice has been less responsive to in vitro culture. We used Illumina Hiseq 2000 sequencing platform for comparative transcriptome analysis between two rice subspecies at six different developmental stages combined with a tag-based digital gene expression profiling. Global gene expression among different samples showed greater complexity in japonica rice compared to indica which may be due to polyphyletic origin of two rice subspecies. Expression pattern in initial stage indicate major differences in proembryogenic callus induction phase that may serve as key regulator to observe differences between both subspecies. Our data suggests that phytohormone signaling pathways consist of elaborate networks with frequent crosstalk, thereby allowing plants to regulate somatic embryogenesis pathway. However, this crosstalk varies between the two rice subspecies. Down regulation of positive regulators of meristem development (i.e. KNOX, OsARF5) and up regulation of its counterparts (OsRRs, MYB, GA20ox1/GA3ox2) in japonica may be responsible for its better regeneration and differentiation of somatic embryos. Comprehensive gene expression information in the present experiment may also facilitate to understand the monocot specific meristem regulation for dedifferentiation of somatic cell to embryogenic cells.

De novo sequencing and analysis of the cranberry fruit transcriptome to identify putative genes involved in flavonoid biosynthesis, transport and regulation.

BackgroundCranberries (Vaccinium macrocarpon Ait.), renowned for their excellent health benefits, are an important berry crop. Here, we performed transcriptome sequencing of one cranberry cultivar, from fruits at two different developmental stages, on the Illumina HiSeq 2000 platform. Our main goals were to identify putative genes for major metabolic pathways of bioactive compounds and compare the expression patterns between white fruit (W) and red fruit (R) in cranberry.ResultsIn this study, two cDNA libraries of W and R were constructed. Approximately 119 million raw sequencing reads were generated and assembled de novo, yielding 57,331 high quality unigenes with an average length of 739 bp. Using BLASTx, 38,460 unigenes were identified as putative homologs of annotated sequences in public protein databases, including NCBI NR, NT, Swiss-Prot, KEGG, COG and GO. Of these, 21,898 unigenes mapped to 128 KEGG pathways, with the metabolic pathways, secondary metabolites, glycerophospholipid metabolism, ether lipid metabolism, starch and sucrose metabolism, purine metabolism, and pyrimidine metabolism being well represented. Among them, many candidate genes were involved in flavonoid biosynthesis, transport and regulation. Furthermore, digital gene expression (DEG) analysis identified 3,257 unigenes that were differentially expressed between the two fruit developmental stages. In addition, 14,473 simple sequence repeats (SSRs) were detected.ConclusionsOur results present comprehensive gene expression information about the cranberry fruit transcriptome that could facilitate our understanding of the molecular mechanisms of fruit development in cranberries. Although it will be necessary to validate the functions carried out by these genes, these results could be used to improve the quality of breeding programs for the cranberry and related species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1842-4) contains supplementary material, which is available to authorized users.

Characterization of Adelphocoris suturalis (Hemiptera: Miridae) Transcriptome from Different Developmental Stages.

Adelphocoris suturalis is one of the most serious pest insects of Bt cotton in China, however its molecular genetics, biochemistry and physiology are poorly understood. We used high throughput sequencing platform to perform de novo transcriptome assembly and gene expression analyses across different developmental stages (eggs, 2nd and 5th instar nymphs, female and male adults). We obtained 20 GB of clean data and revealed 88,614 unigenes, including 23,830 clusters and 64,784 singletons. These unigene sequences were annotated and classified by Gene Ontology, Clusters of Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes databases. A large number of differentially expressed genes were discovered through pairwise comparisons between these developmental stages. Gene expression profiles were dramatically different between life stage transitions, with some of these most differentially expressed genes being associated with sex difference, metabolism and development. Quantitative real-time PCR results confirm deep-sequencing findings based on relative expression levels of nine randomly selected genes. Furthermore, over 791,390 single nucleotide polymorphisms and 2,682 potential simple sequence repeats were identified. Our study provided comprehensive transcriptional gene expression information for A. suturalis that will form the basis to better understanding of development pathways, hormone biosynthesis, sex differences and wing formation in mirid bugs.

Transcriptome profiling identifies differentially expressed genes in Huoyan goose ovaries between the laying period and ceased period.

The Huoyan goose is famous for its high egg-laying performance and is listed as a nationally protected domestic animal by the Chinese government. To elucidate the key regulatory genes involved in Huoyan goose egg laying, RNA from ovarian tissue during the ceased and laying periods was sequenced using the Illumina HiSeq 2000 sequencing platform. More than 12 million reads were produced in ceased and laying libraries that included 11,896,423 and 12,534,799 clean reads, respectively. More than 20% of the reads were matched to the reference genome, and 23% of the reads were matched to reference genes. Genes with a false discovery rate (FDR) ≤0.001 and log2ratio ≧1 or ≤−1 were characterized as differentially expressed, and 344 up-regulated and 344 down-regulated genes were classified into functional categories. Twelve genes that are mainly involved in pathways for reproduction regulation, such as steroid hormone biosynthesis, GnRH signaling pathways, oocyte meiosis, progesterone-mediated oocyte maturation, steroid biosynthesis, calcium signaling pathways, and G-protein coupled receptor signaling pathway were selected for validation by a quantitative real-time polymerase chain reaction (qRT-PCR) analysis, the qRT-PCR results are consistent with the general expression patterns of those genes from the Illumina sequencing. These data provide comprehensive gene expression information at the transcriptional level that might increase our understanding of the Huoyan goose's reproductive biology.

Transcriptome Analysis of Early Anther Development of Cotton Revealed Male Sterility Genes for Major Metabolic Pathways

Anther development in flowering plants is critical for plant breeding and reproduction and is regulated by elaborate coordination of many genes. However, the functions of most genes related to this developmental process remain unknown and understanding of the molecular mechanism of cotton (Gossypium hirsutum L.) genetic male sterility (GMS) is still scant. To better understand the functions of genes related to anther development, we performed a digital gene expression (DGE) analysis between an upland cotton GMS line and its maintainer line. Compared with the maintainer line, we identified 916 up-regulated and 826 down-regulated genes in the GMS line, including 12 transcription factors. Transcriptome profiling analysis showed that many key genes were involved in pentose and glucuronate interconversions, starch and sucrose metabolism, galactose metabolism, alpha-linolenic acid metabolism, peroxisome, monoterpenoid biosynthesis, and sesquiterpenoid biosynthesis. Our analysis provides comprehensive gene expression information at the transcriptional level and lays the foundation1s for further functional analysis of candidate genes required for anther development, and will help understand the molecular mechanism of GMS in cotton.