51
|
de Boer TE, Roelofs D, Vooijs R, Holmstrup M, Amorim MJB. Population-specific transcriptional differences associated with freeze tolerance in a terrestrial worm. Ecol Evol 2018; 8:3774-3786. [PMID: 29686857 PMCID: PMC5901168 DOI: 10.1002/ece3.3602] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 12/25/2022] Open
Abstract
Enchytraeus albidus is a terrestrial earthworm widespread along the coasts of northern Europe and the Arctic. This species tolerates freezing of body fluids and survives winters in a frozen state. Their acclimatory physiological mechanisms behind freeze tolerance involve increased fluidity of membrane lipids during cold exposure and accumulation of cryoprotectants (glucose) during the freezing process. Gene regulatory processes of these physiological responses have not been studied, partly because no gene expression tools were developed. The main aim of this study was to understand whether the freeze tolerance mechanisms have a transcriptomic basis in E. albidus. For that purpose, first the transcriptome of E. albidus was assembled with RNAseq data. Second, two strains from contrasting thermal environments (Germany and Greenland) were compared by mapping barcoded RNAseq data onto the assembled transcriptome. Both of these strains are freeze tolerant, but Greenland is extremely freeze tolerant. Results showed more plastic responses in the Greenland strain as well as higher constitutive expression of particular stress response genes. These altered transcriptional networks are associated with an adapted homeostasis coping with prolonged freezing conditions in Greenland animals. Previously identified physiological alterations in freeze‐tolerant strains of E. albidus are underpinned at the transcriptome level. These processes involve anion transport in the hemolymph, fatty acid metabolism, metabolism, and transport of cryoprotective sugars as well as protection against oxidative stress. Pathway analysis supported most of these processes, and identified additional differentially expressed pathways such as peroxisome and Toll‐like receptor signaling. We propose that the freeze‐tolerant phenotype is the consequence of genetic adaptation to cold stress and may have driven evolutionary divergence of the two strains.
Collapse
Affiliation(s)
| | - Dick Roelofs
- Department of Ecological Science Faculty of Earth and Life Sciences VU University, Amsterdam Amsterdam The Netherlands
| | - Riet Vooijs
- Department of Ecological Science Faculty of Earth and Life Sciences VU University, Amsterdam Amsterdam The Netherlands
| | | | - Mónica J B Amorim
- Department of Biology and CESAM (Centre for Environmental and Marine Studies) University of Aveiro Aveiro Portugal
| |
Collapse
|
52
|
Transcriptome Analyses of Mosaic (MSC) Mitochondrial Mutants of Cucumber in a Highly Inbred Nuclear Background. G3-GENES GENOMES GENETICS 2018; 8:953-965. [PMID: 29330162 PMCID: PMC5844315 DOI: 10.1534/g3.117.300321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cucumber (Cucumis sativus L.) has a large, paternally transmitted mitochondrial genome. Cucumber plants regenerated from cell cultures occasionally show paternally transmitted mosaic (MSC) phenotypes, characterized by slower growth, chlorotic patterns on the leaves and fruit, lower fertility, and rearrangements in their mitochondrial DNAs (mtDNAs). MSC lines 3, 12, and 16 originated from different cell cultures all established using the highly inbred, wild-type line B. These MSC lines possess different rearrangements and under-represented regions in their mtDNAs. We completed RNA-seq on normalized and non-normalized cDNA libraries from MSC3, MSC12, and MSC16 to study their nuclear gene-expression profiles relative to inbred B. Results from both libraries indicated that gene expression in MSC12 and MSC16 were more similar to each other than MSC3. Forty-one differentially expressed genes (DEGs) were upregulated and one downregulated in the MSC lines relative to B. Gene functional classifications revealed that more than half of these DEGs are associated with stress-response pathways. Consistent with this observation, we detected elevated levels of hydrogen peroxide throughout leaf tissue in all MSC lines compared to wild-type line B. These results demonstrate that independently produced MSC lines with different mitochondrial polymorphisms show unique and shared nuclear responses. This study revealed genes associated with stress response that could become selection targets to develop cucumber cultivars with increased stress tolerance, and further support of cucumber as a model plant to study nuclear-mitochondrial interactions.
Collapse
|
53
|
Mořkovský L, Janoušek V, Reif J, Rídl J, Pačes J, Choleva L, Janko K, Nachman MW, Reifová R. Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility. Mol Ecol 2018; 27:949-958. [PMID: 29319911 DOI: 10.1111/mec.14479] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/15/2017] [Accepted: 12/16/2017] [Indexed: 12/24/2022]
Abstract
Hybrid sterility is a common first step in the evolution of postzygotic reproductive isolation. According to Haldane's Rule, it affects predominantly the heterogametic sex. While the genetic basis of hybrid male sterility in organisms with heterogametic males has been studied for decades, the genetic basis of hybrid female sterility in organisms with heterogametic females has received much less attention. We investigated the genetic basis of reproductive isolation in two closely related avian species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (L. luscinia), that hybridize in a secondary contact zone and produce viable hybrid progeny. In accordance with Haldane's Rule, hybrid females are sterile, while hybrid males are fertile, allowing gene flow to occur between the species. Using transcriptomic data from multiple individuals of both nightingale species, we identified genomic islands of high differentiation (FST ) and of high divergence (Dxy ), and we analysed gene content and patterns of molecular evolution within these islands. Interestingly, we found that these islands were enriched for genes related to female meiosis and metabolism. The islands of high differentiation and divergence were also characterized by higher levels of linkage disequilibrium than the rest of the genome in both species indicating that they might be situated in genomic regions of low recombination. This study provides one of the first insights into genetic basis of hybrid female sterility in organisms with heterogametic females.
Collapse
Affiliation(s)
- Libor Mořkovský
- Department of Zoology, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Václav Janoušek
- Department of Zoology, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Jakub Rídl
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics, The Czech Academy of Sciences, Prague 4, Czech Republic
| | - Jan Pačes
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics, The Czech Academy of Sciences, Prague 4, Czech Republic
| | - Lukáš Choleva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Liběchov, Czech Republic
| | - Michael W Nachman
- Museum of Comparative Zoology and Integrative Biology, University of California, Berkeley, CA, USA
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Prague 2, Czech Republic
| |
Collapse
|
54
|
Zhang SF, Zhang Z, Kong XB, Wang HB, Liu F. Dynamic Changes in Chemosensory Gene Expression during the Dendrolimus punctatus Mating Process. Front Physiol 2018; 8:1127. [PMID: 29375398 PMCID: PMC5767605 DOI: 10.3389/fphys.2017.01127] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/20/2017] [Indexed: 12/13/2022] Open
Abstract
The insect chemosensory system is pivotal for interactions with their environments, and moths have especially sensitive olfaction. Exploration of the connection between the plasticity of olfactory-guided and molecular level pathways in insects is important for understanding the olfactory recognition mechanisms of insects. The pine caterpillar moth, Dendrolimus punctatus Walker, is a dominant conifer defoliator in China, and mating is the priority for adults of this species, during which sex pheromone recognition and oviposition site location are the main activities; these activities are all closely related to chemosensory genes. Thus, we aimed to identify chemosensory related genes and monitor the spectrum of their dynamic expression during the entire mating process in D. punctatus. In this study, we generated transcriptome data from male and female adult D. punctatus specimens at four mating stages: eclosion, calling, copulation, and post-coitum. These data were analyzed using bioinformatics tools to identify the major olfactory-related gene families and determine their expression patterns during mating. Levels of odorant binding proteins (OBPs), chemosensory proteins (CSPs), and odorant receptors (ORs) were closely correlated with mating behavior. Comparison with ORs from other Dendrolimus and Lepidoptera species led to the discovery of a group of ORs specific to Dendrolimus. Furthermore, we identified several genes encoding OBPs and ORs that were upregulated after mating in females; these genes may mediate the location of host plants for oviposition via plant-emitted volatiles. This work will facilitate functional research into D. punctatus chemosensory genes, provide information about the relationship between chemosensory genes and important physiological activities, and promote research into the mechanisms underlying insect olfactory recognition.
Collapse
Affiliation(s)
| | - Zhen Zhang
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, State Forestry Administration, Beijing, China
| | | | | | | |
Collapse
|
55
|
Hawkins AK, Garza ER, Dietz VA, Hernandez OJ, Hawkins WD, Burrell AM, Pepper AE. Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant. Genome Biol Evol 2017; 9:3478-3494. [PMID: 29220486 PMCID: PMC5751042 DOI: 10.1093/gbe/evx259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2017] [Indexed: 12/26/2022] Open
Abstract
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.
Collapse
|
56
|
Fantastic Beasts and How To Sequence Them: Ecological Genomics for Obscure Model Organisms. Trends Genet 2017; 34:121-132. [PMID: 29198378 DOI: 10.1016/j.tig.2017.11.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/30/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023]
Abstract
The application of genomic approaches to 'obscure model organisms' (OMOs), meaning species with no prior genomic resources, enables increasingly sophisticated studies of the genomic basis of evolution, acclimatization, and adaptation in real ecological contexts. I consider here ecological questions that can be addressed using OMOs, and indicate optimal sequencing and data-handling solutions for each case. With this I hope to promote the diversity of OMO-based projects that would capitalize on the peculiarities of the natural history of OMOs and could feasibly be completed within the scope of a single PhD thesis.
Collapse
|
57
|
Dupuis JR, Mcdonald CM, Acorn JH, Sperling FAH. Genomics-informed species delimitation to support morphological identification of anglewing butterflies (Lepidoptera: Nymphalidae: Polygonia). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Julian R Dupuis
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, USA
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - Christianne M Mcdonald
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - John H Acorn
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
58
|
A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection. mSphere 2017; 2:mSphere00307-17. [PMID: 28932815 PMCID: PMC5597969 DOI: 10.1128/msphere.00307-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/23/2017] [Indexed: 11/20/2022] Open
Abstract
Recent high-throughput sequencing (HTS) investigations have resulted in unexpected discoveries of known and novel viruses in a variety of sample types, including research materials, clinical materials, and biological products. Therefore, HTS can be a powerful tool for supplementing current methods for demonstrating the absence of adventitious or unwanted viruses in biological products, particularly when using a new cell line. However, HTS is a complex technology with different platforms, which needs standardization for evaluation of biologics. This collaborative study was undertaken to investigate detection of different virus types using two different HTS platforms. The results of the independently performed studies demonstrated a similar sensitivity of virus detection, regardless of the different sample preparation and processing procedures and bioinformatic analyses done in the three laboratories. Comparable HTS detection of different virus types supports future development of reference virus materials for standardization and validation of different HTS platforms. The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses makes it a powerful tool for broad microbial investigations, such as evaluation of novel cell substrates that may be used for the development of new biological products. However, like any new assay, regulatory applications of HTS need method standardization. Therefore, our three laboratories initiated a study to evaluate performance of HTS for potential detection of viral adventitious agents by spiking model viruses in different cellular matrices to mimic putative materials for manufacturing of biologics. Four model viruses were selected based upon different physical and biochemical properties and commercial availability: human respiratory syncytial virus (RSV), Epstein-Barr virus (EBV), feline leukemia virus (FeLV), and human reovirus (REO). Additionally, porcine circovirus (PCV) was tested by one laboratory. Independent samples were prepared for HTS by spiking intact viruses or extracted viral nucleic acids, singly or mixed, into different HeLa cell matrices (resuspended whole cells, cell lysate, or total cellular RNA). Data were obtained using different sequencing platforms (Roche 454, Illumina HiSeq1500 or HiSeq2500). Bioinformatic analyses were performed independently by each laboratory using available tools, pipelines, and databases. The results showed that comparable virus detection was obtained in the three laboratories regardless of sample processing, library preparation, sequencing platform, and bioinformatic analysis: between 0.1 and 3 viral genome copies per cell were detected for all of the model viruses used. This study highlights the potential for using HTS for sensitive detection of adventitious viruses in complex biological samples containing cellular background. IMPORTANCE Recent high-throughput sequencing (HTS) investigations have resulted in unexpected discoveries of known and novel viruses in a variety of sample types, including research materials, clinical materials, and biological products. Therefore, HTS can be a powerful tool for supplementing current methods for demonstrating the absence of adventitious or unwanted viruses in biological products, particularly when using a new cell line. However, HTS is a complex technology with different platforms, which needs standardization for evaluation of biologics. This collaborative study was undertaken to investigate detection of different virus types using two different HTS platforms. The results of the independently performed studies demonstrated a similar sensitivity of virus detection, regardless of the different sample preparation and processing procedures and bioinformatic analyses done in the three laboratories. Comparable HTS detection of different virus types supports future development of reference virus materials for standardization and validation of different HTS platforms.
Collapse
|
59
|
Zhang SF, Liu HH, Kong XB, Wang HB, Liu F, Zhang Z. Identification and Expression Profiling of Chemosensory Genes in Dendrolimus punctatus Walker. Front Physiol 2017; 8:471. [PMID: 28736530 PMCID: PMC5500615 DOI: 10.3389/fphys.2017.00471] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 06/21/2017] [Indexed: 11/13/2022] Open
Abstract
Dendrolimus punctatus Walker is a serious pest affecting conifers in southern China. As extensive pesticide spraying is currently required to control D. punctatus, new control strategies are urgently needed. Chemosensory genes represent potential molecular targets for development of alternative pest control strategies, and the expression characteristics of these genes provide an indication of their function. To date, little information is available regarding chemosensory genes in D. punctatus or their expression profiles at different development stages and in various tissues. Here, we assembled and analyzed the transcriptomes of D. punctatus collected at different developmental stages and in a range of organs, using next-generation sequencing. A total of 171 putative chemosensory genes were identified, encoding 53 odorant binding proteins, 26 chemosensory proteins, 60 odorant receptors (OR), 12 gustatory receptors (GR), 18 ionotropic receptors (IR), and 2 sensory neuron membrane proteins (SNMPs). Expression analysis indicated that the antennae possess the largest number of highly expressed olfactory genes and that olfactory gene expression patterns in the eggs, larvae, and head were similar to one another, with each having moderate numbers of highly expressed olfactory genes. Fat body, ovary, midgut, and testis tissues also had similar olfactory gene expression patterns, including few highly expressed olfactory genes. Of particular note, we identified only two pheromone binding proteins and no pheromone receptors in D. punctatus, similar to our previous findings in Dendrolimus houi and Dendrolimus kikuchii, suggesting that insects of the Dendrolimus genus have different pheromone recognition characteristics to other Lepidopteran insects. Overall, this extensive expression profile analysis provides a clear map of D. punctatus chemosensory genes, and will facilitate functional studies and the development of new pest control methods in the future.
Collapse
Affiliation(s)
- Su-Fang Zhang
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, State Forestry AdministrationBeijing, China
| | - Hui-Hui Liu
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, State Forestry AdministrationBeijing, China
| | - Xiang-Bo Kong
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, State Forestry AdministrationBeijing, China
| | - Hong-Bin Wang
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, State Forestry AdministrationBeijing, China
| | - Fu Liu
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, State Forestry AdministrationBeijing, China
| | - Zhen Zhang
- Key Laboratory of Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, State Forestry AdministrationBeijing, China
| |
Collapse
|
60
|
Dupuis J, Brunet B, Bird H, Lumley L, Fagua G, Boyle B, Levesque R, Cusson M, Powell J, Sperling F. Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex. Mol Phylogenet Evol 2017; 111:158-168. [DOI: 10.1016/j.ympev.2017.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/27/2017] [Accepted: 04/03/2017] [Indexed: 01/02/2023]
|
61
|
An innovative strategy to clone positive modifier genes of defects caused by mtDNA mutations: MRPS18C as suppressor gene of m.3946G>A mutation in MT-ND1 gene. Hum Genet 2017; 136:885-896. [PMID: 28526948 DOI: 10.1007/s00439-017-1812-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/13/2017] [Indexed: 12/31/2022]
Abstract
We have developed a new functional complementation approach to clone modifier genes which overexpression is able to suppress the biochemical defects caused by mtDNA mutations (suppressor genes). This strategy consists in transferring human genes into respiratory chain-deficient fibroblasts, followed by a metabolic selection in a highly selective medium. We used a normalized expression cDNA library in an episomal vector (pREP4) to transfect the fibroblasts, and a medium with glutamine and devoid of any carbohydrate source to select metabolically. Growing the patient's fibroblasts in this selective medium, the deficient cells rapidly disappear unless they are rescued by the cDNA of a suppressor gene. The use of an episomal vector allows us to carry out several rounds of transfection/selection (cyclical phenotypic rescue) to enrich the rescue with true clones of suppressor genes. Using fibroblasts from a patient with epileptic encephalopathy with the m.3946G>A (p.E214K) mutation in the MT-ND1 gene, several candidate genes were identified and one of them was characterized functionally. Thus, overexpression of MRPS18C gene (that encode for bS18m protein) suppressed the molecular defects produced by this mtDNA mutation, recovering the complex I activity and reducing the ROS produced by this complex to normal levels. We suggest that modulation of bS18m expression may be an effective therapeutic strategy for the patients with this mutation.
Collapse
|
62
|
Automated multiplex genome-scale engineering in yeast. Nat Commun 2017; 8:15187. [PMID: 28469255 PMCID: PMC5418614 DOI: 10.1038/ncomms15187] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 03/08/2017] [Indexed: 12/23/2022] Open
Abstract
Genome-scale engineering is indispensable in understanding and engineering microorganisms, but the current tools are mainly limited to bacterial systems. Here we report an automated platform for multiplex genome-scale engineering in Saccharomyces cerevisiae, an important eukaryotic model and widely used microbial cell factory. Standardized genetic parts encoding overexpression and knockdown mutations of >90% yeast genes are created in a single step from a full-length cDNA library. With the aid of CRISPR-Cas, these genetic parts are iteratively integrated into the repetitive genomic sequences in a modular manner using robotic automation. This system allows functional mapping and multiplex optimization on a genome scale for diverse phenotypes including cellulase expression, isobutanol production, glycerol utilization and acetic acid tolerance, and may greatly accelerate future genome-scale engineering endeavours in yeast.
Collapse
|
63
|
Mubemba B, Thompson P, Odendaal L, Coetzee P, Venter E. Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis. J Virol Methods 2017; 243:10-14. [DOI: 10.1016/j.jviromet.2017.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 10/20/2022]
|
64
|
Saaristo M, Wong BBM, Mincarelli L, Craig A, Johnstone CP, Allinson M, Lindström K, Craft JA. Characterisation of the transcriptome of male and female wild-type guppy brains with RNA-Seq and consequences of exposure to the pharmaceutical pollutant, 17α-ethinyl estradiol. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 186:28-39. [PMID: 28246045 DOI: 10.1016/j.aquatox.2017.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 02/09/2017] [Accepted: 02/14/2017] [Indexed: 06/06/2023]
Abstract
Waterways are increasingly being contaminated by chemical compounds that can disrupt the endocrinology of organisms. One such compound is 17α-ethinyl estradiol (EE2), a synthetic estrogen used in the contraceptive pill. Despite considerable research interest in the effects of EE2 on reproduction and gene expression, surprisingly, only a few studies have capitalised on technologies, such as next-generation sequencing (NGS), to uncover the molecular pathways related to EE2 exposure. Accordingly, using high-throughput sequencing technologies, the aim of our study was to explore the effects of EE2 on brain transcriptome in wild-type male and female guppy (Poecilia reticulata). We conducted two sets of experiments, where fish were exposed to EE2 (measured concentrations: 8ng/L and 38ng/L) in a flow-through system for 21days. The effects on the brain transcriptome on both males and females were assessed using Illumina sequencing (MiSeq and HiSeq) platform followed by bioinformatics analysis (edgeR, DESeq2). Here, we report that exposure to EE2 caused both up- and downregulation of specific transcript abundances, and affected transcript abundance in a sex-specific manner. Specifically, we found 773 transcripts, of which 60 were male-specific, 61 female-specific and 285 treatment-specific. EE2 affected expression of 165 transcripts in males, with 88 downregulated and 77 upregulated, while in females, 120 transcripts were affected with 62 downregulated and 58 upregulated. Finally, RT-qPCR validation demonstrated that expression of transcripts related to transposable elements, neuroserpin and heat shock protein were significantly affected by EE2-exposure. Our study is the first to report brain transcriptome libraries for guppies exposed to EE2. Not only does our study provide a valuable resource, it offers insights into the mechanisms underlying the feminizing effects on the brains of organisms exposed to environmentally realistic concentrations of EE2.
Collapse
Affiliation(s)
- Minna Saaristo
- School of Biological Sciences, Monash University, 3800 Victoria, Australia; Environmental and Marine Biology, Åbo Akademi University, 20500 Turku, Finland.
| | - Bob B M Wong
- School of Biological Sciences, Monash University, 3800 Victoria, Australia
| | - Laura Mincarelli
- Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, UK
| | - Allison Craig
- Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, UK
| | | | - Mayumi Allinson
- Victorian Centre for Aquatic Pollution Identification and Management (CAPIM), School of Chemistry, 3010 Victoria, Australia
| | - Kai Lindström
- Environmental and Marine Biology, Åbo Akademi University, 20500 Turku, Finland
| | - John A Craft
- Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, UK
| |
Collapse
|
65
|
Translation complex profile sequencing to study the in vivo dynamics of mRNA–ribosome interactions during translation initiation, elongation and termination. Nat Protoc 2017; 12:697-731. [DOI: 10.1038/nprot.2016.189] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
66
|
De novo assembly of the sea trout (Salmo trutta m. trutta) skin transcriptome to identify putative genes involved in the immune response and epidermal mucus secretion. PLoS One 2017; 12:e0172282. [PMID: 28212382 PMCID: PMC5315281 DOI: 10.1371/journal.pone.0172282] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/02/2017] [Indexed: 01/02/2023] Open
Abstract
In fish, the skin is a multifunctional organ and the first barrier against pathogens. Salmonids differ in their susceptibility to microorganisms due to varied skin morphology and gene expression patterns. The brown trout is a salmonid species with important commercial and ecological value in Europe. However, there is a lack of knowledge regarding the genes involved in the immune response and mucus secretion in the skin of this fish. Thus, we characterized the skin transcriptome of anadromous brown trout using next-generation sequencing (NGS). A total of 1,348,306 filtered reads were obtained and assembled into 75,970 contigs. Of these contigs 48.57% were identified using BLAST tool searches against four public databases. KEGG pathway and Gene Ontology analyses revealed that 13.40% and 34.57% of the annotated transcripts, respectively, represent a variety of biological processes and functions. Among the identified KEGG Orthology categories, the best represented were signal transduction (23.28%) and immune system (8.82%), with a variety of genes involved in immune pathways, implying the differentiation of immune responses in the trout skin. We also identified and transcriptionally characterized 8 types of mucin proteins–the main structural components of the mucosal layer. Moreover, 140 genes involved in mucin synthesis were identified, and 1,119 potential simple sequence repeats (SSRs) were detected in 3,134 transcripts.
Collapse
|
67
|
Effective detection of variation in single-cell transcriptomes using MATQ-seq. Nat Methods 2017; 14:267-270. [PMID: 28092691 DOI: 10.1038/nmeth.4145] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 12/06/2016] [Indexed: 12/26/2022]
Abstract
The quantification of transcriptional variation in single cells, particularly within the same cell population, is currently limited by the low sensitivity and high technical noise of single-cell RNA-seq assays. We report multiple annealing and dC-tailing-based quantitative single-cell RNA-seq (MATQ-seq), a highly sensitive and quantitative method for single-cell sequencing of total RNA. By systematically determining technical noise, we show that MATQ-seq captures genuine biological variation between whole transcriptomes of single cells.
Collapse
|
68
|
Al-Faifi SA, Migdadi HM, Algamdi SS, Khan MA, Al-Obeed RS, Ammar MH, Jakse J. Analysis of Expressed Sequence Tags (EST) in Date Palm. Methods Mol Biol 2017; 1638:283-313. [PMID: 28755231 DOI: 10.1007/978-1-4939-7159-6_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Expressed sequence tags (EST) were generated from a normalized cDNA library of the date palm Sukkari cv. to understand the high-quality and better field performance of this well-known commercial cultivar. A total of 6943 high-quality ESTs were generated, out of them 6671 are submitted to the GenBank dbEST (LIBEST_028537). The generated ESTs were assembled into 6362 unigenes, consisting of 494 (14.4%) contigs and 5868 (84.53%) singletons. The functional annotation shows that the majority of the ESTs are associated with binding (44%), catalytic (40%), transporter (5%), and structural molecular (5%) activities. The blastx results show that 73% of unigenes are significantly similar to known plant genes and 27% are novel. The latter could be of particular interest in date palm genetic studies. Further analysis shows that some ESTs are categorized as stress/defense- and fruit development-related genes. These newly generated ESTs could significantly enhance date palm EST databases in the public domain and are available to scientists and researchers across the globe. This knowledge will facilitate the discovery of candidate genes that govern important developmental and agronomical traits in date palm. It will provide important resources for developing genetic tools, comparative genomics, and genome evolution among date palm cultivars.
Collapse
Affiliation(s)
- Sulieman A Al-Faifi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Hussein M Migdadi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia.
| | - Salem S Algamdi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Mohammad Altaf Khan
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Rashid S Al-Obeed
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Megahed H Ammar
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Jerenj Jakse
- Biotechnical Faculty, Agronomy Department, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
69
|
Pardo BG, Álvarez-Dios JA, Cao A, Ramilo A, Gómez-Tato A, Planas JV, Villalba A, Martínez P. Construction of an Ostrea edulis database from genomic and expressed sequence tags (ESTs) obtained from Bonamia ostreae infected haemocytes: Development of an immune-enriched oligo-microarray. FISH & SHELLFISH IMMUNOLOGY 2016; 59:331-344. [PMID: 27815201 DOI: 10.1016/j.fsi.2016.10.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/17/2016] [Accepted: 10/30/2016] [Indexed: 06/06/2023]
Abstract
The flat oyster, Ostrea edulis, is one of the main farmed oysters, not only in Europe but also in the United States and Canada. Bonamiosis due to the parasite Bonamia ostreae has been associated with high mortality episodes in this species. This parasite is an intracellular protozoan that infects haemocytes, the main cells involved in oyster defence. Due to the economical and ecological importance of flat oyster, genomic data are badly needed for genetic improvement of the species, but they are still very scarce. The objective of this study is to develop a sequence database, OedulisDB, with new genomic and transcriptomic resources, providing new data and convenient tools to improve our knowledge of the oyster's immune mechanisms. Transcriptomic and genomic sequences were obtained using 454 pyrosequencing and compiled into an O. edulis database, OedulisDB, consisting of two sets of 10,318 and 7159 unique sequences that represent the oyster's genome (WG) and de novo haemocyte transcriptome (HT), respectively. The flat oyster transcriptome was obtained from two strains (naïve and tolerant) challenged with B. ostreae, and from their corresponding non-challenged controls. Approximately 78.5% of 5619 HT unique sequences were successfully annotated by Blast search using public databases. A total of 984 sequences were identified as being related to immune response and several key immune genes were identified for the first time in flat oyster. Additionally, transcriptome information was used to design and validate the first oligo-microarray in flat oyster enriched with immune sequences from haemocytes. Our transcriptomic and genomic sequencing and subsequent annotation have largely increased the scarce resources available for this economically important species and have enabled us to develop an OedulisDB database and accompanying tools for gene expression analysis. This study represents the first attempt to characterize in depth the O. edulis haemocyte transcriptome in response to B. ostreae through massively sequencing and has aided to improve our knowledge of the immune mechanisms of flat oyster. The validated oligo-microarray and the establishment of a reference transcriptome will be useful for large-scale gene expression studies in this species.
Collapse
Affiliation(s)
- Belén G Pardo
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - José Antonio Álvarez-Dios
- Departamento de Matemática Aplicada, Facultad de Matemáticas, Universidade de Santiago de Compostela, 15781 Santiago de Compostela, Spain.
| | - Asunción Cao
- Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain.
| | - Andrea Ramilo
- Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain.
| | - Antonio Gómez-Tato
- Departamento de Matemáticas, Facultad de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Josep V Planas
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08007, Barcelona, Spain.
| | - Antonio Villalba
- Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain; Departamento de Ciencias de la Vida, Universidad de Alcalá, 28871 Alcalá de Henares, Spain.
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| |
Collapse
|
70
|
Penselin D, Münsterkötter M, Kirsten S, Felder M, Taudien S, Platzer M, Ashelford K, Paskiewicz KH, Harrison RJ, Hughes DJ, Wolf T, Shelest E, Graap J, Hoffmann J, Wenzel C, Wöltje N, King KM, Fitt BDL, Güldener U, Avrova A, Knogge W. Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses. BMC Genomics 2016; 17:953. [PMID: 27875982 PMCID: PMC5118889 DOI: 10.1186/s12864-016-3299-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/15/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young age of the five species currently known, this genus appears to be well-suited to address the question at the molecular level of how pathogenic fungi adapt to their hosts. RESULTS The genomes of the different Rhynchosporium species were sequenced, assembled and annotated using ab initio gene predictors trained on several fungal genomes as well as on Rhynchosporium expressed sequence tags. Structures of the rDNA regions and genome-wide single nucleotide polymorphisms provided a hypothesis for intra-genus evolution. Homology screening detected core meiotic genes along with most genes crucial for sexual recombination in ascomycete fungi. In addition, a large number of cell wall-degrading enzymes that is characteristic for hemibiotrophic and necrotrophic fungi infecting monocotyledonous hosts were found. Furthermore, the Rhynchosporium genomes carry a repertoire of genes coding for polyketide synthases and non-ribosomal peptide synthetases. Several of these genes are missing from the genome of the closest sequenced relative, the poplar pathogen Marssonina brunnea, and are possibly involved in adaptation to the grass hosts. Most importantly, six species-specific genes coding for protein effectors were identified in R. commune. Their deletion yielded mutants that grew more vigorously in planta than the wild type. CONCLUSION Both cryptic sexuality and secondary metabolites may have contributed to host adaptation. Most importantly, however, the growth-retarding activity of the species-specific effectors suggests that host adaptation of R. commune aims at extending the biotrophic stage at the expense of the necrotrophic stage of pathogenesis. Like other apoplastic fungi Rhynchosporium colonizes the intercellular matrix of host leaves relatively slowly without causing symptoms, reminiscent of the development of endophytic fungi. Rhynchosporium may therefore become an object for studying the mutualism-parasitism transition.
Collapse
Affiliation(s)
- Daniel Penselin
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kirsten
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Marius Felder
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Stefan Taudien
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Matthias Platzer
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Kevin Ashelford
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | | | | | - David J. Hughes
- Applied Bioinformatics, Rothamsted Research, Harpenden, Hertfordshire UK
| | - Thomas Wolf
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Ekaterina Shelest
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Jenny Graap
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Jan Hoffmann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Claudia Wenzel
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany ,Present address: Food Quality and Nutrition, Agroscope, Bern, Switzerland
| | - Nadine Wöltje
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Kevin M. King
- Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire UK
| | - Bruce D. L. Fitt
- Biological and Environmental Sciences, University of Hertfordshire, Hatfield, Hertfordshire UK
| | - Ulrich Güldener
- Department of Genome-Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
| | - Anna Avrova
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Wolfgang Knogge
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| |
Collapse
|
71
|
Song H, Zhao X, Hu W, Wang X, Shen T, Yang L. Comparative Transcriptional Analysis of Loquat Fruit Identifies Major Signal Networks Involved in Fruit Development and Ripening Process. Int J Mol Sci 2016; 17:ijms17111837. [PMID: 27827928 PMCID: PMC5133838 DOI: 10.3390/ijms17111837] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/24/2016] [Accepted: 10/26/2016] [Indexed: 11/28/2022] Open
Abstract
Loquat (Eriobotrya japonica Lindl.) is an important non-climacteric fruit and rich in essential nutrients such as minerals and carotenoids. During fruit development and ripening, thousands of the differentially expressed genes (DEGs) from various metabolic pathways cause a series of physiological and biochemical changes. To better understand the underlying mechanism of fruit development, the Solexa/Illumina RNA-seq high-throughput sequencing was used to evaluate the global changes of gene transcription levels. More than 51,610,234 high quality reads from ten runs of fruit development were sequenced and assembled into 48,838 unigenes. Among 3256 DEGs, 2304 unigenes could be annotated to the Gene Ontology database. These DEGs were distributed into 119 pathways described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A large number of DEGs were involved in carbohydrate metabolism, hormone signaling, and cell-wall degradation. The real-time reverse transcription (qRT)-PCR analyses revealed that several genes related to cell expansion, auxin signaling and ethylene response were differentially expressed during fruit development. Other members of transcription factor families were also identified. There were 952 DEGs considered as novel genes with no annotation in any databases. These unigenes will serve as an invaluable genetic resource for loquat molecular breeding and postharvest storage.
Collapse
Affiliation(s)
- Huwei Song
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, College of Life Science, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, College of Life Science, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
| | - Weicheng Hu
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, College of Life Science, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
| | - Xinfeng Wang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, College of Life Science, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
| | - Ting Shen
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, College of Life Science, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
| | - Liming Yang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, College of Life Science, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an 223300, Jiangsu, China.
| |
Collapse
|
72
|
Merrill KR, Coleman CE, Meyer SE, Leger EA, Collins KA. Development of single-nucleotide polymorphism markers for Bromus tectorum (Poaceae) from a partially sequenced transcriptome. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600068. [PMID: 27843723 PMCID: PMC5104524 DOI: 10.3732/apps.1600068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/17/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Bromus tectorum (Poaceae) is an annual grass species that is invasive in many areas of the world but most especially in the U.S. Intermountain West. Single-nucleotide polymorphism (SNP) markers were developed for use in investigating the geospatial and ecological diversity of B. tectorum in the Intermountain West to better understand the mechanisms behind its successful invasion. METHODS AND RESULTS Normalized cDNA libraries from six diverse B. tectorum individuals were pooled and sequenced using 454 sequencing. Ninety-five SNP assays were developed for use on 96.96 arrays with the Fluidigm EP1 genotyping platform. Verification of the 95 SNPs by genotyping 251 individuals from 12 populations is reported, along with amplification data from four related Bromus species. CONCLUSIONS These SNP markers are polymorphic across populations of B. tectorum, are optimized for high-throughput applications, and may be applicable to other, related Bromus species.
Collapse
Affiliation(s)
- Keith R. Merrill
- Shrub Sciences Laboratory, United States Forest Service, Rocky Mountain Research Station, 735 North 500 East, Provo, Utah 84606 USA
- Department of Plant and Wildlife Sciences, 4105 Life Sciences Building, Brigham Young University, Provo, Utah 84602 USA
| | - Craig E. Coleman
- Department of Plant and Wildlife Sciences, 4105 Life Sciences Building, Brigham Young University, Provo, Utah 84602 USA
| | - Susan E. Meyer
- Shrub Sciences Laboratory, United States Forest Service, Rocky Mountain Research Station, 735 North 500 East, Provo, Utah 84606 USA
| | - Elizabeth A. Leger
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, 1664 N. Virginia Street, MS 186, Reno, Nevada 89557 USA
| | - Katherine A. Collins
- Department of Plant and Wildlife Sciences, 4105 Life Sciences Building, Brigham Young University, Provo, Utah 84602 USA
| |
Collapse
|
73
|
Bostick M, Bolduc N, Lehman A, Farmer A. Strand‐Specific Transcriptome Sequencing Using SMART Technology. ACTA ACUST UNITED AC 2016; 116:4.27.1-4.27.18. [DOI: 10.1002/cpmb.22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Magnolia Bostick
- Takara Bio USA, Inc. (formerly Clontech Laboratories, Inc.) Mountain View California
| | - Nathalie Bolduc
- Takara Bio USA, Inc. (formerly Clontech Laboratories, Inc.) Mountain View California
| | - Alisa Lehman
- Takara Bio USA, Inc. (formerly Clontech Laboratories, Inc.) Mountain View California
| | - Andrew Farmer
- Takara Bio USA, Inc. (formerly Clontech Laboratories, Inc.) Mountain View California
| |
Collapse
|
74
|
Calduch-Giner JA, Sitjà-Bobadilla A, Pérez-Sánchez J. Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax). Front Physiol 2016; 7:359. [PMID: 27610085 PMCID: PMC4997091 DOI: 10.3389/fphys.2016.00359] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/05/2016] [Indexed: 01/23/2023] Open
Abstract
High-quality sequencing reads from the intestine of European sea bass were assembled, annotated by similarity against protein reference databases and combined with nucleotide sequences from public and private databases. After redundancy filtering, 24,906 non-redundant annotated sequences encoding 15,367 different gene descriptions were obtained. These annotated sequences were used to design a custom, high-density oligo-microarray (8 × 15 K) for the transcriptomic profiling of anterior (AI), middle (MI), and posterior (PI) intestinal segments. Similar molecular signatures were found for AI and MI segments, which were combined in a single group (AI-MI) whereas the PI outstood separately, with more than 1900 differentially expressed genes with a fold-change cutoff of 2. Functional analysis revealed that molecular and cellular functions related to feed digestion and nutrient absorption and transport were over-represented in AI-MI segments. By contrast, the initiation and establishment of immune defense mechanisms became especially relevant in PI, although the microarray expression profiling validated by qPCR indicated that these functional changes are gradual from anterior to posterior intestinal segments. This functional divergence occurred in association with spatial transcriptional changes in nutrient transporters and the mucosal chemosensing system via G protein-coupled receptors. These findings contribute to identify key indicators of gut functions and to compare different fish feeding strategies and immune defense mechanisms acquired along the evolution of teleosts.
Collapse
Affiliation(s)
- Josep A Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Biology, Culture and Pathology of Marine Species, Institute of Aquaculture Torre de la Sal (IATS-CSIC) Castellón, Spain
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Biology, Culture and Pathology of Marine Species, Institute of Aquaculture Torre de la Sal (IATS-CSIC) Castellón, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Biology, Culture and Pathology of Marine Species, Institute of Aquaculture Torre de la Sal (IATS-CSIC) Castellón, Spain
| |
Collapse
|
75
|
Oikonomopoulos S, Wang YC, Djambazian H, Badescu D, Ragoussis J. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations. Sci Rep 2016; 6:31602. [PMID: 27554526 PMCID: PMC4995519 DOI: 10.1038/srep31602] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 07/21/2016] [Indexed: 12/21/2022] Open
Abstract
To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA libraries were generated using a template switching protocol to facilitate the direct comparison between different sequencing platforms. The MinION performance was assessed for its ability to sequence the cDNAs directly with good accuracy in terms of abundance and full length. The abundance of the ERCC cDNA molecules sequenced by MinION agreed with their expected concentration. No length or GC content bias was observed. The majority of cDNAs were sequenced as full length. Additionally, a complex cDNA population derived from a human HEK-293 cell line was sequenced on an Illumina HiSeq 2500, PacBio RS II and ONT MinION platforms. We observed that there was a good agreement in the measured cDNA abundance between PacBio RS II and ONT MinION (rpearson = 0.82, isoforms with length more than 700bp) and between Illumina HiSeq 2500 and ONT MinION (rpearson = 0.75). This indicates that the ONT MinION can sequence quantitatively both long and short full length cDNA molecules.
Collapse
Affiliation(s)
- Spyros Oikonomopoulos
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, 740 Dr. Penfield Avenue, McGill University, Montréal, Québec, Canada
| | - Yu Chang Wang
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, 740 Dr. Penfield Avenue, McGill University, Montréal, Québec, Canada
| | - Haig Djambazian
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, 740 Dr. Penfield Avenue, McGill University, Montréal, Québec, Canada
| | - Dunarel Badescu
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, 740 Dr. Penfield Avenue, McGill University, Montréal, Québec, Canada
| | - Jiannis Ragoussis
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, 740 Dr. Penfield Avenue, McGill University, Montréal, Québec, Canada
- Department of Bioengineering, McGill University, Montréal, Québec, Canada
- Center of Innovation in Personalized Medicine, Cancer and Mutagen Unit, King Fahd Center for Medical Research, Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
76
|
Dupuis JR, Sperling FAH. Hybrid dynamics in a species group of swallowtail butterflies. J Evol Biol 2016; 29:1932-1951. [DOI: 10.1111/jeb.12931] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 04/22/2016] [Accepted: 06/27/2016] [Indexed: 01/15/2023]
Affiliation(s)
- J. R. Dupuis
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
| | - F. A. H. Sperling
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
| |
Collapse
|
77
|
Fang N, Akinci‐Tolun R. Depletion of Ribosomal RNA Sequences from Single‐Cell RNA‐Sequencing Library. ACTA ACUST UNITED AC 2016; 115:7.27.1-7.27.20. [DOI: 10.1002/cpmb.11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
78
|
Leclerc M, Kresdorn N, Horres R. Asterias rubens: Evidence of NF-kappa B genes. Meta Gene 2016; 8:30-2. [PMID: 27014588 PMCID: PMC4792854 DOI: 10.1016/j.mgene.2015.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/01/2015] [Accepted: 12/13/2015] [Indexed: 11/25/2022] Open
Abstract
In the present paper we show a survey of the Asterias rubens sea star genome for genes associated with NF-kappa-B proteins implied in the immune response. The NF-kappa B gene, into 2 subunits, was found in this invertebrate.
Collapse
|
79
|
Pyrosequencing the Midgut Transcriptome of the Banana Weevil Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) Reveals Multiple Protease-Like Transcripts. PLoS One 2016; 11:e0151001. [PMID: 26949943 PMCID: PMC4780788 DOI: 10.1371/journal.pone.0151001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/21/2016] [Indexed: 11/25/2022] Open
Abstract
The banana weevil Cosmopolites sordidus is an important and serious insect pest in most banana and plantain-growing areas of the world. In spite of the economic importance of this insect pest very little genomic and transcriptomic information exists for this species. In the present study, we characterized the midgut transcriptome of C. sordidus using massive 454-pyrosequencing. We generated over 590,000 sequencing reads that assembled into 30,840 contigs with more than 400 bp, representing a significant expansion of existing sequences available for this insect pest. Among them, 16,427 contigs contained one or more GO terms. In addition, 15,263 contigs were assigned an EC number. In-depth transcriptome analysis identified genes potentially involved in insecticide resistance, peritrophic membrane biosynthesis, immunity-related function and defense against pathogens, and Bacillus thuringiensis toxins binding proteins as well as multiple enzymes involved with protein digestion. This transcriptome will provide a valuable resource for understanding larval physiology and for identifying novel target sites and management approaches for this important insect pest.
Collapse
|
80
|
Li Y, Zhang J, Zhao J, Zhao L, Cheng Y, Li Z. A simple molecular beacon with duplex-specific nuclease amplification for detection of microRNA. Analyst 2016; 141:1071-6. [DOI: 10.1039/c5an02312b] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A target recycling amplification method based on a simple molecular beacon and duplex-specific nuclease has been developed for microRNA detection.
Collapse
Affiliation(s)
- Yingcun Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
| | - Jiangyan Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
| | - Jingjing Zhao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
| | - Likun Zhao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
| | - Yongqiang Cheng
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
| | - Zhengping Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
| |
Collapse
|
81
|
Trumbić Ž, Bekaert M, Taggart JB, Bron JE, Gharbi K, Mladineo I. Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758). BMC Genomics 2015; 16:1007. [PMID: 26607231 PMCID: PMC4659210 DOI: 10.1186/s12864-015-2208-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The largest of the tuna species, Atlantic bluefin tuna (Thunnus thynnus), inhabits the North Atlantic Ocean and the Mediterranean Sea and is considered to be an endangered species, largely a consequence of overfishing. T. thynnus aquaculture, referred to as fattening or farming, is a capture based activity dependent on yearly renewal from the wild. Thus, the development of aquaculture practices independent of wild resources can provide an important contribution towards ensuring security and sustainability of this species in the longer-term. The development of such practices is today greatly assisted by large scale transcriptomic studies. RESULTS We have used pyrosequencing technology to sequence a mixed-tissue normalised cDNA library, derived from adult T. thynnus. A total of 976,904 raw sequence reads were assembled into 33,105 unique transcripts having a mean length of 893 bases and an N50 of 870. Of these, 33.4% showed similarity to known proteins or gene transcripts and 86.6% of them were matched to the congeneric Pacific bluefin tuna (Thunnus orientalis) genome, compared to 70.3% for the more distantly related Nile tilapia (Oreochromis niloticus) genome. Transcript sequences were used to develop a novel 15 K Agilent oligonucleotide DNA microarray for T. thynnus and comparative tissue gene expression profiles were inferred for gill, heart, liver, ovaries and testes. Functional contrasts were strongest between gills and ovaries. Gills were particularly associated with immune system, signal transduction and cell communication, while ovaries displayed signatures of glycan biosynthesis, nucleotide metabolism, transcription, translation, replication and repair. CONCLUSIONS Sequence data generated from a novel mixed-tissue T. thynnus cDNA library provide an important transcriptomic resource that can be further employed for study of various aspects of T. thynnus ecology and genomics, with strong applications in aquaculture. Tissue-specific gene expression profiles inferred through the use of novel oligo-microarray can serve in the design of new and more focused transcriptomic studies for future research of tuna physiology and assessment of the welfare in a production environment.
Collapse
Affiliation(s)
- Željka Trumbić
- University Department of Marine Studies, University of Split, Split, Croatia.
| | - Michaël Bekaert
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, UK.
| | - John B Taggart
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, UK.
| | - James E Bron
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, UK.
| | - Karim Gharbi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, Scotland, UK.
| | - Ivona Mladineo
- Institute of Oceanography and Fisheries, Split, Croatia.
| |
Collapse
|
82
|
Chen XG, Jiang X, Gu J, Xu M, Wu Y, Deng Y, Zhang C, Bonizzoni M, Dermauw W, Vontas J, Armbruster P, Huang X, Yang Y, Zhang H, He W, Peng H, Liu Y, Wu K, Chen J, Lirakis M, Topalis P, Van Leeuwen T, Hall AB, Jiang X, Thorpe C, Mueller RL, Sun C, Waterhouse RM, Yan G, Tu ZJ, Fang X, James AA. Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution. Proc Natl Acad Sci U S A 2015; 112:E5907-15. [PMID: 26483478 PMCID: PMC4640774 DOI: 10.1073/pnas.1516410112] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Asian tiger mosquito, Aedes albopictus, is a highly successful invasive species that transmits a number of human viral diseases, including dengue and Chikungunya fevers. This species has a large genome with significant population-based size variation. The complete genome sequence was determined for the Foshan strain, an established laboratory colony derived from wild mosquitoes from southeastern China, a region within the historical range of the origin of the species. The genome comprises 1,967 Mb, the largest mosquito genome sequenced to date, and its size results principally from an abundance of repetitive DNA classes. In addition, expansions of the numbers of members in gene families involved in insecticide-resistance mechanisms, diapause, sex determination, immunity, and olfaction also contribute to the larger size. Portions of integrated flavivirus-like genomes support a shared evolutionary history of association of these viruses with their vector. The large genome repertory may contribute to the adaptability and success of Ae. albopictus as an invasive species.
Collapse
Affiliation(s)
- Xiao-Guang Chen
- Department of Pathogen Biology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China;
| | - Xuanting Jiang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Jinbao Gu
- Department of Pathogen Biology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Meng Xu
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Yang Wu
- Department of Pathogen Biology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yuhua Deng
- Department of Pathogen Biology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Chi Zhang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Mariangela Bonizzoni
- Program in Public Health, University of California, Irvine, CA 92697; Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - John Vontas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 73100 Heraklion, Greece; Faculty of Crop Science, Pesticide Science Lab, Agricultural University of Athens, 11855 Athens, Greece
| | - Peter Armbruster
- Department of Biology, Georgetown University, Washington, DC 20057
| | - Xin Huang
- Department of Biology, Georgetown University, Washington, DC 20057
| | - Yulan Yang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Hao Zhang
- Department of Pathogen Biology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Weiming He
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Hongjuan Peng
- Department of Pathogen Biology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yongfeng Liu
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Kun Wu
- Department of Pathogen Biology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jiahua Chen
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Manolis Lirakis
- Department of Biology, University of Crete, Heraklion, GR-74100, Crete, Greece
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 73100 Heraklion, Greece
| | - Thomas Van Leeuwen
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Andrew Brantley Hall
- Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech University, Blacksburg, VA 24061; Department of Biochemistry, Fralin Life Science Institute, Virginia Tech University, Blacksburg, VA 24061
| | - Xiaofang Jiang
- Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech University, Blacksburg, VA 24061; Department of Biochemistry, Fralin Life Science Institute, Virginia Tech University, Blacksburg, VA 24061
| | - Chevon Thorpe
- Cellular and Molecular Physiology, Edward Via College of Osteopathic Medicine, Blacksburg, VA 24060
| | | | - Cheng Sun
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Robert Michael Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139; The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Guiyun Yan
- Department of Pathogen Biology, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou 510515, China; Program in Public Health, University of California, Irvine, CA 92697
| | - Zhijian Jake Tu
- Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech University, Blacksburg, VA 24061; Department of Biochemistry, Fralin Life Science Institute, Virginia Tech University, Blacksburg, VA 24061
| | - Xiaodong Fang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China;
| | - Anthony A James
- Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry, University of California, Irvine, CA 92697
| |
Collapse
|
83
|
Pauchet Y, Wielsch N, Wilkinson PA, Sakaluk SK, Svatoš A, ffrench-Constant RH, Hunt J, Heckel DG. What's in the Gift? Towards a Molecular Dissection of Nuptial Feeding in a Cricket. PLoS One 2015; 10:e0140191. [PMID: 26439494 PMCID: PMC4595131 DOI: 10.1371/journal.pone.0140191] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/22/2015] [Indexed: 01/11/2023] Open
Abstract
Nuptial gifts produced by males and transferred to females during copulation are common in insects. Yet, their precise composition and subsequent physiological effects on the female recipient remain unresolved. Male decorated crickets Gryllodes sigillatus transfer a spermatophore to the female during copulation that is composed of an edible gift, the spermatophylax, and the ampulla that contains the ejaculate. After transfer of the spermatophore, the female detaches the spermatophylax and starts to eat it while sperm from the ampulla are evacuated into the female reproductive tract. When the female has finished consuming the spermatophylax, she detaches the ampulla and terminates sperm transfer. Hence, one simple function of the spermatophylax is to ensure complete sperm transfer by distracting the female from prematurely removing the ampulla. However, the majority of orally active components of the spermatophylax itself and their subsequent effects on female behavior have not been identified. Here, we report the first analysis of the proteome of the G. sigillatus spermatophylax and the transcriptome of the male accessory glands that make these proteins. The accessory gland transcriptome was assembled into 17,691 transcripts whilst about 30 proteins were detected within the mature spermatophylax itself. Of these 30 proteins, 18 were encoded by accessory gland encoded messages. Most spermatophylax proteins show no similarity to proteins with known biological functions and are therefore largely novel. A spermatophylax protein shows similarity to protease inhibitors suggesting that it may protect the biologically active components from digestion within the gut of the female recipient. Another protein shares similarity with previously characterized insect polypeptide growth factors suggesting that it may play a role in altering female reproductive physiology concurrent with fertilization. Characterization of the spermatophylax proteome provides the first step in identifying the genes encoding these proteins in males and in understanding their biological functions in the female recipient.
Collapse
Affiliation(s)
- Yannick Pauchet
- Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
- * E-mail:
| | - Natalie Wielsch
- Mass spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Paul A. Wilkinson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Scott K. Sakaluk
- Behavior, Ecology, Evolution & Systematics Section, School of Biological Sciences, Illinois State University, Normal, IL, United States of America
| | - Aleš Svatoš
- Mass spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Richard H. ffrench-Constant
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - John Hunt
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - David G. Heckel
- Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| |
Collapse
|
84
|
Ocaña S, Seoane P, Bautista R, Palomino C, Claros GM, Torres AM, Madrid E. Large-Scale Transcriptome Analysis in Faba Bean (Vicia faba L.) under Ascochyta fabae Infection. PLoS One 2015; 10:e0135143. [PMID: 26267359 PMCID: PMC4534337 DOI: 10.1371/journal.pone.0135143] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/17/2015] [Indexed: 12/21/2022] Open
Abstract
Faba bean is an important food crop worldwide. However, progress in faba bean genomics lags far behind that of model systems due to limited availability of genetic and genomic information. Using the Illumina platform the faba bean transcriptome from leaves of two lines (29H and Vf136) subjected to Ascochyta fabae infection have been characterized. De novo transcriptome assembly provided a total of 39,185 different transcripts that were functionally annotated, and among these, 13,266 were assigned to gene ontology against Arabidopsis. Quality of the assembly was validated by RT-qPCR amplification of selected transcripts differentially expressed. Comparison of faba bean transcripts with those of better-characterized plant genomes such as Arabidopsis thaliana, Medicago truncatula and Cicer arietinum revealed a sequence similarity of 68.3%, 72.8% and 81.27%, respectively. Moreover, 39,060 single nucleotide polymorphism (SNP) and 3,669 InDels were identified for genotyping applications. Mapping of the sequence reads generated onto the assembled transcripts showed that 393 and 457 transcripts were overexpressed in the resistant (29H) and susceptible genotype (Vf136), respectively. Transcripts involved in plant-pathogen interactions such as leucine rich proteins (LRR) or plant growth regulators involved in plant adaptation to abiotic and biotic stresses were found to be differently expressed in the resistant line. The results reported here represent the most comprehensive transcript database developed so far in faba bean, providing valuable information that could be used to gain insight into the pathways involved in the resistance mechanism against A. fabae and to identify potential resistance genes to be further used in marker assisted selection.
Collapse
Affiliation(s)
- Sara Ocaña
- Área de Mejora y Biotecnología, IFAPA Centro Alameda del Obispo, Apdo 3092, E-14080, Córdoba, Spain
| | - Pedro Seoane
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, E-29071, Málaga, Spain
| | - Rocio Bautista
- Plataforma Andaluza de Bioinformática, Universidad de Málaga, E-29071, Málaga, Spain
| | - Carmen Palomino
- Área de Mejora y Biotecnología, IFAPA Centro Alameda del Obispo, Apdo 3092, E-14080, Córdoba, Spain
| | - Gonzalo M. Claros
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, E-29071, Málaga, Spain
- Plataforma Andaluza de Bioinformática, Universidad de Málaga, E-29071, Málaga, Spain
| | - Ana M. Torres
- Área de Mejora y Biotecnología, IFAPA Centro Alameda del Obispo, Apdo 3092, E-14080, Córdoba, Spain
| | - Eva Madrid
- Institute for Sustainable Agriculture, CSIC, Apdo 4084, E-14080, Córdoba, Spain
| |
Collapse
|
85
|
Cruz A, Rodrigues R, Pinheiro M, Mendo S. Transcriptomes analysis of Aeromonas molluscorum Av27 cells exposed to tributyltin (TBT): Unravelling the effects from the molecular level to the organism. MARINE ENVIRONMENTAL RESEARCH 2015; 109:132-9. [PMID: 26171931 PMCID: PMC4541717 DOI: 10.1016/j.marenvres.2015.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/24/2015] [Accepted: 06/26/2015] [Indexed: 06/04/2023]
Abstract
Aeromonas molluscorum Av27 cells were exposed to 0, 5 and 50 μM of TBT and the respective transcriptomes were obtained by pyrosequencing. Gene Ontology revealed that exposure to 5 μM TBT results in a higher number of repressed genes in contrast with 50 μM of TBT, where the number of over-expressed genes is greater. At both TBT concentrations, higher variations in gene expression were found in the functional categories associated with enzymatic activities, transport/binding and oxidation-reduction. A number of proteins are affected by TBT, such as the acriflavin resistance protein, several transcription-related proteins, several Hsps, ABC transporters, CorA and ZntB and other outer membrane efflux proteins, all of these involved in cellular metabolic processes, important to maintain overall cell viability. Using the STRING tool, several proteins with unknown function were related with others involved in degradation processes, such as the pyoverdine chromophore biosynthetic protein, that has been described as playing a role in the Sn-C cleavage of organotins. This approach has allowed a better understanding of the molecular effects of exposure of bacterial cells to TBT. Furthermore it contributes to the knowledge of the functional genomic aspects of bacteria exposed to this pollutant. Furthermore, the transcriptomic data gathered, and now publically available, constitute a valuable resource for comparative genome analysis.
Collapse
Affiliation(s)
- Andreia Cruz
- Biology Department & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - Raquel Rodrigues
- Biology Department & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Miguel Pinheiro
- Advanced Services Unit, Biocant - Biotechnology Innovation Center, 3060-325, Cantanhede, Portugal; School of Medicine, University of St. Andrews, North Haugh, KY16 9TF, St. Andrews, UK
| | - Sónia Mendo
- Biology Department & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| |
Collapse
|
86
|
Callol A, Reyes-López FE, Roig FJ, Goetz G, Goetz FW, Amaro C, MacKenzie SA. An Enriched European Eel Transcriptome Sheds Light upon Host-Pathogen Interactions with Vibrio vulnificus. PLoS One 2015. [PMID: 26207370 PMCID: PMC4514713 DOI: 10.1371/journal.pone.0133328] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Infectious diseases are one of the principal bottlenecks for the European eel recovery. The aim of this study was to develop a new molecular tool to be used in host-pathogen interaction experiments in the eel. To this end, we first stimulated adult eels with different pathogen-associated molecular patterns (PAMPs), extracted RNA from the immune-related tissues and sequenced the transcriptome. We obtained more than 2x106 reads that were assembled and annotated into 45,067 new descriptions with a notable representation of novel transcripts related with pathogen recognition, signal transduction and the immune response. Then, we designed a DNA-microarray that was used to analyze the early immune response against Vibrio vulnificus, a septicemic pathogen that uses the gills as the portal of entry into the blood, as well as the role of the main toxin of this species (RtxA13) on this early interaction. The gill transcriptomic profiles obtained after bath infecting eels with the wild type strain or with a mutant deficient in rtxA13 were analyzed and compared. Results demonstrate that eels react rapidly and locally against the pathogen and that this immune-response is rtxA13-dependent as transcripts related with cell destruction were highly up-regulated only in the gills from eels infected with the wild-type strain. Furthermore, significant differences in the immune response against the wild type and the mutant strain also suggest that host survival after V. vulnificus infection could depend on an efficient local phagocytic activity. Finally, we also found evidence of the presence of an interbranchial lymphoid tissue in European eel gills although further experiments will be necessary to identify such tissue.
Collapse
Affiliation(s)
- Agnès Callol
- Departament de Microbiologia i Ecologia, Universitat de Valencia, Burjassot, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Felipe E. Reyes-López
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Department de Biologia cel·lular, Fisiologia Animal i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Francisco J. Roig
- Departament de Microbiologia i Ecologia, Universitat de Valencia, Burjassot, Spain
| | - Giles Goetz
- Northwest Fisheries Science Center, Seattle, United States of America
| | | | - Carmen Amaro
- Departament de Microbiologia i Ecologia, Universitat de Valencia, Burjassot, Spain
| | - Simon A. MacKenzie
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
- * E-mail:
| |
Collapse
|
87
|
Tzika AC, Ullate-Agote A, Grbic D, Milinkovitch MC. Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics. Genome Biol Evol 2015; 7:1827-41. [PMID: 26133641 PMCID: PMC4494049 DOI: 10.1093/gbe/evv106] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the “Reptilian Transcriptomes Database 2.0,” which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva.
Collapse
Affiliation(s)
- Athanasia C Tzika
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, Switzerland SIB Swiss Institute of Bioinformatics, Switzerland Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Switzerland
| | - Asier Ullate-Agote
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, Switzerland SIB Swiss Institute of Bioinformatics, Switzerland Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Switzerland
| | - Djordje Grbic
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, Switzerland SIB Swiss Institute of Bioinformatics, Switzerland Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Switzerland
| | - Michel C Milinkovitch
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, Switzerland SIB Swiss Institute of Bioinformatics, Switzerland Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Switzerland
| |
Collapse
|
88
|
Ashrafi H, Hulse-Kemp AM, Wang F, Yang SS, Guan X, Jones DC, Matvienko M, Mockaitis K, Chen ZJ, Stelly DM, Van Deynze A. A Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery. THE PLANT GENOME 2015; 8:eplantgenome2014.10.0068. [PMID: 33228299 DOI: 10.3835/plantgenome2014.10.0068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/17/2015] [Indexed: 06/11/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) has a narrow germplasm base, which constrains marker development and hampers intraspecific breeding. A pressing need exists for high-throughput single nucleotide polymorphism (SNP) markers that can be readily applied to germplasm in breeding and breeding-related research programs. Despite progress made in developing new sequencing technologies during the past decade, the cost of sequencing remains substantial when one is dealing with numerous samples and large genomes. Several strategies have been proposed to lower the cost of sequencing for multiple genotypes of large-genome species like cotton, such as transcriptome sequencing and reduced-representation DNA sequencing. This paper reports the development of a transcriptome assembly of the inbred line Texas Marker-1 (TM-1), a genetic standard for cotton, its usefulness as a reference for RNA sequencing (RNA-seq)-based SNP identification, and the availability of transcriptome sequences of four other cotton cultivars. An assembly of TM-1 was made using Roche 454 transcriptome reads combined with an assembly of all available public expressed sequence tag (EST) sequences of TM-1. The TM-1 assembly consists of 72,450 contigs with a total of 70 million bp. Functional predictions of the transcripts were estimated by alignment to selected protein databases. Transcriptome sequences of the five lines, including TM-1, were obtained using an Illumina Genome Analyzer-II, and the short reads were mapped to the TM-1 assembly to discover SNPs among the five lines. We identified >14,000 unfiltered allelic SNPs, of which ∼3,700 SNPs were retained for assay development after applying several rigorous filters. This paper reports availability of the reference transcriptome assembly and shows its utility in developing intraspecific SNP markers in upland cotton.
Collapse
Affiliation(s)
- Hamid Ashrafi
- Univ. of California-Davis, Dep. of Plant Sciences and Seed Biotechnology Center, One Shields Ave., Davis, CA, 95616
| | | | - Fei Wang
- Texas A&M Univ., Dep. of Soil and Crop Sciences, College Station, TX, 77843
| | - S Samuel Yang
- Texas A&M Univ., Dep. of Soil and Crop Sciences, College Station, TX, 77843
| | - Xueying Guan
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The Univ. of Texas at Austin, Austin, TX, 78712
| | | | - Marta Matvienko
- Univ. of California-Davis, Genome Center, One Shields Ave., Davis, CA, 95616
| | | | - Z Jeffrey Chen
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The Univ. of Texas at Austin, Austin, TX, 78712
| | - David M Stelly
- Texas A&M Univ., Dep. of Soil and Crop Sciences, College Station, TX, 77843
| | - Allen Van Deynze
- Univ. of California-Davis, Dep. of Plant Sciences and Seed Biotechnology Center, One Shields Ave., Davis, CA, 95616
| |
Collapse
|
89
|
Miguel A, de Vega-Bartol J, Marum L, Chaves I, Santo T, Leitão J, Varela MC, Miguel CM. Characterization of the cork oak transcriptome dynamics during acorn development. BMC PLANT BIOLOGY 2015; 15:158. [PMID: 26109289 PMCID: PMC4479327 DOI: 10.1186/s12870-015-0534-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/26/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Cork oak (Quercus suber L.) has a natural distribution across western Mediterranean regions and is a keystone forest tree species in these ecosystems. The fruiting phase is especially critical for its regeneration but the molecular mechanisms underlying the biochemical and physiological changes during cork oak acorn development are poorly understood. In this study, the transcriptome of the cork oak acorn, including the seed, was characterized in five stages of development, from early development to acorn maturation, to identify the dominant processes in each stage and reveal transcripts with important functions in gene expression regulation and response to water. RESULTS A total of 80,357 expressed sequence tags (ESTs) were de novo assembled from RNA-Seq libraries representative of the several acorn developmental stages. Approximately 7.6 % of the total number of transcripts present in Q. suber transcriptome was identified as acorn specific. The analysis of expression profiles during development returned 2,285 differentially expressed (DE) transcripts, which were clustered into six groups. The stage of development corresponding to the mature acorn exhibited an expression profile markedly different from other stages. Approximately 22 % of the DE transcripts putatively code for transcription factors (TF) or transcriptional regulators, and were found almost equally distributed among the several expression profile clusters, highlighting their major roles in controlling the whole developmental process. On the other hand, carbohydrate metabolism, the biological pathway most represented during acorn development, was especially prevalent in mid to late stages as evidenced by enrichment analysis. We further show that genes related to response to water, water deprivation and transport were mostly represented during the early (S2) and the last stage (S8) of acorn development, when tolerance to water desiccation is possibly critical for acorn viability. CONCLUSIONS To our knowledge this work represents the first report of acorn development transcriptomics in oaks. The obtained results provide novel insights into the developmental biology of cork oak acorns, highlighting transcripts putatively involved in the regulation of the gene expression program and in specific processes likely essential for adaptation. It is expected that this knowledge can be transferred to other oak species of great ecological value.
Collapse
Affiliation(s)
- Andreia Miguel
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - José de Vega-Bartol
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Liliana Marum
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
- KLÓN, Innovative Technologies from Cloning, Biocant Park, Núcleo 4, Lote 4A, 3060-197, Cantanhede, Portugal.
| | - Inês Chaves
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Tatiana Santo
- Laboratory of Genomics and Genetic Improvement, BioFIG, FCT, Universidade do Algarve, E.8, Campus de Gambelas, Faro, 8300, Portugal.
| | - José Leitão
- Laboratory of Genomics and Genetic Improvement, BioFIG, FCT, Universidade do Algarve, E.8, Campus de Gambelas, Faro, 8300, Portugal.
| | - Maria Carolina Varela
- INIAV- Instituto Nacional de Investigação Agrária e Veterinária, IP, Quinta do, Marquês, Oeiras, 2780-159, Portugal.
| | - Célia M Miguel
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| |
Collapse
|
90
|
Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life. PLoS One 2015; 10:e0130600. [PMID: 26075903 PMCID: PMC4468109 DOI: 10.1371/journal.pone.0130600] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/21/2015] [Indexed: 11/19/2022] Open
Abstract
Background Collembola (springtails) represent a soil-living lineage of hexapods in between insects and crustaceans. Consequently, their genomes may hold key information on the early processes leading to evolution of Hexapoda from a crustacean ancestor. Method We assembled and annotated transcriptomes of the Collembola Folsomia candida and Orchesella cincta, and performed comparative analysis with protein-coding gene sequences of three crustaceans and three insects to identify adaptive signatures associated with the evolution of hexapods within the pancrustacean clade. Results Assembly of the springtail transcriptomes resulted in 37,730 transcripts with predicted open reading frames for F. candida and 32,154 for O. cincta, of which 34.2% were functionally annotated for F. candida and 38.4% for O. cincta. Subsequently, we predicted orthologous clusters among eight species and applied the branch-site test to detect episodic positive selection in the Hexapoda and Collembola lineages. A subset of 250 genes showed significant positive selection along the Hexapoda branch and 57 in the Collembola lineage. Gene Ontology categories enriched in these genes include metabolism, stress response (i.e. DNA repair, immune response), ion transport, ATP metabolism, regulation and development-related processes (i.e. eye development, neurological development). Conclusions We suggest that the identified gene families represent processes that have played a key role in the divergence of hexapods within the pancrustacean clade that eventually evolved into the most species-rich group of all animals, the hexapods. Furthermore, some adaptive signatures in collembolans may provide valuable clues to understand evolution of hexapods on land.
Collapse
|
91
|
Xiao Y, Sheng ZM, Taubenberger JK. Isolating Viral and Host RNA Sequences from Archival Material and Production of cDNA Libraries for High-Throughput DNA Sequencing. ACTA ACUST UNITED AC 2015; 37:1E.8.1-16. [PMID: 26344216 DOI: 10.1002/9780471729259.mc01e08s37] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The vast majority of surgical biopsy and post-mortem tissue samples are formalin-fixed and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. As an example, the viral RNA genome of the 1918 pandemic influenza A virus was previously determined in a 9-year effort by overlapping RT-PCR from post-mortem samples. Using the protocols described here, the full genome of the 1918 virus was determined at high coverage in one high-throughput sequencing run of a cDNA library derived from total RNA of a 1918 FFPE sample after duplex-specific nuclease treatments. This basic methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of infectious diseases.
Collapse
Affiliation(s)
- Yongli Xiao
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Zong-Mei Sheng
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jeffery K Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
92
|
Jensen MK, Vogt JK, Bressendorff S, Seguin-Orlando A, Petersen M, Sicheritz-Pontén T, Mundy J. Transcriptome and genome size analysis of the Venus flytrap. PLoS One 2015; 10:e0123887. [PMID: 25886597 PMCID: PMC4401711 DOI: 10.1371/journal.pone.0123887] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/23/2015] [Indexed: 11/30/2022] Open
Abstract
The insectivorous Venus flytrap (Dionaea muscipula) is renowned from Darwin’s studies of plant carnivory and the origins of species. To provide tools to analyze the evolution and functional genomics of D. muscipula, we sequenced a normalized cDNA library synthesized from mRNA isolated from D. muscipula flowers and traps. Using the Oases transcriptome assembler 79,165,657 quality trimmed reads were assembled into 80,806 cDNA contigs, with an average length of 679 bp and an N50 length of 1,051 bp. A total of 17,047 unique proteins were identified, and assigned to Gene Ontology (GO) and classified into functional categories. A total of 15,547 full-length cDNA sequences were identified, from which open reading frames were detected in 10,941. Comparative GO analyses revealed that D. muscipula is highly represented in molecular functions related to catalytic, antioxidant, and electron carrier activities. Also, using a single copy sequence PCR-based method, we estimated that the genome size of D. muscipula is approx. 3 Gb. Our genome size estimate and transcriptome analyses will contribute to future research on this fascinating, monotypic species and its heterotrophic adaptations.
Collapse
Affiliation(s)
| | - Josef Korbinian Vogt
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Morten Petersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail: (TS); (JM)
| | - John Mundy
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (TS); (JM)
| |
Collapse
|
93
|
De novo sequencing of the Hypericum perforatum L. flower transcriptome to identify potential genes that are related to plant reproduction sensu lato. BMC Genomics 2015; 16:254. [PMID: 25887758 PMCID: PMC4451943 DOI: 10.1186/s12864-015-1439-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/06/2015] [Indexed: 02/07/2023] Open
Abstract
Background St. John’s wort (Hypericum perforatum L.) is a medicinal plant that produces important metabolites with antidepressant and anticancer activities. Recently gained biological information has shown that this species is also an attractive model system for the study of a naturally occurring form of asexual reproduction called apomixis, which allows cloning plants through seeds. In aposporic gametogenesis, one or multiple somatic cells belonging to the ovule nucellus change their fate by dividing mitotically and developing functionally unreduced embryo sacs by mimicking sexual gametogenesis. Although the introduction of apomixis into agronomically important crops could have revolutionary implications for plant breeding, the genetic control of this mechanism of seed formation is still not well understood for most of the model species investigated so far. We used Roche 454 technology to sequence the entire H. perforatum flower transcriptome of whole flower buds and single flower verticils collected from obligately sexual and unrelated highly or facultatively apomictic genotypes, which enabled us to identify RNAs that are likely exclusive to flower organs (i.e., sepals, petals, stamens and carpels) or reproductive strategies (i.e., sexual vs. apomictic). Results Here we sequenced and annotated the flower transcriptome of H. perforatum with particular reference to reproductive organs and processes. In particular, in our study we characterized approximately 37,000 transcripts found expressed in male and/or female reproductive organs, including tissues or cells of sexual and apomictic flower buds. Ontological annotation was applied to identify major biological processes and molecular functions involved in flower development and plant reproduction. Starting from this dataset, we were able to recover and annotate a large number of transcripts related to meiosis, gametophyte/gamete formation, and embryogenesis, as well as genes that are exclusively or preferentially expressed in sexual or apomictic libraries. Real-Time RT-qPCR assays on pistils and anthers collected at different developmental stages from accessions showing alternative modes of reproduction were used to identify potential genes that are related to plant reproduction sensu lato in H. perforatum. Conclusions Our approach of sequencing flowers from two fully obligate sexual genotypes and two unrelated highly apomictic genotypes, in addition to different flower parts dissected from a facultatively apomictic accession, enabled us to analyze the complexity of the flower transcriptome according to its main reproductive organs as well as for alternative reproductive behaviors. Both annotation and expression data provided original results supporting the hypothesis that apomixis in H. perforatum relies upon spatial or temporal mis-expression of genes acting during female sexual reproduction. The present analyses aim to pave the way toward a better understanding of the molecular basis of flower development and plant reproduction, by identifying genes or RNAs that may differentiate or regulate the sexual and apomictic reproductive pathways in H. perforatum. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1439-y) contains supplementary material, which is available to authorized users.
Collapse
|
94
|
Duplex-specific nuclease-mediated bioanalysis. Trends Biotechnol 2015; 33:180-8. [DOI: 10.1016/j.tibtech.2014.12.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/22/2014] [Accepted: 12/30/2014] [Indexed: 12/21/2022]
|
95
|
de Assis Fonseca FC, Firmino AAP, de Macedo LLP, Coelho RR, de Sousa Júnior JDA, Silva-Junior OB, Togawa RC, Pappas GJ, de Góis LAB, da Silva MCM, Grossi-de-Sá MF. Sugarcane giant borer transcriptome analysis and identification of genes related to digestion. PLoS One 2015; 10:e0118231. [PMID: 25706301 PMCID: PMC4338194 DOI: 10.1371/journal.pone.0118231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/11/2015] [Indexed: 11/25/2022] Open
Abstract
Sugarcane is a widely cultivated plant that serves primarily as a source of sugar and ethanol. Its annual yield can be significantly reduced by the action of several insect pests including the sugarcane giant borer (Telchin licus licus), a lepidopteran that presents a long life cycle and which efforts to control it using pesticides have been inefficient. Although its economical relevance, only a few DNA sequences are available for this species in the GenBank. Pyrosequencing technology was used to investigate the transcriptome of several developmental stages of the insect. To maximize transcript diversity, a pool of total RNA was extracted from whole body insects and used to construct a normalized cDNA database. Sequencing produced over 650,000 reads, which were de novo assembled to generate a reference library of 23,824 contigs. After quality score and annotation, 43% of the contigs had at least one BLAST hit against the NCBI non-redundant database, and 40% showed similarities with the lepidopteran Bombyx mori. In a further analysis, we conducted a comparison with Manduca sexta midgut sequences to identify transcripts of genes involved in digestion. Of these transcripts, many presented an expansion or depletion in gene number, compared to B. mori genome. From the sugarcane giant borer (SGB) transcriptome, a number of aminopeptidase N (APN) cDNAs were characterized based on homology to those reported as Cry toxin receptors. This is the first report that provides a large-scale EST database for the species. Transcriptome analysis will certainly be useful to identify novel developmental genes, to better understand the insect's biology and to guide the development of new strategies for insect-pest control.
Collapse
Affiliation(s)
- Fernando Campos de Assis Fonseca
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Alexandre Augusto Pereira Firmino
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Leonardo Lima Pepino de Macedo
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Roberta Ramos Coelho
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | | | - Orzenil Bonfim Silva-Junior
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | | | | | | | | | - Maria Fátima Grossi-de-Sá
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| |
Collapse
|
96
|
Bahamonde PA, McMaster ME, Servos MR, Martyniuk CJ, Munkittrick KR. Molecular pathways associated with the intersex condition in rainbow darter (Etheostoma caeruleum) following exposures to municipal wastewater in the Grand River basin, ON, Canada. Part B. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 159:302-316. [PMID: 25542366 DOI: 10.1016/j.aquatox.2014.11.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 06/04/2023]
Abstract
Rainbow darter (Etheostoma caeruleum; RBD) is a small benthic fish found in North America. This species is sensitive to sewage effluent, and intersex is found in up to 80% of males in near-field areas in the Grand River, Ontario, Canada. To learn more about the molecular signaling cascades associated with intersex, a developed customized oligonucleotide microarray (4×180 K) using next generation sequencing was developed to characterize the transcriptome in the gonad of male and female RBD. Gene expression profiling was performed in males and females from both a reference site and a polluted site. Males with and without intersex condition from the areas closest to effluent outfalls were compared to males and females from a reference site. Microarray analysis revealed that there was increased mRNA abundance for genes associated with oogenesis in intersex males (i.e. the presence of eggs within the testis), and a decrease in mRNA abundance for genes associated with spermatid development. In females exposed to effluent, cell processes related with hatching and ovulation were down-regulated, and genes involved in immune responses were increased in abundance. In the non-intersex males exposed to effluent, cell processes such as sperm cell adhesion were decreased at the transcript level relative to males from the reference site. Microarray analysis revealed that heat shock proteins (HSP) were significantly increased in non-intersex males exposed to effluent; however, HSPs were not differentially expressed in intersex males exposed to the effluent. Genes involved in sex differentiation (sox9, foxl2 and dmrt1) and reproduction (esr1, esrb, ar, vtg, cyp19a1 and cyp11a) were measured in males, females, and intersex individuals. Consistent with the intersex condition, many transcripts showed an intermediate expression level in intersex males when compared to phenotypic males and females. This study improves our knowledge regarding the molecular pathways that underlie the intersex condition and develops a suite of qPCR bioassays in RBD that are able to discriminate pollutant-exposed males without intersex from those males with intersex. Part A of this study reports on the effects of municipal wastewater effluents (MWWEs) on RBD in the Grand River and demonstrates that there are disruptions in higher level endpoints that include altered steroid levels. Here we develop a new tool for assessing and monitoring the intersex condition in RBD in polluted natural environments and begin to characterize gene networks that are associated with the condition.
Collapse
Affiliation(s)
- P A Bahamonde
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, NB, Canada E2L 4L5.
| | - M E McMaster
- Emerging Methods Branch, Aquatic Contaminant Research Division, Water Science and Technology Directorate, Environment Canada, Burlington, ON, Canada L7R 4A6
| | - M R Servos
- Canadian Rivers Institute and University of Waterloo, Department of Biology, Waterloo, ON, Canada N2L 3G1
| | - C J Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, NB, Canada E2L 4L5
| | - K R Munkittrick
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, NB, Canada E2L 4L5
| |
Collapse
|
97
|
Li B, Li X, Wang M, Yang Z, Yin H, Ai S. Photoelectrochemical biosensor for highly sensitive detection of microRNA based on duplex-specific nuclease-triggered signal amplification. J Solid State Electrochem 2015. [DOI: 10.1007/s10008-015-2747-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
98
|
Ramond JB, Makhalanyane TP, Tuffin MI, Cowan DA. Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members. Lett Appl Microbiol 2015; 60:359-66. [PMID: 25495929 DOI: 10.1111/lam.12380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/28/2014] [Accepted: 12/05/2014] [Indexed: 12/30/2022]
Abstract
UNLABELLED Normalization is a procedure classically employed to detect rare sequences in cellular expression profiles (i.e. cDNA libraries). Here, we present a normalization protocol involving the direct treatment of extracted environmental metagenomic DNA with S1 nuclease, referred to as normalization of metagenomic DNA: NmDNA. We demonstrate that NmDNA, prior to post hoc PCR-based experiments (16S rRNA gene T-RFLP fingerprinting and clone library), increased the diversity of sequences retrieved from environmental microbial communities by detection of rarer sequences. This approach could be used to enhance the resolution of detection of ecologically relevant rare members in environmental microbial assemblages and therefore is promising in enabling a better understanding of ecosystem functioning. SIGNIFICANCE AND IMPACT OF THE STUDY This study is the first testing 'normalization' on environmental metagenomic DNA (mDNA). The aim of this procedure was to improve the identification of rare phylotypes in environmental communities. Using hypoliths as model systems, we present evidence that this post-mDNA extraction molecular procedure substantially enhances the detection of less common phylotypes and could even lead to the discovery of novel microbial genotypes within a given environment.
Collapse
Affiliation(s)
- J-B Ramond
- Centre for Microbial Ecology and Genomics (CMEG), Genomic Research Institute, University of Pretoria, Pretoria, South Africa; Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville, South Africa
| | | | | | | |
Collapse
|
99
|
Bedada G, Westerbergh A, Müller T, Galkin E, Bdolach E, Moshelion M, Fridman E, Schmid KJ. Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts. BMC Genomics 2014; 15:995. [PMID: 25408241 PMCID: PMC4251939 DOI: 10.1186/1471-2164-15-995] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 11/04/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Wild barley is adapted to highly diverse environments throughout its geographical distribution range. Transcriptome sequencing of differentially adapted wild barley ecotypes from contrasting environments contributes to the identification of genes and genetic variation involved in abiotic stress tolerance and adaptation. RESULTS Two differentially adapted wild barley ecotypes from desert (B1K2) and Mediterranean (B1K30) environments were analyzed for drought stress response under controlled conditions. The desert ecotype lost more water under both irrigation and drought, but exhibited higher relative water content (RWC) and better water use efficiency (WUE) than the coastal ecotype. We sequenced normalized cDNA libraries from drought-stressed leaves of both ecotypes with the 454 platform to identify drought-related transcripts. Over half million reads per ecotype were de novo assembled into 20,439 putative unique transcripts (PUTs) for B1K2, 21,494 for B1K30 and 28,720 for the joint assembly. Over 50% of PUTs of each ecotype were not shared with the other ecotype. Furthermore, 16% (3,245) of B1K2 and 17% (3,674) of B1K30 transcripts did not show orthologous sequence hits in the other wild barley ecotype and cultivated barley, and are candidates of ecotype-specific transcripts. Over 800 unique transcripts from each ecotype homologous to over 30 different stress-related genes were identified. We extracted 1,017 high quality SNPs that differentiated the two ecotypes. The genetic distance between the desert ecotype and cultivated barley was 1.9-fold higher than between the Mediterranean ecotype and cultivated barley. Moreover, the desert ecotype harbored a larger proportion of non-synonymous SNPs than the Mediterranean ecotype suggesting different demographic histories of these ecotypes. CONCLUSIONS The results indicate a strong physiological and genomic differentiation between the desert and Mediterranean wild barley ecotypes and a closer relationship of the Mediterranean to cultivated barley. A significant number of novel transcripts specific to wild barley were identified. The higher SNP density and larger proportion of SNPs with functional effects in the desert ecotype suggest different demographic histories and effects of natural selection in Mediterranean and desert wild barley. The data are a valuable genomic resource for an improved genome annotation, transcriptome studies of drought adaptation and a source of new genetic markers for future barley improvement.
Collapse
MESH Headings
- Adaptation, Physiological/genetics
- Base Sequence
- Biological Evolution
- Conserved Sequence
- Crops, Agricultural/genetics
- Crops, Agricultural/physiology
- Droughts
- Ecotype
- Gene Expression Regulation, Plant
- Gene Ontology
- Genes, Plant
- Hordeum/genetics
- Molecular Sequence Annotation
- Plant Leaves/genetics
- Plant Transpiration/genetics
- Polymorphism, Single Nucleotide/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombination, Genetic/genetics
- Reference Standards
- Sequence Analysis, RNA
- Soil/chemistry
- Species Specificity
- Stress, Physiological/genetics
- Transcription Factors/metabolism
- Transcriptome/genetics
- Water/metabolism
Collapse
Affiliation(s)
- Girma Bedada
- />Department of Plant Biology, Uppsala BioCenter, Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Anna Westerbergh
- />Department of Plant Biology, Uppsala BioCenter, Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Thomas Müller
- />Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, D-70599 Stuttgart, Germany
| | - Eyal Galkin
- />Institute of Plant Science and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Eyal Bdolach
- />Institute of Plant Science and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Menachem Moshelion
- />Institute of Plant Science and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Eyal Fridman
- />Institute of Plant Science and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Karl J Schmid
- />Department of Plant Biology, Uppsala BioCenter, Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- />Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, D-70599 Stuttgart, Germany
| |
Collapse
|
100
|
Hulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda ABV, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM. Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. BMC Genomics 2014. [PMID: 25359292 DOI: 10.1186/1471‐2164‐15‐945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection. RESULTS Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3-79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays. CONCLUSIONS This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
| |
Collapse
|