Digital gene expression for non-model organisms

Research Note: Transcriptome analysis of skeletal muscles of black-boned chickens, including 2 types (wild and mutated) of Taihe black-boned silky fowl and 1 type (wild) of Yugan black-boned chicken

The large amount of melanin deposited in Taihe black-boned silky fowl and other black-boned chicken breeds is a highly valued trait due to its desirable nutritional and functional properties, such as antiaging, immune-enhancing, and antifatigue properties. To identify the candidate genes and pathways potentially responsible for melanogenesis in Taihe black-boned silky fowl, digital gene expression tag (DGE-tag)-based transcriptome analyses were performed for 2 groups: wild-type Taihe black-boned silky fowl (TH-1245) vs. mutated Taihe black-boned silky fowl (BY-1245) and TH-1245 vs. wild-type Yugan black-boned chicken (YG-1245). In total, 430 and 765 differentially expressed genes (DEGs) were identified and 13 DEGs displaying different gene expression patterns between the 2 groups were considered valuable for further investigation, such as ANKRD1, MYOZ2, and MYOD1. Furthermore, 6 functionally grouped networks composed of 36 significant GO terms, mainly involved in muscle-related and signaling-related biological processes, were screened by functional enrichment network analysis. In addition, protein-protein interaction (PPI) network analysis identifies 2 top clusters containing 20 hub genes for 2 comparison groups. MYL1 and RPS14 were considered the most potential candidate genes among all hub genes. The Gene Set Enrichment Analysis (GSEA) results showed that the terms and pathways, such as muscle system process, arachidonic acid metabolism, melanogenesis, and tyrosine metabolism, may play important roles in the melanogenesis and further investigations were needed to clarify the relationships between these pathways and melanin. Overall, these results are helpful for furthering our understanding of melanogenesis in breast muscle of Taihe black-boned silky fowl and Yugan black-boned chicken.

Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves

Polyploidy has been suggested to negatively impact environmental stress tolerance, resulting in increased susceptibility to extreme climate events. In this study, we compared the genomic and physiological response of diploid (2n) and triploid (3n) Pacific oysters (Crassostrea gigas) to conditions present during an atmospheric heatwave that impacted the Pacific Northwestern region of the United States in the summer of 2021. Climate stressors were applied either singly (single stressor; elevated seawater temperature, 30°C) or in succession (multiple stressor; elevated seawater temperature followed by aerial emersion at 44°C), replicating conditions present within the intertidal over a tidal cycle during the event. Oyster mortality rate was elevated within stress treatments with respect to the control and was significantly higher in triploids than diploids following multiple stress exposure (36.4% vs. 14.8%). Triploids within the multiple stressor treatment exhibited signs of energetic limitation, including metabolic depression, a significant reduction in ctenidium Na+ /K+ ATPase activity, and the dysregulated expression of genes associated with stress response, innate immunity, glucose metabolism, and mitochondrial function. Functional enrichment analysis of ploidy-specific gene sets identified that biological processes associated with metabolism, stress tolerance, and immune function were overrepresented within triploids across stress treatments. Our results suggest that triploidy impacts the transcriptional regulation of key processes that underly the stress response of Pacific oysters, resulting in downstream shifts in physiological tolerance limits that may increase susceptibility to extreme climate events that present multiple environmental stressors. The impact of chromosome set manipulation on the climate resilience of marine organisms has important implications for domestic food security within future climate scenarios, especially as triploidy induction becomes an increasingly popular tool to elicit reproductive control across a wide range of species used within marine aquaculture.

Genetics and Evolution of Mammalian Coat Pigmentation

The diversity of mammalian coat colors, and their potential adaptive significance, have long fascinated scientists as well as the general public. The recent decades have seen substantial improvement in our understanding of their genetic bases and evolutionary relevance, revealing novel insights into the complex interplay of forces that influence these phenotypes. At the same time, many aspects remain poorly known, hampering a comprehensive understanding of these phenomena. Here we review the current state of this field and indicate topics that should be the focus of additional research. We devote particular attention to two aspects of mammalian pigmentation, melanism and pattern formation, highlighting recent advances and outstanding challenges, and proposing novel syntheses of available information. For both specific areas, and for pigmentation in general, we attempt to lay out recommendations for establishing novel model systems and integrated research programs that target the genetics and evolution of these phenotypes throughout the Mammalia.

Identification and quantification of domestic feline cytochrome P450 transcriptome across multiple tissues

Understanding of cytochrome P450 (CYP) isoform distribution and function in the domestic feline is limited. Only a few studies have defined individual CYP isoforms across metabolically relevant tissues, hampering the ability to predict drug metabolism and potential drug-drug interactions. Using RNA sequencing (RNA-seq), transcriptomes from the 99 Lives Cat Genome Sequencing Initiative databank combined with experimentally acquired whole transcriptome sequencing of healthy, adult male (n = 2) and female (n = 2) domestic felines, expression of 42 CYP isoforms were identified in 20 different tissues. Thirty-seven of these isoforms had not been previously reported in cats. Depending on the tissue, three to twenty-nine CYP isoform transcripts were expressed. The feline genome annotations did not differentiate CYP2E1 and 2E2 genes, demonstrating poor annotation for this gene using the reference genome. As the majority of the sequences are based on automated pipelines, complete cDNA sequences for translation into CYP protein sequences could not be determined. This study is the first to identify and characterize 37 additional CYP isoforms in feline tissues, increasing the number of identified CYP from the previously reported seven isoforms to 42 across 20 tissues.

Fipronil-induced toxic effects in zebrafish (Danio rerio) larvae by using digital gene expression profiling

Fipronil residue has caused widespread concern around the world, especially after the recent "toxic eggs" event in seven European countries. To evaluate the effects of fipronil on vertebrates, zebrafish larvae were used as an animal model to examine the lethal effect, developmental phenotypes at high doses, and possible mechanisms of toxicity by employing digital gene expression (DGE) profiling at environmentally relevant doses. The results of acute toxicity test indicated that treatment with fipronil from 75 h post-fertilization (hpf) led to the death of larvae with a 96-h LC50 value of 459 μg/L, as well as abnormal development including bent spine and shortened body length. Besides, we obtained high-quality-sequencing DGE profilings at fipronil concentrations of 0.5, 5, and 50 μg/L, respectively. The results revealed that 44 differentially expressed genes, 10 GO terms, and 3 KEGG pathways were overlapped among the three concentrations. MIDN, one of the 44 differentially expressed genes, showed dose-dependent responses at the transcriptional level, indicating that it was possibly a potential biomarker to reflect fipronil toxicity in zebrafish. Furthermore, we presumed that the changing transcriptional level of AP-1 family was possibly a reason for bent spine and shortened body length in larvae exposed to fipronil. Concurrently, altered abundance of transcripts of the ELOVL family in a key step of fatty acid elongation could possibly lead to the accumulation of long-chain fatty acids. Collectively, our results suggested that exposure to fipronil caused lethal and developmental toxicity in zebrafish larvae, and demonstrated the need for a comprehensive understanding of the potential mechanisms of fipronil toxicity due to fipronil's frequent presence in the environment and its potential threat to human health.

A direct link between MITF, innate immunity, and hair graying

Melanocyte stem cells (McSCs) and mouse models of hair graying serve as useful systems to uncover mechanisms involved in stem cell self-renewal and the maintenance of regenerating tissues. Interested in assessing genetic variants that influence McSC maintenance, we found previously that heterozygosity for the melanogenesis associated transcription factor, Mitf, exacerbates McSC differentiation and hair graying in mice that are predisposed for this phenotype. Based on transcriptome and molecular analyses of Mitf^mi-vga9/+ mice, we report a novel role for MITF in the regulation of systemic innate immune gene expression. We also demonstrate that the viral mimic poly(I:C) is sufficient to expose genetic susceptibility to hair graying. These observations point to a critical suppressor of innate immunity, the consequences of innate immune dysregulation on pigmentation, both of which may have implications in the autoimmune, depigmenting disease, vitiligo.

Hair pigmentation over the course of a lifetime depends on melanocyte stem cells that reside in the hair follicle. As old hairs fall out and new hairs grow in, melanocyte stem cells serve as a reservoir for the melanocytes that produce the pigment that gives hair its visible color. The loss of these stem cells leads to the growth of nonpigmented, or gray, hairs. Evaluating mouse models of hair graying can reveal key aspects of melanocyte stem cell biology. Using this approach, we discovered a novel role for the melanogenesis associated transcription factor, MITF, in repressing the expression of innate immune genes within cells of the melanocyte lineage. The importance of this repression is revealed in animals that have a predisposition for hair graying. In these animals, artificial elevation of the innate immune response, either through a genetic mechanism or via exposure to viral mimic, results in significant melanocyte and melanocyte stem cell loss and leads to the production of an increased number of gray hairs. These observations highlight the negative effects of innate immune activation on melanocyte and melanocyte stem cell physiology and suggest a connection between viral infection and hair graying.

Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation

From allozymes in 1983 to whole genomes in 2015, genetic studies of the cheetah have been extensive. In this chapter we provide an overview of the available literature. Overall, patterns of genetic variation provided evidence of low variability and suggest this loss occurred thousands of years ago. Differences between published subspecies were supported genetically. At a local scale, populations were generally considered panmictic with minor genetic structure. Although cheetahs have persisted despite low genetic variability, important questions arise from these findings: Does the cheetah have the ability to adapt to and evolve with future changes in environmental and infectious pressure? How would cheetahs cope with further loss of genetic diversity? Connectivity in the wild should be maintained via prevention of habitat loss, while management of small isolated populations may require reestablishing gene flow. Genetics could assist captive-breeding decisions and provide forensic evidence as to the geographical origin of illegally traded animals.

Comparative tissue transcriptomics highlights dynamic differences among tissues but conserved metabolic transcript prioritization in preparation for arousal from torpor

During the hibernation season, 13-lined ground squirrels spend days to weeks in torpor with body temperatures near freezing then spontaneously rewarm. The molecular drivers of the drastic physiological changes that orchestrate and permit torpor are not well understood. Although transcription effectively ceases at the low body temperatures of torpor, previous work has demonstrated that some transcripts are protected from bulk degradation in brown adipose tissue (BAT), consistent with the importance of their protein products for metabolic heat generation during arousal from torpor. We examined the transcriptome of skeletal muscle, heart, and liver to determine the patterns of differentially expressed genes in these tissues, and whether, like BAT, a subset of these were relatively increased during torpor. EDGE-tags were quantified from five distinct physiological states representing the seasonal and torpor-arousal cycles of 13-lined ground squirrels. Supervised clustering on relative transcript abundances with Random Forest separated the two states bracketing prolonged torpor, entrance into and aroused from torpor, in all three tissues. Independent analyses identified 3347, 6784, and 2433 differentially expressed transcripts among all sampling points in heart, skeletal muscle, and liver, respectively. There were few differentially expressed genes in common across all three tissues; these were enriched in mitochondrial and apoptotic pathway components. Divisive clustering of these data revealed unique cohorts of transcripts that increased across the torpor bout in each tissue with patterns reflecting various combinations of cycling within and between seasons as well as between torpor and arousal. Transcripts that increased across the torpor bout were likewise tissue specific. These data shed new light on the biochemical pathways that alter in concert with hibernation phenotype and provide a rich resource for further hypothesis-based studies.

Candidate egg case silk genes for the spider Argiope argentata from differential gene expression analyses

Orb-web weaving spiders produce a variety of task-specific silks from specialized silk glands. The genetics underlying the synthesis of specific silk types are largely unknown, and transcriptome analysis could be a powerful approach for identifying candidate genes. However, de novo assembly and expression profiling of silk glands with RNA-sequencing (RNAseq) are problematic because the few known gene transcripts for silk proteins are extremely long and highly repetitive. To identify candidate genes for tubuliform (egg case) silk synthesis by the orb-weaver Argiope argentata (Araneidae), we estimated transcript abundance using two sequencing methods: RNAseq reads from throughout the length of mRNA molecules, and 3' digital gene expression reads from the 3' region of mRNA molecules. Both analyses identified similar sets of genes as differentially expressed when comparing tubuliform and nonsilk gland tissue. However, incompletely assembled silk gene transcripts were identified as differentially expressed because of RNAseq read alignments to highly repetitive regions, confounding interpretation of RNAseq results. Homologues of egg case silk protein (ECP) genes were upregulated in tubuliform glands. This discovery is the first description of ECP homologues in an araneid. We also propose additional candidate genes involved in synthesis of tubuliform or other silk types.

Effects of MicroRNA-23a on Differentiation and Gene Expression Profiles in 3T3-L1 Adipocytes

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate growth, development, and programmed death of cells. A newly-published study has shown that miRNA-23a could regulate 3T3-L1 adipocyte differentiation. Here, we identified miRNA-23a as a negative regulator of 3T3-L1 adipocyte differentiation again. Over-expression of miRNA-23a inhibited differentiation and decreased lipogenesis as well as down-regulated mRNA and protein expression of both peroxisome proliferator-activated receptor (PPAR) γ and fatty acid binding protein (FABP) 4, whereas knock down of miRNA-23a showed the opposite effects on differentiation as well as increasing the number of apoptotic cells. Additionally, digital gene expression profiling sequencing (DGE-Seq) was used to assay changes in gene expression profiles following alterations in the level of miR-23a. In total, over-expression or knock down of miRNA-23a significantly changed the expression of 313 and 425 genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these genes were mainly involved in the stress response, immune system, metabolism, cell cycle, among other pathways. Additionally, the signal transducer and activator of transcription 1 (Stat1) was shown to be a target of miRNA-23a by computational and dual-luciferase reporter assays that indicated Janus Kinase (Jak)-Stat signal pathway was implicated in regulating adipogenesis mediated by miRNA-23a in adipocytes.

Digital Gene Expression Profiling to Explore Differentially Expressed Genes Associated with Terpenoid Biosynthesis during Fruit Development in Litsea cubeba

Mountain pepper (Litseacubeba (Lour.) Pers.) (Lauraceae) is an important industrial crop as an ingredient in cosmetics, pesticides, food additives and potential biofuels. These properties are attributed to monoterpenes and sesquiterpenes. However, there is still no integrated model describing differentially expressed genes (DEGs) involved in terpenoid biosynthesis during the fruit development of L. cubeba. Here, we performed digital gene expression (DGE) using the Illumina NGS platform to evaluated changes in gene expression during fruit development in L. cubeba. DGE generated expression data for approximately 19354 genes. Fruit at 60 days after flowering (DAF) served as the control, and a total of 415, 1255, 449 and 811 up-regulated genes and 505, 1351, 1823 and 1850 down-regulated genes were identified at 75, 90, 105 and 135 DAF, respectively. Pathway analysis revealed 26 genes involved in terpenoid biosynthesis pathways. Three DEGs had continued increasing or declining trends during the fruit development. The quantitative real-time PCR (qRT-PCR) results of five differentially expressed genes were consistent with those obtained from Illumina sequencing. These results provide a comprehensive molecular biology background for research on fruit development, and information that should aid in metabolic engineering to increase the yields of L. cubeba essential oil.

Analysis of digital gene expression profiling in hemocytes of white shrimp Litopenaeus vannamei under nitrite stress

Accumulation of nitrite in water is highly toxic to aquatic animals. To understand immune responses in shrimp under such environmental stress, a digital gene expression (DGE) technology was applied to detect the gene expression profile of the Litopenaeus vannamei hemocytes in response to nitrite for 48 h. A total of 1922 differently expressed unigenes were generated. Of these transcripts, 1269 and 653 genes were up- or down-regulated respectively. Functional categorization and pathways of the differentially expressed genes revealed that immune defense, xenobiotics biodegradation and metabolism, amino acid and nucleobase metabolic process, apoptosis were the differentially regulated processes occurring during nitrite stress. We selected 19 differential expression transcripts (DETs) to validate the sequencing results by real time quantitative PCR (qPCR). The Pearson's correlation coefficient (R) of the 19 DETs was 0.843, which confirmed the consistency and accuracy between these two approaches. Subsequently, we screened 10 genes to examine the changes in the time course of gene expression in more detail. The results indicated that expressions of ATP-binding cassette transporter (ABC transporter), caspase10, QM protein, C type lectin 4 (CTL4), protein disulfide isomerase (PDI), serine protease inhibitor 8 (SPI8), transglutaminase (TGase), chitinase1, inhibitors of apoptosis proteins (IAP) and cytochrome P450 enzyme (CYP450) were induced to participate in the anti-stress defense against nitrite. These results will provide a reference for follow-up study of molecular toxicology and valuable gene information for better understanding of immune response in L. vannamei under environmental stress.

Digital gene expression analysis with sample multiplexing and PCR duplicate detection: A straightforward protocol

Tag-Seq is a high-throughput approach used for discovering SNPs and characterizing gene expression. In comparison to RNA-Seq, Tag-Seq eases data processing and allows detection of rare mRNA species using only one tag per transcript molecule. However, reduced library complexity raises the issue of PCR duplicates, which distort gene expression levels. Here we present a novel Tag-Seq protocol that uses the least biased methods for RNA library preparation combined with a novel approach for joint PCR template and sample labeling. In our protocol, input RNA is fragmented by hydrolysis, and poly(A)-bearing RNAs are selected and directly ligated to mixed DNA-RNA P5 adapters. The P5 adapters contain i5 barcodes composed of sample-specific (moderately) degenerate base regions (mDBRs), which later allow detection of PCR duplicates. The P7 adapter is attached via reverse transcription with individual i7 barcodes added during the amplification step. The resulting libraries can be sequenced on an Illumina sequencer. After sample demultiplexing and PCR duplicate removal with a free software tool we designed, the data are ready for downstream analysis. Our protocol was tested on RNA samples from predator-induced and control Daphnia microcrustaceans.

Identification of novel direct targets of Drosophila Sine oculis and Eyes absent by integration of genome-wide data sets

Drosophila eye development is a complex process that involves many transcription factors (TFs) and interactions with their cofactors and targets. The TF Sine oculis (So) and its cofactor Eyes absent (Eya) are highly conserved and are both necessary and sufficient for eye development. Despite their many important roles during development, the direct targets of So are still largely unknown. Therefore the So-dependent regulatory network governing eye determination and differentiation is poorly understood. In this study, we intersected gene expression profiles of so or eya mutant eye tissue prepared from three different developmental stages and identified 1731 differentially expressed genes across the Drosophila genome. A combination of co-expression analyses and motif discovery identified a set of twelve putative direct So targets, including three known and nine novel targets. We also used our previous So ChIP-seq data to assess motif predictions for So and identified a canonical So binding motif. Finally, we performed in vivo enhancer reporter assays to test predicted enhancers from six candidate target genes and find that at least one enhancer from each gene is expressed in the developing eye disc and that their expression patterns overlap with that of So. We furthermore confirmed that the expression level of predicted direct So targets, for which antibodies are available, are reduced in so or eya post-mitotic knockout eye discs. In summary, we expand the set of putative So targets and show for the first time that the combined use of expression profiling of so with its cofactor eya is an effective method to identify novel So targets. Moreover, since So is highly conserved throughout the metazoa, our results provide the basis for future functional studies in a wide variety of organisms.

Transcriptomic Analysis of Differentially Expressed Genes during Flower Organ Development in Genetic Male Sterile and Male Fertile Tagetes erecta by Digital Gene-Expression Profiling

Tagetes erecta is an important commercial plant of Asteraceae family. The male sterile (MS) and male fertile (MF) two-type lines of T. erecta have been utilized in F1 hybrid production for many years, but no report has been made to identify the genes that specify its male sterility that is caused by homeotic conversion of floral organs. In this study, transcriptome assembly and digital gene expression profiling were performed to generate expression profiles of MS and MF plants. A cDNA library was generated from an equal mixture of RNA isolated from MS and MF flower buds (1 mm and 4 mm in diameter). Totally, 87,473,431 clean tags were obtained and assembled into 128,937 transcripts among which 65,857 unigenes were identified with an average length of 1,188 bp. About 52% of unigenes (34,176) were annotated in Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KO (KEGG Ortholog database) and/or GO. Taking the above transcriptome as reference, 125 differentially expressed genes were detected in both developmental stages of MS and MF flower buds. MADS-box genes were presumed to be highly related to male sterility in T. erecta based on histological and cytological observations. Twelve MADS-box genes showed significantly different expression levels in flower buds 4 mm in diameter, whereas only one gene expressed significantly different in flower buds 1 mm in diameter between MS and MF plants. This is the first transcriptome analysis in T. erecta and will provide a valuable resource for future genomic studies, especially in flower organ development and/or differentiation.

PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome

A major objective of systems biology is to quantitatively integrate multiple parameters from genome-wide measurements. To integrate gene expression with dynamics in poly(A) tail length and adenylation site, we developed a targeted next-generation sequencing approach, Poly(A)-Test RNA-sequencing. PAT-seq returns (i) digital gene expression, (ii) polyadenylation site/s, and (iii) the polyadenylation-state within and between eukaryotic transcriptomes. PAT-seq differs from previous 3' focused RNA-seq methods in that it depends strictly on 3' adenylation within total RNA samples and that the full-native poly(A) tail is included in the sequencing libraries. Here, total RNA samples from budding yeast cells were analyzed to identify the intersect between adenylation state and gene expression in response to loss of the major cytoplasmic deadenylase Ccr4. Furthermore, concordant changes to gene expression and adenylation-state were demonstrated in the classic Crabtree-Warburg metabolic shift. Because all polyadenylated RNA is interrogated by the approach, alternative adenylation sites, noncoding RNA and RNA-decay intermediates were also identified. Most important, the PAT-seq approach uses standard sequencing procedures, supports significant multiplexing, and thus replication and rigorous statistical analyses can for the first time be brought to the measure of 3'-UTR dynamics genome wide.

Genome-wide analysis reveals dynamic changes in expression of microRNAs during vascular cambium development in Chinese fir, Cunninghamia lanceolata

MicroRNAs (miRNAs) are small noncoding regulatory RNAs that play key roles in the process of plant development. To date, extensive studies of miRNAs have been performed in a few model plants, but few efforts have focused on small RNAs (sRNAs) in conifers because of the lack of reference sequences for their enormous genomes. In this study, Solexa sequencing of three sRNA libraries obtained from dormant, reactivating, and active vascular cambium in Chinese fir (Cunninghamia lanceolata) using tangential cryosectioning identified 20 known miRNA families and 18 novel potential miRNAs, of which nine novel miRNA precursors were validated by RT-PCR and sequencing. More than half of these novel miRNAs displayed stage-specific expression patterns in the vascular cambium. Furthermore, analysing the 103 miRNAs and their predicted targets indicated that about 70% appeared to negatively regulate their targets, of which two target genes involved in the regulation of cambial cell division were validated via RNA ligase-mediated rapid amplification of 5'-cDNA ends (RLM 5'-RACE) and transient co-expression in Nicotiana benthamiana leaves. Interestingly, miRNA156 and miRNA172 may regulate the phase transition in vascular cambium from dormancy to active growth. These results provide new insights into the important regulatory functions of miRNAs in vascular cambium development and wood formation in conifers.

Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea

BACKGROUND

The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the neoblasts. Nonetheless, a reliable reference for this type of studies is still lacking.

RESULTS

Taking advantage of digital gene expression (DGE) sequencing technology we compare all the available transcriptomes for S. mediterranea and improve their annotation. These results are accessible via web for the community of researchers. Using the quantitative nature of DGE, we describe the transcriptional profile of neoblasts and present 42 new neoblast genes, including several cancer-related genes and transcription factors. Furthermore, we describe in detail the Smed-meis-like gene and the three Nuclear Factor Y subunits Smed-nf-YA, Smed-nf-YB-2 and Smed-nf-YC.

CONCLUSIONS

DGE is a valuable tool for gene discovery, quantification and annotation. The application of DGE in S. mediterranea confirms the planarian stem cells or neoblasts as a complex population of pluripotent and multipotent cells regulated by a mixture of transcription factors and cancer-related genes.

Anti-obese effect of glucosamine and chitosan oligosaccharide in high-fat diet-induced obese rats

Objective: This study is to evaluate the anti-obese effects of glucosamine (GLC) and chitosan oligosaccharide (COS) on high-fat diet-induced obese rats. Methods: The rats were randomly divided into twelve groups: a normal diet group (NF), a high-fat diet group (HF), Orlistat group, GLC high-, middle-, and low-dose groups (GLC-H, GLC-M, GLC-L), COS1 (COS, number-average molecular weight ≤1000) high-, middle-, and low-dose groups (COS1-H, COS1-M, COS1-L), and COS2 (COS, number-average molecular weight ≤3000) high-, middle-, and low-dose groups (COS2-H, COS2-M, COS2-L). All groups received oral treatment by gavage once daily for a period of six weeks. Results: Rats fed with COS1 gained the least weight among all the groups (P < 0.01), and these rats lost more weight than those treated with Orlistat. In addition to the COS2-H and Orlistat groups, the serum total cholesterol (CHO) and low-density lipoprotein cholesterol (LDL-C) levels were significantly reduced in all treatment groups compared to the HF group (P < 0.01). The various doses of GLC, COS1 and COS2 reduced the expression levels of PPARγ and LXRα mRNA in the white adipose tissue. Conclusions: The results above demonstrated that GLC, COS1, and COS2 improved dyslipidemia and prevented body weight gains by inhibiting the adipocyte differentiation in obese rats induced by a high-fat diet. Thus, these agents may potentially be used to treat obesity.

Transcriptome analysis of canola (Brassica napus) under salt stress at the germination stage

Canola (Brassica napus) is one of the most important oil crops in the world. However, its yield has been constrained by salt stress. In this study, transcriptome profiles were explored using Digital Gene Expression (DGE) at 0, 3, 12 and 24 hours after H2O (control) and NaCl treatments on B. napus roots at the germination stage. Comparisons of gene-expression between the control and the treatment were conducted after tag-mapping to the sequenced Brassica rapa genome. The differentially expressed genes during the time course of salt stress were focused on, and 163 genes were identified to be differentially expressed at all the time points. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that some of the genes were involved in proline metabolism, inositol metabolism, carbohydrate metabolic processes and oxidation-reduction processes and may play vital roles in the salt-stress response at the germination stage. Thus, this study provides new candidate salt stress responding genes, which may function in novel putative nodes in the molecular pathways of salt stress resistance.

Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator

During hibernation, animals cycle between torpor and arousal. These cycles involve dramatic but poorly understood mechanisms of dynamic physiological regulation at the level of gene expression. Each cycle, Brown Adipose Tissue (BAT) drives periodic arousal from torpor by generating essential heat. We applied digital transcriptome analysis to precisely timed samples to identify molecular pathways that underlie the intense activity cycles of hibernator BAT. A cohort of transcripts increased during torpor, paradoxical because transcription effectively ceases at these low temperatures. We show that this increase occurs not by elevated transcription but rather by enhanced stabilization associated with maintenance and/or extension of long poly(A) tails. Mathematical modeling further supports a temperature-sensitive mechanism to protect a subset of transcripts from ongoing bulk degradation instead of increased transcription. This subset was enriched in a C-rich motif and genes required for BAT activation, suggesting a model and mechanism to prioritize translation of key proteins for thermogenesis.

DOI:http://dx.doi.org/10.7554/eLife.04517.001

Many mammals hibernate to avoid food scarcity and harsh conditions during winter. Hibernation involves entering a state called torpor, which drastically reduces the amount of energy used by the body. During torpor, body temperature also decreases. This is particularly exemplified in ground squirrels, whose body temperature can hover at just above or even below the point of freezing. However, hibernating mammals cannot remain in this state continuously over the months of hibernation but instead cycle between bouts of torpor lasting for 1–3 weeks and brief periods of ‘arousal’ lasting between 12–24 hr, during which their body rapidly warms up.

The heat required to start warming up the hibernator is generated from a specialized form of fat called brown adipose tissue. Normally, the bursts of metabolic activity that are required to create this heat depend on certain proteins being produced. Making a protein involves ‘translating’ its sequence from template molecules called messenger RNA (mRNA), which are ‘transcribed’ from the gene that encodes the protein. During the low body temperatures experienced during torpor, both of these processes stop. So how is the hibernator able to quickly and efficiently heat itself up during the arousal periods of hibernation?

Grabek et al. investigated this by analyzing the relative levels of mRNA in the brown adipose tissue of hibernating 13-lined ground squirrels. Using a special technique to sample and sequence small fragments of mRNA taken from brown adipose tissue, Grabek et al. compiled a profile of the mRNA molecules present at different points in the torpor–arousal cycle and compared this with a similar profile taken from squirrels that were not hibernating.

From this analysis, Grabek et al. detected that a particular group of mRNA molecules that are required for producing heat increase in abundance during torpor, even though body temperature is low enough to stop gene transcription. This increased abundance does not occur because more of the mRNA molecules are made; instead, the mRNA molecules are modified to become more stable and long lasting. Once the animal warms up during arousal, gene transcription is reactivated and more new mRNA molecules are made.

Grabek et al. suggest that the key mRNAs required for brown adipose tissue function are selectively stabilized during torpor through a temperature-dependent protective mechanism. These mRNAs are then preferentially translated into proteins during arousal to rapidly and efficiently heat the hibernator. Most other mRNA molecules degrade throughout torpor, and so their numbers decline as replacements are not transcribed until body temperature briefly recovers during arousal. Whether this protective mechanism is also used in other tissues during torpor remains a question for future work.

DOI:http://dx.doi.org/10.7554/eLife.04517.002

Gene set by de novo assembly of Perilla species and expression profiling between P. frutescens (L.) var. frutescens and var. crispa

Perilla frutescens (L.) Britt. is a self-pollinating annual species and is widely cultivated in China, Korea and Japan as an economic crop and a source of medicine and spices. In this study, we sequenced one cultivar variety (PF98095) of P. frutescens (L.) var. frutescens Britt., which was assembled as reference and other three varieties (PF11109, weedy of var. frutescens, PF06336 and PF06353, cultivars of varieties crispa) in order to carry out comparative expression profiling within cultivar and weedy in varieties frutescens and between varieties frutescens and varieties crispa of cultivar type in P. frutescens. Assembly of PF98095, annotation mapping, DEG (differentially expressed gene) profiling, and comparative analysis were performed. We found that more than 65% of the reads were mapped to the reference of P. frutescens gene set. Moreover, we detected 22,962 DEGs in the weedy variety compared to the cultivar, and also, 22,138 and 23,845 DEGs were identified in two cultivars according to the reference, respectively. The DEGs and functional classification were developed to analyze the differences between weedy and cultivar and between varieties frutescens and varieties crispa of Perilla. Furthermore, candidate genes for the different color and seed size of Perilla were identified that could be further investigated in future study. The herein results may play a significant role, and contribute in functional transcriptome studies of Perilla.

Transcriptomic Analysis for Different Sex Types of Ricinus communis L. during Development from Apical Buds to Inflorescences by Digital Gene Expression Profiling

The castor plant (Ricinus communis L.) is a versatile industrial oilseed crop with a diversity of sex patterns, its hybrid breeding for improving yield and high purity is still hampered by genetic instability of female and poor knowledge of sex expression mechanisms. To obtain some hints involved in sex expression and provide the basis for further insight into the molecular mechanisms of castor plant sex determination, we performed DGE analysis to investigate differences between the transcriptomes of apices and racemes derived from female (JXBM0705P) and monoecious (JXBM0705M) lines. A total of 18 DGE libraries were constructed from the apices and racemes of a wild monoecious line and its isogenic female derivative at three stages of apex development, in triplicate. Approximately 5.7 million clean tags per library were generated and mapped to the reference castor genome. Transcriptomic analysis showed that identical dynamic changes of gene expression were indicated in monoecious and female apical bud during its development from vegetation to reproduction, with more genes expressed at the raceme formation and infant raceme stages compare to the early leaf bud stage. More than 3000 of differentially expressed genes (DEGs) were detected in Ricinus apices at three developmental stages between two different sex types. A number of DEGs involved in hormone response and biosynthesis, such as auxin response and transport, transcription factors, signal transduction, histone demethylation/methylation, programmed cell death, and pollination, putatively associated with sex expression and reproduction were discovered, and the selected DEGs showed consistent expression between qRT-PCR validation and the DGE patterns. Most of those DEGs were suppressed at the early leaf stage in buds of the mutant, but then activated at the following transition stage (5-7-leaf stage) of buds in the mutant, and ultimately, the number of up-regulated DEGs was equal to that of down-regulation in the small raceme of the mutant. In this study, a large number of DEGs and some suggestions involved in sex expression and reproduction were discovered using DGE analysis, which provides large information and valuable hints for next insights into the molecular mechanism of sex determination. It is useful for other further studies in Ricinus.

Current transcriptomics in pig immunity research

Swine performance in the face of disease challenge is becoming progressively more important. To improve the pig’s robustness and resilience against pathogens through selection, a better understanding of the genetic and epigenetic factors in the immune response is required. This review highlights results from the most recent transcriptome research, and the meta-analyses performed, in the context of pig immunity. A technological overview is given including wholegenome microarrays, immune-specific arrays, small-scale high-throughput expression methods, high-density tiling arrays, and next generation sequencing (NGS). Although whole genome microarray techniques will remain complementary to NGS for some time in domestic species, research will transition to sequencing-based methods due to cost-effectiveness and the extra information that such methods provide. Furthermore, upcoming high-throughput epigenomic studies, which will add greatly to our knowledge concerning the impact of epigenetic modifications on pig immune response, are listed in this review. With emphasis on the insights obtained from transcriptomic analyses for porcine immunity, we also discuss the experimental design in pig immunity research and the value of the newly published porcine genome assembly in using the pig as a model for human immune response. We conclude by discussing the importance of establishing community standards to maximize the possibility of integrative computational analyses, such as was clearly beneficial for the human ENCODE project.

Transcriptome characterization and differential expression analysis of cold-responsive genes in young spikes of common wheat

With the frequent occurrence of climatic anomalies, spring frost has become a significant limiting factor on wheat production, especially during the reproductive growth stage. A high-throughput sequencing technology was applied and a total of 54 million clean reads that corresponded to 7.44 Gb of total nucleotides were generated. These reads were then de novo assembled into 120,715 unigenes with an average length of 627 bp. Functional annotations were then obtained by aligning all unigenes with public protein databases. In total, 9657 potential EST-SSRs were identified, and 6310 primer pairs for 1329 SSRs were obtained. Meanwhile, a comparison of four tag-based digital gene expression libraries, which was built from the control and cold-treated young spikes were performed. Overall, 526 up-regulated and 489 down-regulated genes were identified, and GO and KEGG pathway analyses of those genes were further conducted. Based on these results, a series of candidate genes involved in cold response pathways were identified, and 12 of them were confirmed by qRT-PCR. The combination of RNA-Seq and digital gene expression analysis in this study provides a powerful approach for investigating the transcriptional changes and obtained a large number of unigenes annotated to public databases.

Identification of differentially expressed genes in leaf of Reaumuria soongorica under PEG-induced drought stress by digital gene expression profiling

Reaumuria soongorica (Pall.) Maxim., a resurrection semi-shrub, is a typical constructive and dominant species in desert ecosystems in northwestern China. However, the gene expression characteristics of R. soongorica under drought stress have not been elucidated. Digital gene expression analysis was performed using Illumina technique to investigate differentially expressed genes (DEGs) between control and PEG-treated samples of R. soongorica. A total of 212,338 and 211,052 distinct tags were detected in the control and PEG-treated libraries, respectively. A total of 1,325 genes were identified as DEGs, 379 (28.6%) of which were up-regulated and 946 (71.4%) were down-regulated in response to drought stress. Functional annotation analysis identified numerous drought-inducible genes with various functions in response to drought stress. A number of regulatory proteins, functional proteins, and proteins induced by other stress factors in R. soongorica were identified. Alteration in the regulatory proteins (transcription factors and protein kinase) may be involved in signal transduction. Functional proteins, including flavonoid biosynthetic proteins, late embryogenesis abundant (LEA) proteins, small heat shock proteins (sHSP), and aquaporin and proline transporter may play protective roles in response to drought stress. Flavonoids, LEA proteins and sHSP function as reactive oxygen species scavenger or molecular chaperone. Aquaporin and proline transporters regulate the distribution of water and proline throughout the whole plant. The tolerance ability of R. soongorica may be gained through effective signal transduction and enhanced protection of functional proteins to reestablish cellular homeostasis. DEGs obtained in this study may provide useful insights to help further understand the drought-tolerant mechanism of R. soongorica.

Genome-wide survey and expression profiles of the AP2/ERF family in castor bean (Ricinus communis L.)

BACKGROUND

The AP2/ERF transcription factor, one of the largest gene families in plants, plays a crucial role in the regulation of growth and development, metabolism, and responses to biotic and abiotic stresses. Castor bean (Ricinus communis L., Euphobiaceae) is one of most important non-edible oilseed crops and its seed oil is broadly used for industrial applications. The available genome provides a great chance to identify and characterize the global information on AP2/ERF transcription factors in castor bean, which might provide insights in understanding the molecular basis of the AP2/ERF family in castor bean.

RESULTS

A total of 114 AP2/ERF transcription factors were identified based on the genome in castor bean. According to the number of the AP2/ERF domain, the conserved amino acid residues within AP2/ERF domain, the conserved motifs and gene organization in structure, and phylogenetical analysis, the identified 114 AP2/ERF transcription factors were characterized. Global expression profiles among different tissues using high-throughput sequencing of digital gene expression profiles (DGEs) displayed diverse expression patterns that may provide basic information in understanding the function of the AP2/ERF gene family in castor bean.

CONCLUSIONS

The current study is the first report on identification and characterization of the AP2/ERF transcription factors based on the genome of castor bean in the family Euphobiaceae. Results obtained from this study provide valuable information in understanding the molecular basis of the AP2/ERF family in castor bean.

Sequencing-based gene network analysis provides a core set of gene resource for understanding thermal adaptation in Zhikong scallop Chlamys farreri

Marine organisms are commonly exposed to variable environmental conditions, and many of them are under threat from increased sea temperatures caused by global climate change. Generating transcriptomic resources under different stress conditions are crucial for understanding molecular mechanisms underlying thermal adaptation. In this study, we conducted transcriptome-wide gene expression profiling of the scallop Chlamys farreri challenged by acute and chronic heat stress. Of the 13 953 unique tags, more than 850 were significantly differentially expressed at each time point after acute heat stress, which was more than the number of tags differentially expressed (320-350) under chronic heat stress. To obtain a systemic view of gene expression alterations during thermal stress, a weighted gene coexpression network was constructed. Six modules were identified as acute heat stress-responsive modules. Among them, four modules involved in apoptosis regulation, mRNA binding, mitochondrial envelope formation and oxidation reduction were downregulated. The remaining two modules were upregulated. One was enriched with chaperone and the other with microsatellite sequences, whose coexpression may originate from a transcription factor binding site. These results indicated that C. farreri triggered several cellular processes to acclimate to elevated temperature. No modules responded to chronic heat stress, suggesting that the scallops might have acclimated to elevated temperature within 3 days. This study represents the first sequencing-based gene network analysis in a nonmodel aquatic species and provides valuable gene resources for the study of thermal adaptation, which should assist in the development of heat-tolerant scallop lines for aquaculture.

Analysis of the black-chinned tilapia Sarotherodon melanotheron heudelotii reproducing under a wide range of salinities: from RNA-seq to candidate genes

The black-chinned tilapia Sarotherodon melanotheron heudelotii is an ecologically appealing model as it shows exceptional adaptive capacities, especially with regard to salinity. In spite of this, this species is devoid of genomic resources, which impedes the understanding of such remarkable features. De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. It also facilitates the development of quantitative real-time PCR (qPCR) assays for analysing gene expression under different environmental conditions. Nevertheless, obtaining accurate and reliable qPCR results from such data requires a number of validations prior to interpretation. The transcriptome of S. melanotheron was sequenced to discover transcripts potentially involved in the plasticity of male reproduction in response to salinity variations. A set of 54 candidate and reference genes was selected through a digital gene expression (DGE) approach, and a de novo qPCR assay using these genes was validated for further detailed expression analyses. A user-friendly web interface was created for easy handling of the sequence data. This sequence collection represents a major transcriptomic resource for S. melanotheron and will provide a useful tool for functional genomics and genetics studies.

Differential gene expression analysis between anagen and telogen of Capra hircus skin based on the de novo assembled transcriptome sequence

Capra hircus, an economically important livestock, plays an indispensable role in the world animal fiber industry. In the present study, using Illumina/Solexa high throughput sequencing technology, we sequenced and de novo assembled the goat skin transcriptome corresponding to the anagen and telogen of the hair growth cycle. Approximately 53Mb of transcriptome sequences consisting of 57,040 high quality contigs was obtained. More than 8300 contigs were predicted to contain a full length coding sequence. Approximately 43% of the total contigs were identified as harboring homologs of sequences from other organisms in the public database. Based on the assembled transcript-derived contigs, we identified about 7000 transcripts that were differentially expressed between the anagen and telogen libraries. These differentially expressed genes were mainly enriched in signal transduction mechanisms, extracellular structures and cytoskeleton from the KOG database and in ECM receptor interaction, focal adhesion and gap junction from the KEGG pathway database, indicating the essential roles of these genes may play in cell-to-cell and cell-to-matrix communications during the active hair growth phase. In addition, many signaling pathway associated ligands and/or receptors were also identified as up-regulated genes during the anagen phase compared with the telogen stage, suggesting that enhanced cross-talk among signaling transduction pathways may be required for anagen of the hair cycle. These differentially expressed genes, especially those that were over-represented in each of the functional clusters and biochemical pathways, provide valuable resources and opportunities for characterizing the gene functions associated with hair fiber growth as well as for breeding elite Cashmere goat species.

Transcriptomic analysis of differentially expressed genes during anther development in genetic male sterile and wild type cotton by digital gene-expression profiling

BACKGROUND

Cotton (Gossypium hirsutum) anther development involves a diverse range of gene interactions between sporophytic and gametophytic tissues. However, only a small number of genes are known to be specifically involved in this developmental process and the molecular mechanism of the genetic male sterility (GMS) is still poorly understand. To fully explore the global gene expression during cotton anther development and identify genes related to male sterility, a digital gene expression (DGE) analysis was adopted.

RESULTS

Six DGE libraries were constructed from the cotton anthers of the wild type (WT) and GMS mutant (in the WT background) in three stages of anther development, resulting in 21,503 to 37,352 genes detected in WT and GMS mutant anthers. Compared with the fertile isogenic WT, 9,595 (30% of the expressed genes), 10,407 (25%), and 3,139 (10%) genes were differentially expressed at the meiosis, tetrad, and uninucleate microspore stages of GMS mutant anthers, respectively. Using both DGE experiments and real-time quantitative RT-PCR, the expression of many key genes required for anther development were suppressed in the meiosis stage and the uninucleate microspore stage in anthers of the mutant, but these genes were activated in the tetrad stage of anthers in the mutant. These genes were associated predominantly with hormone synthesis, sucrose and starch metabolism, the pentose phosphate pathway, glycolysis, flavonoid metabolism, and histone protein synthesis. In addition, several genes that participate in DNA methylation, cell wall loosening, programmed cell death, and reactive oxygen species generation/scavenging were activated during the three anther developmental stages in the mutant.

CONCLUSIONS

Compared to the same anther developmental stage of the WT, many key genes involved in various aspects of anther development show a reverse gene expression pattern in the GMS mutant, which indicates that diverse gene regulation pathways are involved in the GMS mutant anther development. These findings provide the first insights into the mechanism that leads to genetic male sterility in cotton and contributes to a better understanding of the regulatory network involved in anther development in cotton.

The Transcriptome of Brassica napus L. Roots under Waterlogging at the Seedling Stage

Although rapeseed (Brassica napus L.) is known to be affected by waterlogging, the genetic basis of waterlogging tolerance by rapeseed is largely unknown. In this study, the transcriptome under 0 h and 12 h of waterlogging was assayed in the roots of ZS9, a tolerant variety, using digital gene expression (DGE). A total of 4432 differentially expressed genes were identified, indicating that the response to waterlogging in rapeseed is complicated. The assignments of the annotated genes based on GO (Gene Ontology) revealed there were more genes induced under waterlogging in “oxidation reduction”, “secondary metabolism”, “transcription regulation”, and “translation regulation”; suggesting these four pathways are enhanced under waterlogging. Analysis of the 200 most highly expressed genes illustrated that 144 under normal conditions were down-regulated by waterlogging, while up to 191 under waterlogging were those induced in response to stress. The expression of genes involved under waterlogging is mediated by multiple levels of transcriptional, post-transcriptional, translational and post-translational regulation, including phosphorylation and protein degradation; in particular, protein degradation might be involved in the negative regulation in response to this stress. Our results provide new insight into the response to waterlogging and will help to identify important candidate genes.

SOLiD-SAGE of endophyte-infected red fescue reveals numerous effects on host transcriptome and an abundance of highly expressed fungal secreted proteins

One of the most important plant-fungal symbiotic relationships is that of cool season grasses with endophytic fungi of the genera Epichloë and Neotyphodium. These associations often confer benefits, such as resistance to herbivores and improved drought tolerance, to the hosts. One benefit that appears to be unique to fine fescue grasses is disease resistance. As a first step towards understanding the basis of the endophyte-mediated disease resistance in Festuca rubra we carried out a SOLiD-SAGE quantitative transcriptome comparison of endophyte-free and Epichloë festucae-infected F. rubra. Over 200 plant genes involved in a wide variety of physiological processes were statistically significantly differentially expressed between the two samples. Many of the endophyte expressed genes were surprisingly abundant, with the most abundant fungal tag representing over 10% of the fungal mapped tags. Many of the abundant fungal tags were for secreted proteins. The second most abundantly expressed fungal gene was for a secreted antifungal protein and is of particular interest regarding the endophyte-mediated disease resistance. Similar genes in Penicillium and Aspergillus spp. have been demonstrated to have antifungal activity. Of the 10 epichloae whole genome sequences available, only one isolate of E. festucae and Neotyphodium gansuense var inebrians have an antifungal protein gene. The uniqueness of this gene in E. festucae from F. rubra, its transcript abundance, and the secreted nature of the protein, all suggest it may be involved in the disease resistance conferred to the host, which is a unique feature of the fine fescue-endophyte symbiosis.

Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions

The identification of transcription factor binding sites, enhancers, and transcriptional target genes often relies on the integration of gene expression profiling and computational cis-regulatory sequence analysis. Methods for the prediction of cis-regulatory elements can take advantage of comparative genomics to increase signal-to-noise levels. However, gene expression data are usually derived from only one species. Here we investigate tissue-specific cross-species gene expression profiling by high-throughput sequencing, combined with cross-species motif discovery. First, we compared different methods for expression level quantification and cross-species integration using Tag-seq data. Using the optimal pipeline, we derived a set of genes with conserved expression during retinal determination across Drosophila melanogaster, Drosophila yakuba, and Drosophila virilis. These genes are enriched for binding sites of eye-related transcription factors including the zinc-finger Glass, a master regulator of photoreceptor differentiation. Validation of predicted Glass targets using RNA-seq in homozygous glass mutants confirms that the majority of our predictions are expressed downstream from Glass. Finally, we tested nine candidate enhancers by in vivo reporter assays and found eight of them to drive GFP in the eye disc, of which seven colocalize with the Glass protein, namely, scrt, chp, dpr10, CG6329, retn, Lim3, and dmrt99B. In conclusion, we show for the first time the combined use of cross-species expression profiling with cross-species motif discovery as a method to define a core developmental program, and we augment the candidate Glass targetome from a single known target gene, lozenge, to at least 62 conserved transcriptional targets.

Specifying and sustaining pigmentation patterns in domestic and wild cats

Color markings among felid species display both a remarkable diversity and a common underlying periodicity. A similar range of patterns in domestic cats suggests a conserved mechanism whose appearance can be altered by selection. We identified the gene responsible for tabby pattern variation in domestic cats as Transmembrane aminopeptidase Q (Taqpep), which encodes a membrane-bound metalloprotease. Analyzing 31 other felid species, we identified Taqpep as the cause of the rare king cheetah phenotype, in which spots coalesce into blotches and stripes. Histologic, genomic expression, and transgenic mouse studies indicate that paracrine expression of Endothelin3 (Edn3) coordinates localized color differences. We propose a two-stage model in which Taqpep helps to establish a periodic pre-pattern during skin development that is later implemented by differential expression of Edn3.

Genome-wide transcription factor gene prediction and their expressional tissue-specificities in maize

Transcription factors (TFs) are important regulators of gene expression. To better understand TF-encoding genes in maize (Zea mays L.), a genome-wide TF prediction was performed using the updated B73 reference genome. A total of 2298 TF genes were identified, which can be classified into 56 families. The largest family, known as the MYB superfamily, comprises 322 MYB and MYB-related TF genes. The expression patterns of 2 014 (87.64%) TF genes were examined using RNA-seq data, which resulted in the identification of a subset of TFs that are specifically expressed in particular tissues (including root, shoot, leaf, ear, tassel and kernel). Similarly, 98 kernel-specific TF genes were further analyzed, and it was observed that 29 of the kernel-specific genes were preferentially expressed in the early kernel developmental stage, while 69 of the genes were expressed in the late kernel developmental stage. Identification of these TFs, particularly the tissue-specific ones, provides important information for the understanding of development and transcriptional regulation of maize.

Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff

By next generation transcriptome sequencing, it is possible to obtain data on both nucleotide sequence variation and gene expression. We have used this approach (RNA-Seq) to investigate the genetic basis for differences in plumage coloration and mating strategies in a non-model bird species, the ruff (Philomachus pugnax). Ruff males show enormous variation in the coloration of ornamental feathers, used for individual recognition. This polymorphism is linked to reproductive strategies, with dark males (Independents) defending territories on leks against other Independents, whereas white morphs (Satellites) co-occupy Independent's courts without agonistic interactions. Previous work found a strong genetic component for mating strategy, but the genes involved were not identified. We present feather transcriptome data of more than 6,000 de-novo sequenced ruff genes (although with limited coverage for many of them). None of the identified genes showed significant expression divergence between males, but many genetic markers showed nucleotide differentiation between different color morphs and mating strategies. These include several feather keratin genes, splicing factors, and the Xg blood-group gene. Many of the genes with significant genetic structure between mating strategies have not yet been annotated and their functions remain to be elucidated. We also conducted in-depth investigations of 28 pre-identified coloration candidate genes. Two of these (EDNRB and TYR) were specifically expressed in black- and rust-colored males, respectively. We have demonstrated the utility of next generation transcriptome sequencing for identifying and genotyping large number of genetic markers in a non-model species without previous genomic resources, and highlight the potential of this approach for addressing the genetic basis of ecologically important variation.

EST and transcriptome analysis of cephalochordate amphioxus--past, present and future

The cephalochordates, commonly known as amphioxus or lancelets, are now considered the most basal chordate group, and the studies of these organisms therefore offer important insights into various levels of evolutionary biology. In the past two decades, the investigation of amphioxus developmental biology has provided key knowledge for understanding the basic patterning mechanisms of chordates. Comparative genome studies of vertebrates and amphioxus have uncovered clear evidence supporting the hypothesis of two-round whole-genome duplication thought to have occurred early in vertebrate evolution and have shed light on the evolution of morphological novelties in the complex vertebrate body plan. Complementary to the amphioxus genome-sequencing project, a large collection of expressed sequence tags (ESTs) has been generated for amphioxus in recent years; this valuable collection represents a rich resource for gene discovery, expression profiling and molecular developmental studies in the amphioxus model. Here, we review previous EST analyses and available cDNA resources in amphioxus and discuss their value for use in evolutionary and developmental studies. We also discuss the potential advantages of applying high-throughput, next-generation sequencing (NGS) technologies to the field of amphioxus research.

Next generation quantitative genetics in plants

Most characteristics in living organisms show continuous variation, which suggests that they are controlled by multiple genes. Quantitative trait loci (QTL) analysis can identify the genes underlying continuous traits by establishing associations between genetic markers and observed phenotypic variation in a segregating population. The new high-throughput sequencing (HTS) technologies greatly facilitate QTL analysis by providing genetic markers at genome-wide resolution in any species without previous knowledge of its genome. In addition HTS serves to quantify molecular phenotypes, which aids to identify the loci responsible for QTLs and to understand the mechanisms underlying diversity. The constant improvements in price, experimental protocols, computational pipelines, and statistical frameworks are making feasible the use of HTS for any research group interested in quantitative genetics. In this review I discuss the application of HTS for molecular marker discovery, population genotyping, and expression profiling in QTL analysis.