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Rios-Carlos H, Segovia-Ramírez MG, Fujita MK, Rovito SM. Genomic Gigantism is not Associated with Reduced Selection Efficiency in Neotropical Salamanders. J Mol Evol 2024; 92:371-380. [PMID: 38844681 PMCID: PMC11291587 DOI: 10.1007/s00239-024-10177-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/16/2024] [Indexed: 08/03/2024]
Abstract
Genome size variation in eukaryotes has myriad effects on organismal biology from the genomic to whole-organism level. Large genome size may be associated with lower selection efficiency because lower effective population sizes allow fixation of deleterious mutations via genetic drift, increasing genome size and decreasing selection efficiency. Because of a hypothesized negative relationship between genome size and recombination rate per base pair, increased genome size could also increase the effect of linked selection in the genome, decreasing the efficiency with which natural selection can fix or remove mutations. We used a transcriptomic dataset of 15 and a subset of six Neotropical salamander species ranging in genome size from 12 to 87 pg to study the relationship between genome size and efficiency of selection. We estimated dN/dS of salamanders with small and large genomes and tested for relaxation of selection in the larger genomes. Contrary to our expectations, we did not find a significant relationship between genome size and selection efficiency or strong evidence for higher dN/dS values in species with larger genomes for either species set. We also found little evidence for relaxation of selection in species with larger genomes. A positive correlation between genome size and range size (a proxy of population size) in this group disagrees with predictions of stronger drift in species with larger genomes. Our results highlight the complex interactions between the many forces shaping genomic variation in organisms with genomic gigantism.
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Affiliation(s)
- Hairo Rios-Carlos
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, México
| | - María Guadalupe Segovia-Ramírez
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, México
| | - Matthew K Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas, Arlington, TX, USA
| | - Sean M Rovito
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, km 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, Guanajuato, México.
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Castric V, Batista RA, Carré A, Mousavi S, Mazoyer C, Godé C, Gallina S, Ponitzki C, Theron A, Bellec A, Marande W, Santoni S, Mariotti R, Rubini A, Legrand S, Billiard S, Vekemans X, Vernet P, Saumitou-Laprade P. The homomorphic self-incompatibility system in Oleaceae is controlled by a hemizygous genomic region expressing a gibberellin pathway gene. Curr Biol 2024; 34:1967-1976.e6. [PMID: 38626763 DOI: 10.1016/j.cub.2024.03.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/29/2024] [Accepted: 03/25/2024] [Indexed: 04/18/2024]
Abstract
In flowering plants, outcrossing is commonly ensured by self-incompatibility (SI) systems. These can be homomorphic (typically with many different allelic specificities) or can accompany flower heteromorphism (mostly with just two specificities and corresponding floral types). The SI system of the Oleaceae family is unusual, with the long-term maintenance of only two specificities but often without flower morphology differences. To elucidate the genomic architecture and molecular basis of this SI system, we obtained chromosome-scale genome assemblies of Phillyrea angustifolia individuals and related them to a genetic map. The S-locus region proved to have a segregating 543-kb indel unique to one specificity, suggesting a hemizygous region, as observed in all distylous systems so far studied at the genomic level. Only one of the predicted genes in this indel region is found in the olive tree, Olea europaea, genome, also within a segregating indel. We describe complete association between the presence/absence of this gene and the SI types determined for individuals of seven distantly related Oleaceae species. This gene is predicted to be involved in catabolism of the gibberellic acid (GA) hormone, and experimental manipulation of GA levels in developing buds modified the male and female SI responses of the two specificities in different ways. Our results provide a unique example of a homomorphic SI system, where a single conserved gibberellin-related gene in a hemizygous indel underlies the long-term maintenance of two groups of reproductive compatibility.
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Affiliation(s)
- Vincent Castric
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Rita A Batista
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Amélie Carré
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Soraya Mousavi
- CNR, Institute of Biosciences and Bioresources (IBBR), 06128 Perugia, Italy
| | - Clément Mazoyer
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Cécile Godé
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Sophie Gallina
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Chloé Ponitzki
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Anthony Theron
- INRAE, CNRGV French Plant Genomic Resource Center, F-31326 Castanet Tolosan, France
| | - Arnaud Bellec
- INRAE, CNRGV French Plant Genomic Resource Center, F-31326 Castanet Tolosan, France
| | - William Marande
- INRAE, CNRGV French Plant Genomic Resource Center, F-31326 Castanet Tolosan, France
| | - Sylvain Santoni
- UMR DIAPC Diversité et adaptation des plantes cultivées, F-34398 Montpellier, France
| | - Roberto Mariotti
- CNR, Institute of Biosciences and Bioresources (IBBR), 06128 Perugia, Italy
| | - Andrea Rubini
- CNR, Institute of Biosciences and Bioresources (IBBR), 06128 Perugia, Italy
| | - Sylvain Legrand
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Sylvain Billiard
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Xavier Vekemans
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Philippe Vernet
- Univ. Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
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Plazzi F, Le Cras Y, Formaggioni A, Passamonti M. Mitochondrially mediated RNA interference, a retrograde signaling system affecting nuclear gene expression. Heredity (Edinb) 2024; 132:156-161. [PMID: 37714959 PMCID: PMC10923801 DOI: 10.1038/s41437-023-00650-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023] Open
Abstract
Several functional classes of short noncoding RNAs are involved in manifold regulatory processes in eukaryotes, including, among the best characterized, miRNAs. One of the most intriguing regulatory networks in the eukaryotic cell is the mito-nuclear crosstalk: recently, miRNA-like elements of mitochondrial origin, called smithRNAs, were detected in a bivalve species, Ruditapes philippinarum. These RNA molecules originate in the organelle but were shown in vivo to regulate nuclear genes. Since miRNA genes evolve easily de novo with respect to protein-coding genes, in the present work we estimate the probability with which a newly arisen smithRNA finds a suitable target in the nuclear transcriptome. Simulations with transcriptomes of 12 bivalve species suggest that this probability is high and not species specific: one in a hundred million (1 × 10-8) if five mismatches between the smithRNA and the 3' mRNA are allowed, yet many more are allowed in animals. We propose that novel smithRNAs may easily evolve as exaptation of the pre-existing mitochondrial RNAs. In turn, the ability of evolving novel smithRNAs may have played a pivotal role in mito-nuclear interactions during animal evolution, including the intriguing possibility of acting as speciation trigger.
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Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy.
| | - Youn Le Cras
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy
- Magistère Européen de Génétique, Université Paris Cité, 85 Boulevard Saint Germain, 75006, Paris, Italy
| | - Alessandro Formaggioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy
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Loubet I, Meyer L, Michel S, Pernin F, Carrère S, Barrès B, Le Corre V, Délye C. A high diversity of non-target site resistance mechanisms to acetolactate-synthase (ALS) inhibiting herbicides has evolved within and among field populations of common ragweed (Ambrosia artemisiifolia L.). BMC PLANT BIOLOGY 2023; 23:510. [PMID: 37875807 PMCID: PMC10594812 DOI: 10.1186/s12870-023-04524-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/13/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Non-target site resistance (NTSR) to herbicides is a polygenic trait that threatens the chemical control of agricultural weeds. NTSR involves differential regulation of plant secondary metabolism pathways, but its precise genetic determinisms remain fairly unclear. Full-transcriptome sequencing had previously been implemented to identify NTSR genes. However, this approach had generally been applied to a single weed population, limiting our insight into the diversity of NTSR mechanisms. Here, we sought to explore the diversity of NTSR mechanisms in common ragweed (Ambrosia artemisiifolia L.) by investigating six field populations from different French regions where NTSR to acetolactate-synthase-inhibiting herbicides had evolved. RESULTS A de novo transcriptome assembly (51,242 contigs, 80.2% completeness) was generated as a reference to seek genes differentially expressed between sensitive and resistant plants from the six populations. Overall, 4,609 constitutively differentially expressed genes were identified, of which none were common to all populations, and only 197 were shared by several populations. Similarly, population-specific transcriptomic response was observed when investigating early herbicide response. Gene ontology enrichment analysis highlighted the involvement of stress response and regulatory pathways, before and after treatment. The expression of 121 candidate constitutive NTSR genes including CYP71, CYP72, CYP94, oxidoreductase, ABC transporters, gluco and glycosyltransferases was measured in 220 phenotyped plants. Differential expression was validated in at least one ragweed population for 28 candidate genes. We investigated whether expression patterns at some combinations of candidate genes could predict phenotype. Within populations, prediction accuracy decreased when applied to an additional, independent plant sampling. Overall, a wide variety of genes linked to NTSR was identified within and among ragweed populations, of which only a subset was captured in our experiments. CONCLUSION Our results highlight the complexity and the diversity of NTSR mechanisms that can evolve in a weed species in response to herbicide selective pressure. They strongly point to a non-redundant, population-specific evolution of NTSR to ALS inhibitors in ragweed. It also alerts on the potential of common ragweed for rapid adaptation to drastic environmental or human-driven selective pressures.
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Affiliation(s)
- Ingvild Loubet
- INRAE, Agroécologie, Dijon, France
- Université de Lyon, Anses, INRAE, USC CASPER, Lyon, France
| | | | | | | | | | - Benoit Barrès
- Université de Lyon, Anses, INRAE, USC CASPER, Lyon, France
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Coates BS, Deleury E, Gassmann AJ, Hibbard BE, Meinke LJ, Miller NJ, Petzold-Maxwell J, French BW, Sappington TW, Siegfried BD, Guillemaud T. Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots. BMC Genomics 2021; 22:639. [PMID: 34479486 PMCID: PMC8418000 DOI: 10.1186/s12864-021-07932-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/04/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Resistance of pest insect species to insecticides, including B. thuringiensis (Bt) pesticidal proteins expressed by transgenic plants, is a threat to global food security. Despite the western corn rootworm, Diabrotica virgifera virgifera, being a major pest of maize and having populations showing increasing levels of resistance to hybrids expressing Bt pesticidal proteins, the cell mechanisms leading to mortality are not fully understood. RESULTS Twenty unique RNA-seq libraries from the Bt susceptible D. v. virgifera inbred line Ped12, representing all growth stages and a range of different adult and larval exposures, were assembled into a reference transcriptome. Ten-day exposures of Ped12 larvae to transgenic Bt Cry3Bb1 and Gpp34/Tpp35Ab1 maize roots showed significant differential expression of 1055 and 1374 transcripts, respectively, compared to cohorts on non-Bt maize. Among these, 696 were differentially expressed in both Cry3Bb1 and Gpp34/Tpp35Ab1 maize exposures. Differentially-expressed transcripts encoded protein domains putatively involved in detoxification, metabolism, binding, and transport, were, in part, shared among transcripts that changed significantly following exposures to the entomopathogens Heterorhabditis bacteriophora and Metarhizium anisopliae. Differentially expressed transcripts in common between Bt and entomopathogen treatments encode proteins in general stress response pathways, including putative Bt binding receptors from the ATP binding cassette transporter superfamily. Putative caspases, pro- and anti-apoptotic factors, as well as endoplasmic reticulum (ER) stress-response factors were identified among transcripts uniquely up-regulated following exposure to either Bt protein. CONCLUSIONS Our study suggests that the up-regulation of genes involved in ER stress management and apoptotic progression may be important in determining cell fate following exposure of susceptible D. v. virgifera larvae to Bt maize roots. This study provides novel insights into insect response to Bt intoxication, and a possible framework for future investigations of resistance mechanisms.
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Affiliation(s)
- Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, 103 Genetics Laboratory, Iowa State University, Ames, IA, 50011, USA.
| | | | | | | | - Lance J Meinke
- Department of Entomology, University of Nebraska, Lincoln, NE, USA
| | | | | | - B Wade French
- USDA-ARS, North Central Agricultural Research Laboratory, Brookings, SD, USA
| | - Thomas W Sappington
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, 103 Genetics Laboratory, Iowa State University, Ames, IA, 50011, USA
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6
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Kacprzyk J, Locatelli AG, Hughes GM, Huang Z, Clarke M, Gorbunova V, Sacchi C, Stewart GS, Teeling EC. Evolution of mammalian longevity: age-related increase in autophagy in bats compared to other mammals. Aging (Albany NY) 2021; 13:7998-8025. [PMID: 33744862 PMCID: PMC8034928 DOI: 10.18632/aging.202852] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/05/2021] [Indexed: 12/30/2022]
Abstract
Autophagy maintains cellular homeostasis and its dysfunction has been implicated in aging. Bats are the longest-lived mammals for their size, but the molecular mechanisms underlying their extended healthspan are not well understood. Here, drawing on >8 years of mark-recapture field studies, we report the first longitudinal analysis of autophagy regulation in bats. Mining of published population level aging blood transcriptomes (M. myotis, mouse and human) highlighted a unique increase of autophagy related transcripts with age in bats, but not in other mammals. This bat-specific increase in autophagy transcripts was recapitulated by the western blot determination of the autophagy marker, LC3II/I ratio, in skin primary fibroblasts (Myotis myotis,Pipistrellus kuhlii, mouse), that also showed an increase with age in both bat species. Further phylogenomic selection pressure analyses across eutherian mammals (n=70 taxa; 274 genes) uncovered 10 autophagy-associated genes under selective pressure in bat lineages. These molecular adaptations potentially mediate the exceptional age-related increase of autophagy signalling in bats, which may contribute to their longer healthspans.
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Affiliation(s)
- Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Andrea G. Locatelli
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Present Institutional Address: Division of Genetics and Cell Biology, Fondazione Centro San Raffaele, Via Olgettina, Milano 6020132, Italy
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michael Clarke
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY 14627, USA
| | - Carlotta Sacchi
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gavin S. Stewart
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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Tetreau G, Dhinaut J, Galinier R, Audant-Lacour P, Voisin SN, Arafah K, Chogne M, Hilliou F, Bordes A, Sabarly C, Chan P, Walet-Balieu ML, Vaudry D, Duval D, Bulet P, Coustau C, Moret Y, Gourbal B. Deciphering the molecular mechanisms of mother-to-egg immune protection in the mealworm beetle Tenebrio molitor. PLoS Pathog 2020; 16:e1008935. [PMID: 33057453 PMCID: PMC7591081 DOI: 10.1371/journal.ppat.1008935] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/27/2020] [Accepted: 08/28/2020] [Indexed: 12/19/2022] Open
Abstract
In a number of species, individuals exposed to pathogens can mount an immune response and transmit this immunological experience to their offspring, thereby protecting them against persistent threats. Such vertical transfer of immunity, named trans-generational immune priming (TGIP), has been described in both vertebrates and invertebrates. Although increasingly studied during the last decade, the mechanisms underlying TGIP in invertebrates are still elusive, especially those protecting the earliest offspring life stage, i.e. the embryo developing in the egg. In the present study, we combined different proteomic and transcriptomic approaches to determine whether mothers transfer a "signal" (such as fragments of infecting bacteria), mRNA and/or protein/peptide effectors to protect their eggs against two natural bacterial pathogens, namely the Gram-positive Bacillus thuringiensis and the Gram-negative Serratia entomophila. By taking the mealworm beetle Tenebrio molitor as a biological model, our results suggest that eggs are mainly protected by an active direct transfer of a restricted number of immune proteins and of antimicrobial peptides. In contrast, the present data do not support the involvement of mRNA transfer while the transmission of a "signal", if it happens, is marginal and only occurs within 24h after maternal exposure to bacteria. This work exemplifies how combining global approaches helps to disentangle the different scenarios of a complex trait, providing a comprehensive characterization of TGIP mechanisms in T. molitor. It also paves the way for future alike studies focusing on TGIP in a wide range of invertebrates and vertebrates to identify additional candidates that could be specific to TGIP and to investigate whether the TGIP mechanisms found herein are specific or common to all insect species.
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Affiliation(s)
- Guillaume Tetreau
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Julien Dhinaut
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université Bourgogne-Franche Comté, Dijon, France
| | - Richard Galinier
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Pascaline Audant-Lacour
- CNRS, INRAE, Université Nice Côte d’Azur, UMR 1355–7254 Institut Sophia Agrobiotech, Sophia Antipolis, France
| | | | - Karim Arafah
- Plateforme BioPark d'Archamps, ArchParc, Saint Julien en Genevois, France
| | - Manon Chogne
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université Bourgogne-Franche Comté, Dijon, France
| | - Frédérique Hilliou
- CNRS, INRAE, Université Nice Côte d’Azur, UMR 1355–7254 Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Anaïs Bordes
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Camille Sabarly
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université Bourgogne-Franche Comté, Dijon, France
| | - Philippe Chan
- PISSARO Proteomic Platform, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France
| | - Marie-Laure Walet-Balieu
- PISSARO Proteomic Platform, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France
| | - David Vaudry
- PISSARO Proteomic Platform, Institute for Research and Innovation in Biomedicine, University of Rouen, Rouen, France
| | - David Duval
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Philippe Bulet
- Plateforme BioPark d'Archamps, ArchParc, Saint Julien en Genevois, France
- CR Université Grenoble Alpes, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, La Tronche, France
| | - Christine Coustau
- CNRS, INRAE, Université Nice Côte d’Azur, UMR 1355–7254 Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Yannick Moret
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université Bourgogne-Franche Comté, Dijon, France
| | - Benjamin Gourbal
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
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Silva PIT, Silva-Junior OB, Resende LV, Sousa VA, Aguiar AV, Grattapaglia D. A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze. PLoS One 2020; 15:e0230404. [PMID: 32866150 PMCID: PMC7458329 DOI: 10.1371/journal.pone.0230404] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/05/2020] [Indexed: 12/30/2022] Open
Abstract
High-throughput SNP genotyping has become a precondition to move to higher precision and wider genome coverage genetic analysis of natural and breeding populations of non-model species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation, SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual genome-wide patterns of genetic diversity and structure, challenging previous microsatellite-based assessments. Moreover, SNPs corroborated the known major north-south genetic cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public, user-friendly 3K SNP array for A. angustifolia and a catalog of 44,318 SNPs predicted to provide ~29,000 informative SNPs across ~20,000 loci across the genome, will allow tackling still unsettled questions on its evolutionary history, toward a more comprehensive picture of the origin, past dynamics and future trend of the species' genetic resources. Additionally, but not less importantly, the SNP array described, unlocks the potential to adopt genomic prediction methods to accelerate the still very timid efforts of systematic tree breeding of A. angustifolia.
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Affiliation(s)
- Pedro Italo T. Silva
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
- University of Brasília, Cell Biology Department, Campus Universitário, DF, Brasília, Brazil
| | - Orzenil B. Silva-Junior
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
| | - Lucileide V. Resende
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
| | - Valderes A. Sousa
- Empresa Brasileira de Pesquisa Agropecuária–EMBRAPA Florestas, PR, Colombo, Brazil
| | - Ananda V. Aguiar
- Empresa Brasileira de Pesquisa Agropecuária–EMBRAPA Florestas, PR, Colombo, Brazil
| | - Dario Grattapaglia
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, DF, Brasilia, Brazil
- University of Brasília, Cell Biology Department, Campus Universitário, DF, Brasília, Brazil
- Graduate Program in Genomic Sciences, Universidade Católica de Brasília, Brasília, DF, Brazil
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9
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Nachtigall PG, Kashiwabara AY, Durham AM. CodAn: predictive models for precise identification of coding regions in eukaryotic transcripts. Brief Bioinform 2020; 22:5847603. [PMID: 32460307 PMCID: PMC8138839 DOI: 10.1093/bib/bbaa045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/19/2020] [Accepted: 03/06/2020] [Indexed: 12/13/2022] Open
Abstract
Motivation Characterization of the coding sequences (CDSs) is an essential step in transcriptome annotation. Incorrect identification of CDSs can lead to the prediction of non-existent proteins that can eventually compromise knowledge if databases are populated with similar incorrect predictions made in different genomes. Also, the correct identification of CDSs is important for the characterization of the untranslated regions (UTRs), which are known to be important regulators of the mRNA translation process. Considering this, we present CodAn (Coding sequence Annotator), a new approach to predict confident CDS and UTR regions in full or partial transcriptome sequences in eukaryote species. Results Our analysis revealed that CodAn performs confident predictions on full-length and partial transcripts with the strand sense of the CDS known or unknown. The comparative analysis showed that CodAn presents better overall performance than other approaches, mainly when considering the correct identification of the full CDS (i.e. correct identification of the start and stop codons). In this sense, CodAn is the best tool to be used in projects involving transcriptomic data. Availability CodAn is freely available at https://github.com/pedronachtigall/CodAn. Contact aland@usp.br Supplementary information Supplementary data are available at Briefings in Bioinformatics online.
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Affiliation(s)
| | | | - Alan M Durham
- Corresponding author: Alan M. Durham, Department of Computer Science, Instituto de Matematica e Estatistica, Universidade de Sao Paulo (USP), Brazil. Tel.: +55 11 30919877; Fax: +55 11 30919877; E-mail:
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10
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Del Cortona A, Jackson CJ, Bucchini F, Van Bel M, D'hondt S, Škaloud P, Delwiche CF, Knoll AH, Raven JA, Verbruggen H, Vandepoele K, De Clerck O, Leliaert F. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds. Proc Natl Acad Sci U S A 2020; 117:2551-2559. [PMID: 31911467 PMCID: PMC7007542 DOI: 10.1073/pnas.1910060117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, and multiple types of giant-celled forms.
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Affiliation(s)
- Andrea Del Cortona
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | | | - François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Sofie D'hondt
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, CZ-12800 Prague 2, Czech Republic
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom
- School of Biological Sciences, University of Western Australia, WA 6009, Australia
- Climate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium;
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
| | - Frederik Leliaert
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Meise Botanic Garden, 1860 Meise, Belgium
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11
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Suvorova YM, Korotkova MA, Skryabin KG, Korotkov EV. Search for potential reading frameshifts in cds from Arabidopsis thaliana and other genomes. DNA Res 2019; 26:157-170. [PMID: 30726896 PMCID: PMC6476729 DOI: 10.1093/dnares/dsy046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 12/07/2018] [Indexed: 01/01/2023] Open
Abstract
A new mathematical method for potential reading frameshift detection in protein-coding sequences (cds) was developed. The algorithm is adjusted to the triplet periodicity of each analysed sequence using dynamic programming and a genetic algorithm. This does not require any preliminary training. Using the developed method, cds from the Arabidopsis thaliana genome were analysed. In total, the algorithm found 9,930 sequences containing one or more potential reading frameshift(s). This is ∼21% of all analysed sequences of the genome. The Type I and Type II error rates were estimated as 11% and 30%, respectively. Similar results were obtained for the genomes of Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Rattus norvegicus and Xenopus tropicalis. Also, the developed algorithm was tested on 17 bacterial genomes. We compared our results with the previously obtained data on the search for potential reading frameshifts in these genomes. This study discussed the possibility that the reading frameshift seems like a relatively frequently encountered mutation; and this mutation could participate in the creation of new genes and proteins.
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Affiliation(s)
- Y M Suvorova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - M A Korotkova
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Moscow, Russia
| | - K G Skryabin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - E V Korotkov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.,National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Moscow, Russia
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12
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Longitudinal comparative transcriptomics reveals unique mechanisms underlying extended healthspan in bats. Nat Ecol Evol 2019; 3:1110-1120. [DOI: 10.1038/s41559-019-0913-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/01/2019] [Indexed: 12/22/2022]
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13
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Suvorova YM, Pugacheva VM, Korotkov EV. A Database of Potential Reading Frame Shifts in Coding Sequences from Different Eukaryotic Genomes. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350919030217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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14
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Soewarto J, Hamelin C, Bocs S, Mournet P, Vignes H, Berger A, Armero A, Martin G, Dereeper A, Sarah G, Carriconde F, Maggia L. Transcriptome data from three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust ( Austropuccinia psidii). Data Brief 2019; 22:794-811. [PMID: 30766900 PMCID: PMC6362868 DOI: 10.1016/j.dib.2018.12.080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/14/2018] [Accepted: 12/24/2018] [Indexed: 12/30/2022] Open
Abstract
The myrtle rust disease, caused by the fungus Austropuccinia psidii, infects a wide range of host species within the Myrtaceae family worldwide. Since its first report in 2013 in New Caledonia, it was found on various types of native environments where Myrtaceae are the dominant or codominant species, as well as in several commercial nurseries. It is now considered as a significant threat to ecosystems biodiversity and Myrtaceae-related economy. The use of predictive molecular markers for resistance against myrtle rust is currently the most cost-effective and ecological approach to control the disease. Such an approach for neo Caledonian endemic Myrtaceae species was not possible because of the lack of genomic resources. The recent advancement in new generation sequencing technologies accompanied with relevant bioinformatics tools now provide new research opportunity for work in non-model organism at the transcriptomic level. The present study focuses on transcriptome analysis on three Myrtaceae species endemic to New Caledonia (Arillastrum gummiferum, Syzygium longifolium and Tristaniopsis glauca) that display contrasting responses to the pathogen (non-infected vs infected). Differential gene expression (DGE) and variant calling analysis were conducted on each species. We combined a dual approach by using 1) the annotated reference genome of a related Myrtaceae species (Eucalyptus grandis) and 2) a de novo transcriptomes of each species.
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Affiliation(s)
- Julia Soewarto
- Institut Agronomique néo-Calédonien (IAC), 98848 Nouméa, New Caledonia
| | - Chantal Hamelin
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,South Green Bioinformatics Platform, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,South Green Bioinformatics Platform, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Pierre Mournet
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Hélène Vignes
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Angélique Berger
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Alix Armero
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Alexis Dereeper
- IRD, UMR IPME (IRD-UM2-Cirad) 911, avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
| | - Gautier Sarah
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,South Green Bioinformatics Platform, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Fabian Carriconde
- Institut Agronomique néo-Calédonien (IAC), 98848 Nouméa, New Caledonia
| | - Laurent Maggia
- Institut Agronomique néo-Calédonien (IAC), 98848 Nouméa, New Caledonia.,CIRAD, UMR AGAP, 98800 Nouméa, New Caledonia.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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15
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Jaquiéry J, Peccoud J, Ouisse T, Legeai F, Prunier-Leterme N, Gouin A, Nouhaud P, Brisson JA, Bickel R, Purandare S, Poulain J, Battail C, Lemaitre C, Mieuzet L, Le Trionnaire G, Simon JC, Rispe C. Disentangling the Causes for Faster-X Evolution in Aphids. Genome Biol Evol 2018; 10:507-520. [PMID: 29360959 PMCID: PMC5798017 DOI: 10.1093/gbe/evy015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2018] [Indexed: 12/22/2022] Open
Abstract
The faster evolution of X chromosomes has been documented in several species, and results from the increased efficiency of selection on recessive alleles in hemizygous males and/or from increased drift due to the smaller effective population size of X chromosomes. Aphids are excellent models for evaluating the importance of selection in faster-X evolution because their peculiar life cycle and unusual inheritance of sex chromosomes should generally lead to equivalent effective population sizes for X and autosomes. Because we lack a high-density genetic map for the pea aphid, whose complete genome has been sequenced, we first assigned its entire genome to the X or autosomes based on ratios of sequencing depth in males (X0) to females (XX). Then, we computed nonsynonymous to synonymous substitutions ratios (dN/dS) for the pea aphid gene set and found faster evolution of X-linked genes. Our analyses of substitution rates, together with polymorphism and expression data, showed that relaxed selection is likely to be the greatest contributor to faster-X because a large fraction of X-linked genes are expressed at low rates and thus escape selection. Yet, a minor role for positive selection is also suggested by the difference between substitution rates for X and autosomes for male-biased genes (but not for asexual female-biased genes) and by lower Tajima’s D for X-linked compared with autosomal genes with highly male-biased expression patterns. This study highlights the relevance of organisms displaying alternative chromosomal inheritance to the understanding of forces shaping genome evolution.
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Affiliation(s)
- Julie Jaquiéry
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,CNRS UMR 6553 ECOBIO, Université de Rennes 1, France
| | - Jean Peccoud
- CNRS UMR 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, France
| | | | - Fabrice Legeai
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | | | - Anais Gouin
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | - Pierre Nouhaud
- Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | | | - Ryan Bickel
- Department of Biology, University of Rochester
| | - Swapna Purandare
- Multidisciplinary Center for Advance Research and Studies (MCARS), Jamia Millia Islamia, New Delhi, India
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Christophe Battail
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Centre National de Génotypage (CNG), Evry, France
| | - Claire Lemaitre
- INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | | | | | | | - Claude Rispe
- BIOEPAR, INRA, ONIRIS, La Chantrerie, Nantes, France
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16
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Meléndez-Rosa J, Bi K, Lacey EA. Genomic analysis of MHC-based mate choice in the monogamous California mouse. Behav Ecol 2018; 29:1167-1180. [PMID: 30214134 PMCID: PMC6129947 DOI: 10.1093/beheco/ary096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 06/13/2018] [Accepted: 06/22/2018] [Indexed: 01/06/2023] Open
Abstract
Variation at Major Histocompatibility Complex (MHC) genes is thought to be an important mechanism underlying mate choice in vertebrates, with individuals typically predicted to prefer MHC-dissimilar reproductive partners. However, analyses based on individual MHC loci have generated contradictory results regarding the role of these genes in mate-choice decisions. To provide a more comprehensive assessment of relationships between MHC variation and mating behavior, we used an exome capture strategy to characterize variability at 13 MHC loci, 312 innate immune system genes, and 1044 nonimmune genes in 25 obligate monogamous pairs of California mice (Peromyscus californicus) from 2 free-living populations of this species in Monterey County, California. Pairwise genotypic comparisons and analyses of SNP-based allelic differences failed to detect disassortative mating based on MHC variability; reproductive partners were not more dissimilar than randomly generated male-female pairs at MHC, innate or nonimmune loci. Within populations, individuals tended to be more closely related at MHC genes than at innate or nonimmune genes. Consistent with the functional role of immunogenes, the 2 study populations were highly differentiated at MHC and innate genes but not at nonimmune loci. Collectively, our results suggest that MHC genetic variation in California mice reflects local differences in pathogen exposure rather than disassortative mating based on variability at MHC Class I and II genes.
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Affiliation(s)
- Jesyka Meléndez-Rosa
- Department of Integrative Biology, University of California, Berkeley, CA
- Museum of Vertebrate Zoology, University of California, Berkeley Valley Life Sciences Bldg., Berkeley, CA
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley Valley Life Sciences Bldg., Berkeley, CA
- Computational Genomics Resource, MC University of California, Berkeley, CA
| | - Eileen A Lacey
- Department of Integrative Biology, University of California, Berkeley, CA
- Museum of Vertebrate Zoology, University of California, Berkeley Valley Life Sciences Bldg., Berkeley, CA
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17
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De Clerck O, Kao SM, Bogaert KA, Blomme J, Foflonker F, Kwantes M, Vancaester E, Vanderstraeten L, Aydogdu E, Boesger J, Califano G, Charrier B, Clewes R, Del Cortona A, D’Hondt S, Fernandez-Pozo N, Gachon CM, Hanikenne M, Lattermann L, Leliaert F, Liu X, Maggs CA, Popper ZA, Raven JA, Van Bel M, Wilhelmsson PK, Bhattacharya D, Coates JC, Rensing SA, Van Der Straeten D, Vardi A, Sterck L, Vandepoele K, Van de Peer Y, Wichard T, Bothwell JH. Insights into the Evolution of Multicellularity from the Sea Lettuce Genome. Curr Biol 2018; 28:2921-2933.e5. [DOI: 10.1016/j.cub.2018.08.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/21/2018] [Accepted: 08/03/2018] [Indexed: 10/28/2022]
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18
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Ueno S, Nakamura Y, Kobayashi M, Terashima S, Ishizuka W, Uchiyama K, Tsumura Y, Yano K, Goto S. TodoFirGene: Developing Transcriptome Resources for Genetic Analysis of Abies sachalinensis. PLANT & CELL PHYSIOLOGY 2018; 59:1276-1284. [PMID: 29566239 DOI: 10.1093/pcp/pcy058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Todo-matsu (Abies sachalinensis) is one of the most important forestry species in Hokkaido, Japan and is distributed from near sea level to the alpine zone. Due to its wide spatial distribution, the species adapts to its environment, displaying phenotypes of ecological relevance. In order to identify candidate genes under natural selection, we collected the transcriptome from the female and male flower, leaf and inner bark. De novo assembly with 34.7 Gb of sequencing reads produced 158,542 transcripts from 69,618 loci, whose estimated coverage reached 95.6% of conserved eukaryotic genes. Homology searches against publicly available databases identified 134,190 (84.6%) transcripts with at least one hit. In total, 28,944 simple sequence repeats (SSRs) and 80,758 single nucleotide variants (SNVs) were detected from 23,570 (14.9%) and 25,366 (16.0%) transcripts, which were valuable for use in genetic analysis of the species. All the annotations were included in a relational database, TodoFirGene, which provides an interface for various queries and homology search, and can be accessed at http://plantomics.mind.meiji.ac.jp/todomatsu/. This database hosts not only the A. sachalinensis transcriptome but also links to the proteomes of 13 other species, allowing a comparative genomic study of plant species.
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Affiliation(s)
- Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687 Japan
| | - Yukino Nakamura
- School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Masaaki Kobayashi
- School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Shin Terashima
- School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Wataru Ishizuka
- Forestry Research Institute, Hokkaido Research Organization, Koshunai, Bibai, Hokkaido, 079-0198 Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687 Japan
| | - Yoshihiko Tsumura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687 Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572 Japan
| | - Kentaro Yano
- School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Susumu Goto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
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19
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Bolger ME, Arsova B, Usadel B. Plant genome and transcriptome annotations: from misconceptions to simple solutions. Brief Bioinform 2018; 19:437-449. [PMID: 28062412 PMCID: PMC5952960 DOI: 10.1093/bib/bbw135] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/29/2016] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome and transcriptome sequencing has become orders of magnitudes cheaper and more efficient, often the functional annotation process is lagging behind. This might be hampered by the lack of a comprehensive enumeration of simple-to-use tools available to the plant researcher. In this comprehensive review, we present (i) typical ontologies to be used in the plant sciences, (ii) useful databases and resources used for functional annotation, (iii) what to expect from an annotated plant genome, (iv) an automated annotation pipeline and (v) a recipe and reference chart outlining typical steps used to annotate plant genomes/transcriptomes using publicly available resources.
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Affiliation(s)
- Marie E Bolger
- Forschungszentrum Jülich, Wilhelm Johnen Str, Jülich, Germany
| | - Borjana Arsova
- Forschungszentrum Jülich, Wilhelm Johnen Str, Jülich, Germany
- FRS-FNRS Chargé de Recherches, Functional Genomics and Plant Molecular Imaging Center for Protein Engineering (CIP), Dpt of Life Sciences, University of Liège, Quartier de la Vallée, 1, Chemin de la Vallée, 4 - Bât B22, 4000 LIEGE, Belgium
| | - Björn Usadel
- Forschungszentrum Jülich, Wilhelm Johnen Str, Jülich, Germany
- RWTH Aachen University, Institute for Biology I Botany, BioSC, Worringer Weg 3, Aachen, Germany
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20
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Diesner M, Gallot A, Binz H, Gaertner C, Vitecek S, Kahnt J, Schachtner J, Jacquin-Joly E, Gadenne C. Mating-Induced Differential Peptidomics of Neuropeptides and Protein Hormones in Agrotis ipsilon Moths. J Proteome Res 2018; 17:1397-1414. [PMID: 29466015 DOI: 10.1021/acs.jproteome.7b00779] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In many insects, mating induces drastic changes in male and female responses to sex pheromones or host-plant odors. In the male moth Agrotis ipsilon, mating induces a transient inhibition of behavioral and neuronal responses to the female sex pheromone. As neuropeptides and peptide hormones regulate most behavioral processes, we hypothesize that they could be involved in this mating-dependent olfactory plasticity. Here we used next-generation RNA sequencing and a combination of liquid chromatography, matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, and direct tissue profiling to analyze the transcriptome and peptidome of different brain compartments in virgin and mated males and females of A. ipsilon. We identified 37 transcripts encoding putative neuropeptide precursors and 54 putative bioactive neuropeptides from 23 neuropeptide precursors (70 sequences in total, 25 neuropeptide precursors) in different areas of the central nervous system including the antennal lobes, the gnathal ganglion, and the corpora cardiaca-corpora allata complex. Comparisons between virgin and mated males and females revealed tissue-specific differences in peptide composition between sexes and according to physiological state. Mated males showed postmating differences in neuropeptide occurrence, which could participate in the mating-induced olfactory plasticity.
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Affiliation(s)
- Max Diesner
- Department of Biology - Animal Physiology , Philipps University Marburg , D-35032 Marburg , Germany
| | - Aurore Gallot
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (UMR iEES-Paris) , INRA , Route de Saint-Cyr , 78026 Versailles Cedex , France
| | - Hellena Binz
- Institute of Zoology , University of Mainz , Johann-Joachim-Becher-Weg 6 , 55128 Mainz , Germany
| | - Cyril Gaertner
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (UMR iEES-Paris) , INRA , Route de Saint-Cyr , 78026 Versailles Cedex , France
| | - Simon Vitecek
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (UMR iEES-Paris) , INRA , Route de Saint-Cyr , 78026 Versailles Cedex , France
| | - Jörg Kahnt
- Max-Planck-Institute für terrestrische Mikrobiologie, Marburg , Germany
| | - Joachim Schachtner
- Department of Biology - Animal Physiology , Philipps University Marburg , D-35032 Marburg , Germany
| | - Emmanuelle Jacquin-Joly
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (UMR iEES-Paris) , INRA , Route de Saint-Cyr , 78026 Versailles Cedex , France
| | - Christophe Gadenne
- Institut de Génétique, Environnement et Protection des Plantes (UMR IGEPP) , INRA , Agrocampus Ouest, rue Le Nôtre , 49054 Angers cedex 01 , France
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21
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Gschloessl B, Dorkeld F, Berges H, Beydon G, Bouchez O, Branco M, Bretaudeau A, Burban C, Dubois E, Gauthier P, Lhuillier E, Nichols J, Nidelet S, Rocha S, Sauné L, Streiff R, Gautier M, Kerdelhué C. Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae). Mol Ecol Resour 2018; 18:602-619. [PMID: 29352511 DOI: 10.1111/1755-0998.12756] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 12/23/2017] [Accepted: 01/03/2018] [Indexed: 12/15/2022]
Abstract
The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture. Using a well-studied population from Portugal with peculiar phenological characteristics, the karyotype was first determined and a first draft genome of 537 Mb total length was assembled into 68,292 scaffolds (N50 = 164 kb). From this genome assembly, 29,415 coding genes were predicted. To circumvent some limitations for fine-scale physical mapping of genomic regions of interest, a 3X coverage BAC library was also developed. In particular, 11 BACs from this library were individually sequenced to assess the assembly quality. Additionally, de novo transcriptomic resources were generated from various developmental stages sequenced with HiSeq and MiSeq Illumina technologies. The reads were de novo assembled into 62,376 and 63,175 transcripts, respectively. Then, a robust subset of the genome-predicted coding genes, the de novo transcriptome assemblies and previously published 454/Sanger data were clustered to obtain a high-quality and comprehensive reference transcriptome consisting of 29,701 bona fide unigenes. These sequences covered 99% of the cegma and 88% of the busco highly conserved eukaryotic genes and 84% of the busco arthropod gene set. Moreover, 90% of these transcripts could be localized on the draft genome. The described information is available via a genome annotation portal (http://bipaa.genouest.org/sp/thaumetopoea_pityocampa/).
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Affiliation(s)
- B Gschloessl
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - F Dorkeld
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - H Berges
- INRA-CNRGV, Castanet Tolosan Cedex, France
| | - G Beydon
- INRA-CNRGV, Castanet Tolosan Cedex, France
| | - O Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, INRA Auzeville, Castanet Tolosan Cedex, France
| | - M Branco
- Forest Research Center (CEF), Instituto Superior de Agronomia (ISA), University of Lisbon (ULisboa), Lisboa, Portugal
| | - A Bretaudeau
- INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Rennes, France.,INRIA, IRISA, GenOuest Core Facility, Rennes, France
| | - C Burban
- BIOGECO, INRA, Univ. Bordeaux, Cestas, France
| | - E Dubois
- Plateforme MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle IGF-sud, UMR 5203 CNRS-U 661 INSERM-Université de Montpellier, Montpellier Cedex 05, France
| | - P Gauthier
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - E Lhuillier
- INRA, US 1426, GeT-PlaGe, Genotoul, INRA Auzeville, Castanet Tolosan Cedex, France
| | - J Nichols
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, UK
| | - S Nidelet
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.,Plateforme MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle IGF-sud, UMR 5203 CNRS-U 661 INSERM-Université de Montpellier, Montpellier Cedex 05, France
| | - S Rocha
- Forest Research Center (CEF), Instituto Superior de Agronomia (ISA), University of Lisbon (ULisboa), Lisboa, Portugal
| | - L Sauné
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - R Streiff
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - M Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - C Kerdelhué
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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22
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Dias RO, Cardoso C, Pimentel AC, Damasceno TF, Ferreira C, Terra WR. The roles of mucus-forming mucins, peritrophins and peritrophins with mucin domains in the insect midgut. INSECT MOLECULAR BIOLOGY 2018; 27:46-60. [PMID: 28833767 DOI: 10.1111/imb.12340] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Most insects have a gut lined with a peritrophic membrane (PM) consisting of chitin and proteins, mainly peritrophins that have chitin-binding domains. The PM is proposed to originate from mucus-forming mucins (Mf-mucins), which acquired a chitin-binding domain that interlocked with chitin, replacing mucus in function. We evaluated the expression of Mf-mucins and peritrophins by RNA-sequencing (RNA-seq) throughout the midgut of four distantly related insects. Mf-mucins were identified as proteins with high o-glycosylation and a series of uninterrupted Pro/Thr/Ser residues. The results demonstrate that the mucus layer is widespread in insects, and suggest that insect Mf-mucins are derived from those found in other animals by the loss of the cysteine knot and von Willebrand domains. The data also support a role of Mf-mucins in protecting the middle midgut of Musca domestica against acidic buffers. Mf-mucins may also produce a jelly-like material associated with the PM that immobilizes digestive enzymes in Spodoptera frugiperda. Peritrophins with a domain similar to Mf-mucins may be close to the ancestor of peritrophins. Expression data of peritrophins and chitin synthase genes throughout the midgut of M. domestica, S. frugiperda and Tenebrio molitor indicated that peritrophins were incorporated along the PM, according to their preferential sites of formation. Finally, the data support the view that mucus has functions distinct from the PM.
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Affiliation(s)
- R O Dias
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | - C Cardoso
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | - A C Pimentel
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | - T F Damasceno
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | - C Ferreira
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | - W R Terra
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
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23
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Gschloessl B, Dorkeld F, Audiot P, Bretaudeau A, Kerdelhué C, Streiff R. De novo genome and transcriptome resources of the Adzuki bean borer Ostrinia scapulalis (Lepidoptera: Crambidae). Data Brief 2018; 17:781-787. [PMID: 29785409 PMCID: PMC5958680 DOI: 10.1016/j.dib.2018.01.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 11/25/2022] Open
Abstract
We present a draft genome assembly with a de novo prediction and automated functional annotation of coding genes, and a reference transcriptome of the Adzuki bean borer, Ostrinia scapulalis, based on RNA sequencing of various tissues and developmental stages. The genome assembly spans 419 Mb, has a GC content of 37.4% and includes 26,120 predicted coding genes. The reference transcriptome holds 33,080 unigenes and contains a high proportion of a set of genes conserved in eukaryotes and arthropods, used as quality assessment of the reconstructed transcripts. The new genomic and transcriptomic data presented here significantly enrich the public sequence databases for the Crambidae and Lepidoptera, and represent useful resources for future researches related to the evolution and the adaptation of phytophagous moths. The genome and transcriptome assemblies have been deposited and made accessible via a NCBI BioProject (id PRJNA390510) and the LepidoDB database (http://bipaa.genouest.org/sp/ostrinia_scapulalis/).
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Affiliation(s)
- B Gschloessl
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - F Dorkeld
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - P Audiot
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - A Bretaudeau
- INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France.,INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | - C Kerdelhué
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - R Streiff
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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24
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Huang Z, Teeling EC. ExUTR: a novel pipeline for large-scale prediction of 3'-UTR sequences from NGS data. BMC Genomics 2017; 18:847. [PMID: 29110697 PMCID: PMC5674806 DOI: 10.1186/s12864-017-4241-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 10/25/2017] [Indexed: 12/11/2022] Open
Abstract
Background The three prime untranslated region (3′-UTR) is known to play a pivotal role in modulating gene expression by determining the fate of mRNA. Many crucial developmental events, such as mammalian spermatogenesis, tissue patterning, sex determination and neurogenesis, rely heavily on post-transcriptional regulation by the 3′-UTR. However, 3′-UTR biology seems to be a relatively untapped field, with only limited tools and 3′-UTR resources available. To elucidate the regulatory mechanisms of the 3′-UTR on gene expression, firstly the 3′-UTR sequences must be identified. Current 3′-UTR mining tools, such as GETUTR, 3USS and UTRscan, all depend on a well-annotated reference genome or curated 3′-UTR sequences, which hinders their application on a myriad of non-model organisms where the genomes are not available. To address these issues, the establishment of an NGS-based, automated pipeline is urgently needed for genome-wide 3′-UTR prediction in the absence of reference genomes. Results Here, we propose ExUTR, a novel NGS-based pipeline to predict and retrieve 3′-UTR sequences from RNA-Seq experiments, particularly designed for non-model species lacking well-annotated genomes. This pipeline integrates cutting-edge bioinformatics tools, databases (Uniprot and UTRdb) and novel in-house Perl scripts, implementing a fully automated workflow. By taking transcriptome assemblies as inputs, this pipeline identifies 3′-UTR signals based primarily on the intrinsic features of transcripts, and outputs predicted 3′-UTR candidates together with associated annotations. In addition, ExUTR only requires minimal computational resources, which facilitates its implementation on a standard desktop computer with reasonable runtime, making it affordable to use for most laboratories. We also demonstrate the functionality and extensibility of this pipeline using publically available RNA-Seq data from both model and non-model species, and further validate the accuracy of predicted 3′-UTR using both well-characterized 3′-UTR resources and 3P–Seq data. Conclusions ExUTR is a practical and powerful workflow that enables rapid genome-wide 3′-UTR discovery from NGS data. The candidates predicted through this pipeline will further advance the study of miRNA target prediction, cis elements in 3′-UTR and the evolution and biology of 3′-UTRs. Being independent of a well-annotated reference genome will dramatically expand its application to much broader research area, encompassing all species for which RNA-Seq is available. Electronic supplementary material The online version of this article (10.1186/s12864-017-4241-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zixia Huang
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Emma C Teeling
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
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25
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Zheng P, Wang M, Li C, Sun X, Wang X, Sun Y, Sun S. Insights into deep-sea adaptations and host-symbiont interactions: A comparative transcriptome study on Bathymodiolus
mussels and their coastal relatives. Mol Ecol 2017; 26:5133-5148. [DOI: 10.1111/mec.14160] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Ping Zheng
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
| | - Minxiao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- Deep Sea Research Center; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
| | - Chaolun Li
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
- Deep Sea Research Center; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- Laboratory for Marine Ecology and Environmental Science; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | | | - Xiaocheng Wang
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
| | - Yan Sun
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
| | - Song Sun
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
- Laboratory for Marine Ecology and Environmental Science; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
- Jiaozhou Bay Marine Ecosystem Research Station; Chinese Academy of Sciences; Qingdao China
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26
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Sundell D, Street NR, Kumar M, Mellerowicz EJ, Kucukoglu M, Johnsson C, Kumar V, Mannapperuma C, Delhomme N, Nilsson O, Tuominen H, Pesquet E, Fischer U, Niittylä T, Sundberg B, Hvidsten TR. AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula. THE PLANT CELL 2017; 29:1585-1604. [PMID: 28655750 PMCID: PMC5559752 DOI: 10.1105/tpc.17.00153] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/12/2017] [Accepted: 06/24/2017] [Indexed: 05/17/2023]
Abstract
Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer elite varieties will benefit from improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated high-spatial-resolution RNA sequencing data spanning the secondary phloem, vascular cambium, and wood-forming tissues of Populus tremula The transcriptome comprised 28,294 expressed, annotated genes, 78 novel protein-coding genes, and 567 putative long intergenic noncoding RNAs. Most paralogs originating from the Salicaceae whole-genome duplication had diverged expression, with the exception of those highly expressed during secondary cell wall deposition. Coexpression network analyses revealed that regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. A comparative analysis revealed that a majority of these modules are conserved in Picea abies The high spatial resolution of our data enabled identification of novel roles for characterized genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. An associated web resource (AspWood, http://aspwood.popgenie.org) provides interactive tools for exploring the expression profiles and coexpression network.
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Affiliation(s)
- David Sundell
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Manoj Kumar
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umeå, Sweden
| | - Ewa J Mellerowicz
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umeå, Sweden
| | - Melis Kucukoglu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umeå, Sweden
| | - Christoffer Johnsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umeå, Sweden
| | - Vikash Kumar
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umeå, Sweden
| | - Chanaka Mannapperuma
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Ove Nilsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umeå, Sweden
| | - Hannele Tuominen
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Edouard Pesquet
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Urs Fischer
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umeå, Sweden
| | - Totte Niittylä
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umeå, Sweden
| | - Björn Sundberg
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 87 Umeå, Sweden
| | - Torgeir R Hvidsten
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1433 Ås, Norway
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27
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Moreira NR, Cardoso C, Dias RO, Ferreira C, Terra WR. A physiologically-oriented transcriptomic analysis of the midgut of Tenebrio molitor. JOURNAL OF INSECT PHYSIOLOGY 2017; 99:58-66. [PMID: 28341416 DOI: 10.1016/j.jinsphys.2017.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 03/13/2017] [Accepted: 03/20/2017] [Indexed: 06/06/2023]
Abstract
Physiological data showed that T. molitor midgut is buffered at pH 5.6 at the two anterior thirds and at 7.9 at the posterior third. Furthermore, water is absorbed and secreted at the anterior and posterior midgut, respectively, driving a midgut counter flux of fluid. To look for the molecular mechanisms underlying these phenomena and nutrient absorption as well, a transcriptomic approach was used. For this, 11 types of transporters were chosen from the midgut transcriptome obtained by pyrosequencing (Roche 454). After annotation with the aid of databanks and manual curation, the sequences were validated by RT-PCR. The expression level of each gene at anterior, middle and posterior midgut and carcass (larva less midgut) was evaluated by RNA-seq taking into account reference sequences based on 454 contigs and reads obtained by Illumina sequencing. The data showed that sugar and amino acid uniporters and symporters are expressed along the whole midgut. In the anterior midgut are found transporters for NH3 and NH4+ that with a chloride channel may be responsible for acidifying the lumen. At the posterior midgut, bicarbonate-Cl- antiporter with bicarbonate supplied by carbonic anhydrase may alkalinize the lumen. Water absorption caused mainly by an anterior Na+-K+-2Cl- symporter and water secretion caused by a posterior K+-Cl- may drive the midgut counter flux. Transporters that complement the action of those described were also found.
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Affiliation(s)
- Nathalia R Moreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil
| | - Christiane Cardoso
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil
| | - Renata O Dias
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil
| | - Clelia Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil
| | - Walter R Terra
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil.
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28
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Diversity in sequences, post-translational modifications and expected pharmacological activities of toxins from four Conus species revealed by the combination of cutting-edge proteomics, transcriptomics and bioinformatics. Toxicon 2017; 130:116-125. [DOI: 10.1016/j.toxicon.2017.02.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/13/2017] [Accepted: 02/16/2017] [Indexed: 01/05/2023]
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29
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Armero A, Baudouin L, Bocs S, This D. Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut. PLoS One 2017; 12:e0173300. [PMID: 28334050 PMCID: PMC5363918 DOI: 10.1371/journal.pone.0173300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 02/17/2017] [Indexed: 01/20/2023] Open
Abstract
The palms are a family of tropical origin and one of the main constituents of the ecosystems of these regions around the world. The two main species of palm represent different challenges: coconut (Cocos nucifera L.) is a source of multiple goods and services in tropical communities, while oil palm (Elaeis guineensis Jacq) is the main protagonist of the oil market. In this study, we present a workflow that exploits the comparative genomics between a target species (coconut) and a reference species (oil palm) to improve the transcriptomic data, providing a proteome useful to answer functional or evolutionary questions. This workflow reduces redundancy and fragmentation, two inherent problems of transcriptomic data, while preserving the functional representation of the target species. Our approach was validated in Arabidopsis thaliana using Arabidopsis lyrata and Capsella rubella as references species. This analysis showed the high sensitivity and specificity of our strategy, relatively independent of the reference proteome. The workflow increased the length of proteins products in A. thaliana by 13%, allowing, often, to recover 100% of the protein sequence length. In addition redundancy was reduced by a factor greater than 3. In coconut, the approach generated 29,366 proteins, 1,246 of these proteins deriving from new contigs obtained with the BRANCH software. The coconut proteome presented a functional profile similar to that observed in rice and an important number of metabolic pathways related to secondary metabolism. The new sequences found with BRANCH software were enriched in functions related to biotic stress. Our strategy can be used as a complementary step to de novo transcriptome assembly to get a representative proteome of a target species. The results of the current analysis are available on the website PalmComparomics (http://palm-comparomics.southgreen.fr/).
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Affiliation(s)
- Alix Armero
- Montpellier SupAgro, UMR AGAP, Montpellier, France
| | | | - Stéphanie Bocs
- CIRAD, UMR AGAP, Montpellier, France
- South Green Bioinformatics Platform, Montpellier, France
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30
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Cardoso JMS, Anjo SI, Fonseca L, Egas C, Manadas B, Abrantes I. Bursaphelenchus xylophilus and B. mucronatus secretomes: a comparative proteomic analysis. Sci Rep 2016; 6:39007. [PMID: 27941947 PMCID: PMC5150578 DOI: 10.1038/srep39007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/16/2016] [Indexed: 11/09/2022] Open
Abstract
The pinewood nematode, Bursaphelenchus xylophilus, recognized as a worldwide major forest pest, is a migratory endoparasitic nematode with capacity to feed on pine tissues and also on fungi colonizing the trees. Bursaphelenchus mucronatus, the closest related species, differs from B. xylophilus on its pathogenicity, making this nematode a good candidate for comparative analyses. Secretome profiles of B. xylophilus and B. mucronatus were obtained and proteomic differences were evaluated by quantitative SWATH-MS. From the 681 proteins initially identified, 422 were quantified and compared between B. xylophilus and B. mucronatus secretomes and from these, 243 proteins were found differentially regulated: 158 and 85 proteins were increased in B. xylophilus and B. mucronatus secretomes, respectively. While increased proteins in B. xylophilus secretome revealed a strong enrichment in proteins with peptidase activity, the increased proteins in B. mucronatus secretome were mainly related to oxidative stress responses. The changes in peptidases were evaluated at the transcription level by RT-qPCR, revealing a correlation between the mRNA levels of four cysteine peptidases with secretion levels. The analysis presented expands our knowledge about molecular basis of B. xylophilus and B. mucronatus hosts interaction and supports the hypothesis of a key role of secreted peptidases in B. xylophilus pathogenicity.
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Affiliation(s)
- Joana M. S. Cardoso
- CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Sandra I. Anjo
- Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Luís Fonseca
- CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Conceição Egas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Isabel Abrantes
- CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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Wippler J, Kleiner M, Lott C, Gruhl A, Abraham PE, Giannone RJ, Young JC, Hettich RL, Dubilier N. Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis. BMC Genomics 2016; 17:942. [PMID: 27871231 PMCID: PMC5117596 DOI: 10.1186/s12864-016-3293-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 11/15/2016] [Indexed: 02/07/2023] Open
Abstract
Background The gutless marine worm Olavius algarvensis has a completely reduced digestive and excretory system, and lives in an obligate nutritional symbiosis with bacterial symbionts. While considerable knowledge has been gained of the symbionts, the host has remained largely unstudied. Here, we generated transcriptomes and proteomes of O. algarvensis to better understand how this annelid worm gains nutrition from its symbionts, how it adapted physiologically to a symbiotic lifestyle, and how its innate immune system recognizes and responds to its symbiotic microbiota. Results Key adaptations to the symbiosis include (i) the expression of gut-specific digestive enzymes despite the absence of a gut, most likely for the digestion of symbionts in the host's epidermal cells; (ii) a modified hemoglobin that may bind hydrogen sulfide produced by two of the worm’s symbionts; and (iii) the expression of a very abundant protein for oxygen storage, hemerythrin, that could provide oxygen to the symbionts and the host under anoxic conditions. Additionally, we identified a large repertoire of proteins involved in interactions between the worm's innate immune system and its symbiotic microbiota, such as peptidoglycan recognition proteins, lectins, fibrinogen-related proteins, Toll and scavenger receptors, and antimicrobial proteins. Conclusions We show how this worm, over the course of evolutionary time, has modified widely-used proteins and changed their expression patterns in adaptation to its symbiotic lifestyle and describe expressed components of the innate immune system in a marine oligochaete. Our results provide further support for the recent realization that animals have evolved within the context of their associations with microbes and that their adaptive responses to symbiotic microbiota have led to biological innovations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3293-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juliane Wippler
- Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany. .,Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.
| | - Manuel Kleiner
- Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany. .,Energy Bioengineering and Geomicrobiology Research Group, University of Calgary, Calgary, T2N 1N4, AB, Canada.
| | - Christian Lott
- Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.,HYDRA Institute for Marine Sciences, Elba Field Station, Via del Forno 80, 57034, Campo nell' Elba, (LI), Italy
| | - Alexander Gruhl
- Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Paul E Abraham
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Richard J Giannone
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Jacque C Young
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA.,Present Address: Saul Ewing LLP, 1500 Market Street, 37th Floor, Philadelphia, PA, 19102-2186, USA
| | - Robert L Hettich
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Nicole Dubilier
- Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
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Fuzita FJ, Pinkse MWH, Patane JSL, Verhaert PDEM, Lopes AR. High throughput techniques to reveal the molecular physiology and evolution of digestion in spiders. BMC Genomics 2016; 17:716. [PMID: 27604083 PMCID: PMC5013568 DOI: 10.1186/s12864-016-3048-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 08/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spiders are known for their predatory efficiency and for their high capacity of digesting relatively large prey. They do this by combining both extracorporeal and intracellular digestion. Whereas many high throughput ("-omics") techniques focus on biomolecules in spider venom, so far this approach has not yet been applied to investigate the protein composition of spider midgut diverticula (MD) and digestive fluid (DF). RESULTS We here report on our investigations of both MD and DF of the spider Nephilingis (Nephilengys) cruentata through the use of next generation sequencing and shotgun proteomics. This shows that the DF is composed of a variety of hydrolases including peptidases, carbohydrases, lipases and nuclease, as well as of toxins and regulatory proteins. We detect 25 astacins in the DF. Phylogenetic analysis of the corresponding transcript(s) in Arachnida suggests that astacins have acquired an unprecedented role for extracorporeal digestion in Araneae, with different orthologs used by each family. The results of a comparative study of spiders in distinct physiological conditions allow us to propose some digestion mechanisms in this interesting animal taxon. CONCLUSION All the high throughput data allowed the demonstration that DF is a secretion originating from the MD. We identified enzymes involved in the extracellular and intracellular phases of digestion. Besides that, data analyses show a large gene duplication event in Araneae digestive process evolution, mainly of astacin genes. We were also able to identify proteins expressed and translated in the digestive system, which until now had been exclusively associated to venom glands.
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Affiliation(s)
- Felipe J Fuzita
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, 05503-000, Brazil.,Biotechnology Program, University of São Paulo, São Paulo, Brazil
| | - Martijn W H Pinkse
- Laboratory of Analytical Biotechnology and Innovative Peptide Biology, Delft University of Technology, Delft, The Netherlands
| | - José S L Patane
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Peter D E M Verhaert
- Laboratory of Analytical Biotechnology and Innovative Peptide Biology, Delft University of Technology, Delft, The Netherlands.,Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Adriana R Lopes
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, 05503-000, Brazil.
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Petitot AS, Dereeper A, Agbessi M, Da Silva C, Guy J, Ardisson M, Fernandez D. Dual RNA-seq reveals Meloidogyne graminicola transcriptome and candidate effectors during the interaction with rice plants. MOLECULAR PLANT PATHOLOGY 2016; 17:860-74. [PMID: 26610268 PMCID: PMC6638361 DOI: 10.1111/mpp.12334] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 10/09/2015] [Accepted: 10/09/2015] [Indexed: 05/15/2023]
Abstract
Root-knot nematodes secrete proteinaceous effectors into plant tissues to facilitate infection by suppressing host defences and reprogramming the host metabolism to their benefit. Meloidogyne graminicola is a major pest of rice (Oryza sativa) in Asia and Latin America, causing important crop losses. The goal of this study was to identify M. graminicola pathogenicity genes expressed during the plant-nematode interaction. Using the dual RNA-sequencing (RNA-seq) strategy, we generated transcriptomic data of M. graminicola samples covering the pre-parasitic J2 stage and five parasitic stages in rice plants, from the parasitic J2 to the adult female. In the absence of a reference genome, a de novo M. graminicola transcriptome of 66 396 contigs was obtained from those reads that were not mapped on the rice genome. Gene expression profiling across the M. graminicola life cycle revealed key genes involved in nematode development and provided insights into the genes putatively associated with parasitism. The development of a 'secreted protein prediction' pipeline revealed a typical set of proteins secreted by nematodes, as well as a large number of cysteine-rich proteins and putative nuclear proteins. Combined with expression data, this pipeline enabled the identification of 15 putative effector genes, including two homologues of well-characterized effectors from cyst nematodes (CLE-like and VAP1) and a metallothionein. The localization of gene expression was assessed by in situ hybridization for a subset of candidates. All of these data represent important molecular resources for the elucidation of M. graminicola biology and for the selection of potential targets for the development of novel control strategies for this nematode species.
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Affiliation(s)
- Anne-Sophie Petitot
- IRD, UMR IRD-Cirad-UM2 Interactions Plantes-Microbes-Environnement, 34394, Montpellier Cedex 5, France
| | - Alexis Dereeper
- IRD, UMR IRD-Cirad-UM2 Interactions Plantes-Microbes-Environnement, 34394, Montpellier Cedex 5, France
| | - Mawusse Agbessi
- IRD, UMR IRD-Cirad-UM2 Interactions Plantes-Microbes-Environnement, 34394, Montpellier Cedex 5, France
| | - Corinne Da Silva
- CEA, Institut de Génomique, GENOSCOPE - Centre National de Séquençage, 91057, Evry Cedex, France
| | - Julie Guy
- CEA, Institut de Génomique, GENOSCOPE - Centre National de Séquençage, 91057, Evry Cedex, France
| | - Morgane Ardisson
- INRA, UMR Amélioration Génétique et Adaptation des Plantes, 34060, Montpellier Cedex 1, France
| | - Diana Fernandez
- IRD, UMR IRD-Cirad-UM2 Interactions Plantes-Microbes-Environnement, 34394, Montpellier Cedex 5, France
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Gottardini E, Cristofori A, Pellegrini E, La Porta N, Nali C, Baldi P, Sablok G. Suppression Substractive Hybridization and NGS Reveal Differential Transcriptome Expression Profiles in Wayfaring Tree (Viburnum lantana L.) Treated with Ozone. FRONTIERS IN PLANT SCIENCE 2016; 7:713. [PMID: 27313581 PMCID: PMC4887494 DOI: 10.3389/fpls.2016.00713] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 05/09/2016] [Indexed: 05/29/2023]
Abstract
Tropospheric ozone (O3) is a global air pollutant that causes high economic damages by decreasing plant productivity. It enters the leaves through the stomata, generates reactive oxygen species, which subsequent decrease in photosynthesis, plant growth, and biomass accumulation. In order to identify genes that are important for conferring O3 tolerance or sensitivity to plants, a suppression subtractive hybridization analysis was performed on the very sensitive woody shrub, Viburnum lantana, exposed to chronic O3 treatment (60 ppb, 5 h d(-1) for 45 consecutive days). Transcript profiling and relative expression assessment were carried out in asymptomatic leaves, after 15 days of O3 exposure. At the end of the experiment symptoms were observed on all treated leaves and plants, with an injured leaf area per plant accounting for 16.7% of the total surface. Cloned genes were sequenced by 454-pyrosequencing and transcript profiling and relative expression assessment were carried out on sequenced reads. A total of 38,800 and 12,495 high quality reads obtained in control and O3-treated libraries, respectively (average length of 319 ± 156.7 and 255 ± 107.4 bp). The Ensembl transcriptome yielded a total of 1241 unigenes with a total sequence length of 389,126 bp and an average length size of 389 bp (guanine-cytosine content = 49.9%). mRNA abundance was measured by reads per kilobase per million and 41 and 37 ensembl unigenes showed up- and down-regulation respectively. Unigenes functionally associated to photosynthesis and carbon utilization were repressed, demonstrating the deleterious effect of O3 exposure. Unigenes functionally associated to heat-shock proteins and glutathione were concurrently induced, suggesting the role of thylakoid-localized proteins and antioxidant-detoxification pathways as an effective strategy for responding to O3. Gene Ontology analysis documented a differential expression of co-regulated transcripts for several functional categories, including specific transcription factors (MYB and WRKY). This study demonstrates that a complex sequence of events takes place in the cells at intracellular and membrane level following O3 exposure and elucidates the effects of this oxidative stress on the transcriptional machinery of the non-model plant species V. lantana, with the final aim to provide the molecular supportive knowledge for the use of this plant as O3-bioindicator.
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Affiliation(s)
- Elena Gottardini
- Fondazione Edmund Mach, Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation CentreTrento, Italy
| | - Antonella Cristofori
- Fondazione Edmund Mach, Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation CentreTrento, Italy
| | - Elisa Pellegrini
- Department of Agriculture, Food and Environment, University of PisaPisa, Italy
| | - Nicola La Porta
- Fondazione Edmund Mach, Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation CentreTrento, Italy
- MOUNTFOR Project Centre, European Forest InstituteTrento, Italy
- Consiglio Nazionale delle Ricerche, Istituto per la Valorizzazione del Legno e delle Specie ArboreeFlorence, Italy
| | - Cristina Nali
- Department of Agriculture, Food and Environment, University of PisaPisa, Italy
| | - Paolo Baldi
- Fondazione Edmund Mach, Genomics and Biology of Fruit Crops Department, Research and Innovation CentreTrento, Italy
| | - Gaurav Sablok
- Fondazione Edmund Mach, Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation CentreTrento, Italy
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
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Morandin C, Tin MMY, Abril S, Gómez C, Pontieri L, Schiøtt M, Sundström L, Tsuji K, Pedersen JS, Helanterä H, Mikheyev AS. Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants. Genome Biol 2016; 17:43. [PMID: 26951146 PMCID: PMC4780134 DOI: 10.1186/s13059-016-0902-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/12/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Reproductive division of labor in eusocial insects is a striking example of a shared genetic background giving rise to alternative phenotypes, namely queen and worker castes. Queen and worker phenotypes play major roles in the evolution of eusocial insects. Their behavior, morphology and physiology underpin many ecologically relevant colony-level traits, which evolved in parallel in multiple species. RESULTS Using queen and worker transcriptomic data from 16 ant species we tested the hypothesis that conserved sets of genes are involved in ant reproductive division of labor. We further hypothesized that such sets of genes should also be involved in the parallel evolution of other key traits. We applied weighted gene co-expression network analysis, which clusters co-expressed genes into modules, whose expression levels can be summarized by their 'eigengenes'. Eigengenes of most modules were correlated with phenotypic differentiation between queens and workers. Furthermore, eigengenes of some modules were correlated with repeated evolution of key phenotypes such as complete worker sterility, the number of queens per colony, and even invasiveness. Finally, connectivity and expression levels of genes within the co-expressed network were strongly associated with the strength of selection. Although caste-associated sets of genes evolve faster than non-caste-associated, we found no evidence for queen- or worker-associated co-expressed genes evolving faster than one another. CONCLUSIONS These results identify conserved functionally important genomic units that likely serve as building blocks of phenotypic innovation, and allow the remarkable breadth of parallel evolution seen in ants, and possibly other eusocial insects as well.
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Affiliation(s)
- Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland. .,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland.
| | - Mandy M Y Tin
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan
| | - Sílvia Abril
- Department of Environmental Sciences, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Crisanto Gómez
- Department of Environmental Sciences, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Luigi Pontieri
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Liselotte Sundström
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Kazuki Tsuji
- Department of Subtropical Agro-Environmental Sciences, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
| | - Jes Søe Pedersen
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan. .,Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia.
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The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature 2016; 530:331-5. [PMID: 26814964 DOI: 10.1038/nature16548] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/18/2015] [Indexed: 11/09/2022]
Abstract
Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.
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Yamamoto N, Kudo T, Fujiwara S, Takatsuka Y, Hirokawa Y, Tsuzuki M, Takano T, Kobayashi M, Suda K, Asamizu E, Yokoyama K, Shibata D, Tabata S, Yano K. Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae. PLANT & CELL PHYSIOLOGY 2016; 57:e6. [PMID: 26746174 PMCID: PMC4722176 DOI: 10.1093/pcp/pcv195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/27/2015] [Indexed: 05/04/2023]
Abstract
Pleurochrysis is a coccolithophorid genus, which belongs to the Coccolithales in the Haptophyta. The genus has been used extensively for biological research, together with Emiliania in the Isochrysidales, to understand distinctive features between the two coccolithophorid-including orders. However, molecular biological research on Pleurochrysis such as elucidation of the molecular mechanism behind coccolith formation has not made great progress at least in part because of lack of comprehensive gene information. To provide such information to the research community, we built an open web database, the Pleurochrysome (http://bioinf.mind.meiji.ac.jp/phapt/), which currently stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from expressed sequence tag sequences of P. haptonemofera as core information. The UNIGENEs were annotated with gene sequences sharing significant homology, conserved domains, Gene Ontology, KEGG Orthology, predicted subcellular localization, open reading frames and orthologous relationship with genes of 10 other algal species, a cyanobacterium and the yeast Saccharomyces cerevisiae. This sequence and annotation information can be easily accessed via several search functions. Besides fundamental functions such as BLAST and keyword searches, this database also offers search functions to explore orthologous genes in the 12 organisms and to seek novel genes. The Pleurochrysome will promote molecular biological and phylogenetic research on coccolithophorids and other haptophytes by helping scientists mine data from the primary transcriptome of P. haptonemofera.
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Affiliation(s)
- Naoki Yamamoto
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan These authors contributed equally to this work. Present address: International Rice Research Institute, DAPO 7777, Metro Manila 1301, Philippines.
| | - Toru Kudo
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan These authors contributed equally to this work.
| | - Shoko Fujiwara
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan These authors contributed equally to this work.
| | - Yukiko Takatsuka
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan
| | - Yasutaka Hirokawa
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan
| | - Mikio Tsuzuki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan
| | - Tomoyuki Takano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Masaaki Kobayashi
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Kunihiro Suda
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Erika Asamizu
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Koji Yokoyama
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
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Glaser N, Gallot A, Legeai F, Harry M, Kaiser L, Le Ru B, Calatayud PA, Jacquin-Joly E. Differential expression of the chemosensory transcriptome in two populations of the stemborer Sesamia nonagrioides. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 65:28-34. [PMID: 26316282 DOI: 10.1016/j.ibmb.2015.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 06/30/2015] [Accepted: 07/08/2015] [Indexed: 06/04/2023]
Abstract
Among the proposed mechanisms of local adaptation to different ecological environments, transcriptional changes may play an important role. In this study, we investigated whether such variability occurred within the chemosensory organs of a herbivorous insect, for which chemosensation guides most of its host preferences. A European and an African population of the noctuid Sesamia nonagrioides that display significant differences in their ecological preferences were collected on Zea mays and Typha domingensis, respectively. RNAseq were used between the two populations for digital expression profiling of chemosensory organs from larval antennae and palps. Preliminary data on adult female antennae and ovipositors were also collected. We found 6,550 differentially expressed transcripts in larval antennae and palps. Gene ontology enrichment analyses suggested that transcriptional activity was overrepresented in the French population and that virus and defense activities were overrepresented in the Kenyan population. In addition, we found differential expression of a variety of cytochrome P450s, which may be linked to the different host-plant diets. Looking at olfactory genes, we observed differential expression of numerous candidate odorant-binding proteins, chemosensory proteins, and one olfactory receptor, suggesting that differences in olfactory sensitivity participate in insect adaptation.
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Affiliation(s)
- Nicolas Glaser
- INRA, UMR 1392, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Route de Saint-Cyr, F-78026 Versailles Cedex, France; UMR Evolution, Génomes, Comportement et Ecologie, IRD, CNRS, Université Paris Sud, Campus CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Aurore Gallot
- INRA, UMR 1392, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Route de Saint-Cyr, F-78026 Versailles Cedex, France; IRISA, équipe GenScale, Campus universitaire de Beaulieu, 35042 Rennes Cedex, France
| | - Fabrice Legeai
- IRISA, équipe GenScale, Campus universitaire de Beaulieu, 35042 Rennes Cedex, France
| | - Myriam Harry
- UMR Evolution, Génomes, Comportement et Ecologie, IRD, CNRS, Université Paris Sud, Campus CNRS, 91198 Gif-sur-Yvette Cedex, France; Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Laure Kaiser
- UMR Evolution, Génomes, Comportement et Ecologie, IRD, CNRS, Université Paris Sud, Campus CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Bruno Le Ru
- UMR Evolution, Génomes, Comportement et Ecologie, IRD, CNRS, Université Paris Sud, Campus CNRS, 91198 Gif-sur-Yvette Cedex, France; UMR Evolution, Génomes, Comportement et Ecologie IRD, CNRS, Université Paris Sud, c/o icipe, NSBB Project, PO Box 30772-00100, Nairobi, Kenya
| | - Paul-André Calatayud
- UMR Evolution, Génomes, Comportement et Ecologie, IRD, CNRS, Université Paris Sud, Campus CNRS, 91198 Gif-sur-Yvette Cedex, France; UMR Evolution, Génomes, Comportement et Ecologie IRD, CNRS, Université Paris Sud, c/o icipe, NSBB Project, PO Box 30772-00100, Nairobi, Kenya
| | - Emmanuelle Jacquin-Joly
- INRA, UMR 1392, Institut d'Ecologie et des Sciences de l'Environnement de Paris, Route de Saint-Cyr, F-78026 Versailles Cedex, France.
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Aird SD, Aggarwal S, Villar-Briones A, Tin MMY, Terada K, Mikheyev AS. Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly. BMC Genomics 2015; 16:647. [PMID: 26315097 PMCID: PMC4552096 DOI: 10.1186/s12864-015-1832-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 08/07/2015] [Indexed: 12/19/2022] Open
Abstract
Background While many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression level, and evolutionary rate in secreted protein systems. Venomous snakes employ well-integrated systems of proteins and organic constituents to immobilize prey. Venoms are generally optimized to subdue preferred prey more effectively than non-prey, and many venom protein families manifest positive selection and rapid gene family diversification. Although previous studies have illuminated how individual venom protein families evolve, how selection acts on venoms as integrated systems, is unknown. Results Using next-generation transcriptome sequencing and mass spectrometry, we examined microevolution in two pitvipers, allopatrically separated for at least 1.6 million years, and their hybrids. Transcriptomes of parental species had generally similar compositions in regard to protein families, but for a given protein family, the homologs present and concentrations thereof sometimes differed dramatically. For instance, a phospholipase A2 transcript comprising 73.4 % of the Protobothrops elegans transcriptome, was barely present in the P. flavoviridis transcriptome (<0.05 %). Hybrids produced most proteins found in both parental venoms. Protein evolutionary rates were positively correlated with transcriptomic and proteomic abundances, and the most abundant proteins showed positive selection. This pattern holds with the addition of four other published crotaline transcriptomes, from two more genera, and also for the recently published king cobra genome, suggesting that rapid evolution of abundant proteins may be generally true for snake venoms. Looking more broadly at Protobothrops, we show that rapid evolution of the most abundant components is due to positive selection, suggesting an interplay between abundance and adaptation. Conclusions Given log-scale differences in toxin abundance, which are likely correlated with biosynthetic costs, we hypothesize that as a result of natural selection, snakes optimize return on energetic investment by producing more of venom proteins that increase their fitness. Natural selection then acts on the additive genetic variance of these components, in proportion to their contributions to overall fitness. Adaptive evolution of venoms may occur most rapidly through changes in expression levels that alter fitness contributions, and thus the strength of selection acting on specific secretome components. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1832-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steven D Aird
- Okinawa Institute of Science and Technology Graduate University, Tancha 1919-1, Onna-son, Kunigami-gun, Okinawa-ken, 904-0412, Japan.
| | - Shikha Aggarwal
- Okinawa Institute of Science and Technology Graduate University, Tancha 1919-1, Onna-son, Kunigami-gun, Okinawa-ken, 904-0412, Japan. .,University School of Environment Management, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, 110078, India.
| | - Alejandro Villar-Briones
- Okinawa Institute of Science and Technology Graduate University, Tancha 1919-1, Onna-son, Kunigami-gun, Okinawa-ken, 904-0412, Japan.
| | - Mandy Man-Ying Tin
- Okinawa Institute of Science and Technology Graduate University, Tancha 1919-1, Onna-son, Kunigami-gun, Okinawa-ken, 904-0412, Japan.
| | - Kouki Terada
- Okinawa Prefectural Institute of Health and the Environment, Biology and Ecology Group, 2003 Ozato, Ozato, Nanjo-shi, Okinawa, 901-1202, Japan.
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology Graduate University, Tancha 1919-1, Onna-son, Kunigami-gun, Okinawa-ken, 904-0412, Japan. .,Research School of Biology, Australian National University, Canberra, ACT 0200, Australia.
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Gardin JAC, Gouzy J, Carrère S, Délye C. ALOMYbase, a resource to investigate non-target-site-based resistance to herbicides inhibiting acetolactate-synthase (ALS) in the major grass weed Alopecurus myosuroides (black-grass). BMC Genomics 2015; 16:590. [PMID: 26265378 PMCID: PMC4534104 DOI: 10.1186/s12864-015-1804-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 07/31/2015] [Indexed: 12/29/2022] Open
Abstract
Background Herbicide resistance in agrestal weeds is a global problem threatening food security. Non-target-site resistance (NTSR) endowed by mechanisms neutralising the herbicide or compensating for its action is considered the most agronomically noxious type of resistance. Contrary to target-site resistance, NTSR mechanisms are far from being fully elucidated. A part of weed response to herbicide stress, NTSR is considered to be largely driven by gene regulation. Our purpose was to establish a transcriptome resource allowing investigation of the transcriptomic bases of NTSR in the major grass weed Alopecurus myosuroides L. (Poaceae) for which almost no genomic or transcriptomic data was available. Results RNA-Seq was performed from plants in one F2 population that were sensitive or expressing NTSR to herbicides inhibiting acetolactate-synthase. Cloned plants were sampled over seven time-points ranging from before until 73 h after herbicide application. Assembly of over 159M high-quality Illumina reads generated a transcriptomic resource (ALOMYbase) containing 65,558 potentially active contigs (N50 = 1240 nucleotides) predicted to encode 32,138 peptides with 74 % GO annotation, of which 2017 were assigned to protein families presumably involved in NTSR. Comparison with the fully sequenced grass genomes indicated good coverage and correct representation of A. myosuroides transcriptome in ALOMYbase. The part of the herbicide transcriptomic response common to the resistant and the sensitive plants was consistent with the expected effects of acetolactate-synthase inhibition, with striking similarities observed with published Arabidopsis thaliana data. A. myosuroides plants with NTSR were first affected by herbicide action like sensitive plants, but ultimately overcame it. Analysis of differences in transcriptomic herbicide response between resistant and sensitive plants did not allow identification of processes directly explaining NTSR. Five contigs associated to NTSR in the F2 population studied were tentatively identified. They were predicted to encode three cytochromes P450 (CYP71A, CYP71B and CYP81D), one peroxidase and one disease resistance protein. Conclusions Our data confirmed that gene regulation is at the root of herbicide response and of NTSR. ALOMYbase proved to be a relevant resource to support NTSR transcriptomic studies, and constitutes a valuable tool for future research aiming at elucidating gene regulations involved in NTSR in A. myosuroides. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1804-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jérôme Gouzy
- INRA, UMR441 LIPM, F-31326, Castanet-Tolosan, France.
| | | | - Christophe Délye
- INRA, UMR1347 Agroécologie, 17 rue de Sully, F-21000, Dijon, France.
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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.
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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
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Andrade SC, Novo M, Kawauchi GY, Worsaae K, Pleijel F, Giribet G, Rouse GW. Articulating “Archiannelids”: Phylogenomics and Annelid Relationships, with Emphasis on Meiofaunal Taxa. Mol Biol Evol 2015. [DOI: 10.1093/molbev/msv157] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Fuzita FJ, Pinkse MWH, Patane JSL, Juliano MA, Verhaert PDEM, Lopes AR. Biochemical, transcriptomic and proteomic analyses of digestion in the scorpion Tityus serrulatus: insights into function and evolution of digestion in an ancient arthropod. PLoS One 2015; 10:e0123841. [PMID: 25875018 PMCID: PMC4398375 DOI: 10.1371/journal.pone.0123841] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 02/25/2015] [Indexed: 01/29/2023] Open
Abstract
Scorpions are among the oldest terrestrial arthropods and they have passed through small morphological changes during their evolutionary history on land. They are efficient predators capable of capturing and consuming large preys and due to envenomation these animals can become a human health challenge. Understanding the physiology of scorpions can not only lead to evolutionary insights but also is a crucial step in the development of control strategies. However, the digestive process in scorpions has been scarcely studied. In this work, we describe the combinatory use of next generation sequencing, proteomic analysis and biochemical assays in order to investigate the digestive process in the yellow scorpion Tityus serrulatus, mainly focusing in the initial protein digestion. The transcriptome generated database allowed the quantitative identification by mass spectrometry of different enzymes and proteins involved in digestion. All the results suggested that cysteine cathepsins play an important role in protein digestion. Two digestive cysteine cathepsins were isolated and characterized presenting acidic characteristics (pH optima and stability), zymogen conversion to the mature form after acidic activation and a cross-class inhibition by pepstatin. A more elucidative picture of the molecular mechanism of digestion in a scorpion was proposed based on our results from Tityus serrulatus. The midgut and midgut glands (MMG) are composed by secretory and digestive cells. In fasting animals, the secretory granules are ready for the next predation event, containing enzymes needed for alkaline extra-oral digestion which will compose the digestive fluid, such as trypsins, astacins and chitinase. The digestive vacuoles are filled with an acidic proteolytic cocktail to the intracellular digestion composed by cathepsins L, B, F, D and legumain. Other proteins as lipases, carbohydrases, ctenitoxins and a chitolectin with a perithrophin domain were also detected. Evolutionarily, a large gene duplication of cathepsin L occurred in Arachnida with the sequences from ticks being completely divergent from other arachnids probably due to the particular selective pressures over this group.
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Affiliation(s)
- Felipe J. Fuzita
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, Brazil
- Biotechnology Program, University of São Paulo, São Paulo, Brazil
| | - Martijn W. H. Pinkse
- Laboratory of Analytical Biotechnology & Innovative Peptide Biology, Delft University of Technology, Delft, The Netherlands
| | - José S. L. Patane
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | | | - Peter D. E. M. Verhaert
- Laboratory of Analytical Biotechnology & Innovative Peptide Biology, Delft University of Technology, Delft, The Netherlands
| | - Adriana R. Lopes
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, Brazil
- * E-mail:
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Yang Y, Moore MJ, Brockington SF, Soltis DE, Wong GKS, Carpenter EJ, Zhang Y, Chen L, Yan Z, Xie Y, Sage RF, Covshoff S, Hibberd JM, Nelson MN, Smith SA. Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing. Mol Biol Evol 2015; 32:2001-14. [PMID: 25837578 PMCID: PMC4833068 DOI: 10.1093/molbev/msv081] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees, we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole-genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in nonmodel species that is based on homolog groups in addition to inferred ortholog groups.
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Affiliation(s)
- Ya Yang
- Department of Ecology & Evolutionary Biology, University of Michigan
| | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Douglas E Soltis
- Department of Biology, University of Florida Florida Museum of Natural History, University of Florida Genetics Institute, University of Florida
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada Department of Medicine, University of Alberta, Edmonton, AB, Canada BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Eric J Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yong Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Li Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Zhixiang Yan
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Yinlong Xie
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Matthew N Nelson
- School of Plant Biology, The University of Western Australia, Crawley, WA, Australia
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan
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De La Torre AR, Lin YC, Van de Peer Y, Ingvarsson PK. Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families. Genome Biol Evol 2015; 7:1002-15. [PMID: 25747252 PMCID: PMC4419791 DOI: 10.1093/gbe/evv044] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (>50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.
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Affiliation(s)
| | - Yao-Cheng Lin
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium Genomics Research Institute, University of Pretoria, South Africa
| | - Pär K Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Sweden Umeå Plant Science Centre, Umeå, Sweden
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Duhoux A, Carrère S, Gouzy J, Bonin L, Délye C. RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance. PLANT MOLECULAR BIOLOGY 2015; 87:473-87. [PMID: 25636204 DOI: 10.1007/s11103-015-0292-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/26/2015] [Indexed: 05/03/2023]
Abstract
Non-target-site resistance (NTSR) to herbicides that disrupts agricultural weed control is a worldwide concern for food security. NTSR is considered a polygenic adaptive trait driven by differential gene regulation in resistant plants. Little is known about its genetic determinism, which precludes NTSR diagnosis and evolutionary studies. We used Illumina RNA-sequencing to investigate transcriptomic differences between plants from the global major weed rye-grass sensitive or resistant to the acetolactate-synthase (ALS) inhibiting herbicide pyroxsulam. Plants were collected before and along a time-course after herbicide application. De novo transcriptome assembly yielded a resource (LOLbase) including 92,381 contigs representing potentially active transcripts that were assigned putative annotations. Early effects of ALS inhibition consistent with the literature were observed in resistant and sensitive plants, proving LOLbase data were relevant to study herbicide response. Comparison of resistant and sensitive plants identified 30 candidate NTSR contigs. Further validation using 212 plants resistant or sensitive to pyroxsulam and/or to the ALS inhibitors iodosulfuron + mesosulfuron confirmed four contigs (two cytochromes P450, one glycosyl-transferase and one glutathione-S-transferase) were NTSR markers which combined expression levels could reliably identify resistant plants. This work confirmed that NTSR is driven by differential gene expression and involves different mechanisms. It provided tools and foundation for subsequent NTSR investigations.
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Affiliation(s)
- Arnaud Duhoux
- UMR1347 Agroécologie, INRA, 17 rue Sully, 21000, Dijon, France
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47
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Duhoux A, Carrère S, Gouzy J, Bonin L, Délye C. RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance. PLANT MOLECULAR BIOLOGY 2015; 87:473-487. [PMID: 25636204 DOI: 10.1007/s11103-015-0292-293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/26/2015] [Indexed: 05/20/2023]
Abstract
Non-target-site resistance (NTSR) to herbicides that disrupts agricultural weed control is a worldwide concern for food security. NTSR is considered a polygenic adaptive trait driven by differential gene regulation in resistant plants. Little is known about its genetic determinism, which precludes NTSR diagnosis and evolutionary studies. We used Illumina RNA-sequencing to investigate transcriptomic differences between plants from the global major weed rye-grass sensitive or resistant to the acetolactate-synthase (ALS) inhibiting herbicide pyroxsulam. Plants were collected before and along a time-course after herbicide application. De novo transcriptome assembly yielded a resource (LOLbase) including 92,381 contigs representing potentially active transcripts that were assigned putative annotations. Early effects of ALS inhibition consistent with the literature were observed in resistant and sensitive plants, proving LOLbase data were relevant to study herbicide response. Comparison of resistant and sensitive plants identified 30 candidate NTSR contigs. Further validation using 212 plants resistant or sensitive to pyroxsulam and/or to the ALS inhibitors iodosulfuron + mesosulfuron confirmed four contigs (two cytochromes P450, one glycosyl-transferase and one glutathione-S-transferase) were NTSR markers which combined expression levels could reliably identify resistant plants. This work confirmed that NTSR is driven by differential gene expression and involves different mechanisms. It provided tools and foundation for subsequent NTSR investigations.
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Affiliation(s)
- Arnaud Duhoux
- UMR1347 Agroécologie, INRA, 17 rue Sully, 21000, Dijon, France
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Aya K, Kobayashi M, Tanaka J, Ohyanagi H, Suzuki T, Yano K, Takano T, Yano K, Matsuoka M. De Novo Transcriptome Assembly of a Fern, Lygodium japonicum, and a Web Resource Database, Ljtrans DB. ACTA ACUST UNITED AC 2014; 56:e5. [DOI: 10.1093/pcp/pcu184] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Bouzid W, Verdenaud M, Klopp C, Ducancel F, Noirot C, Vétillard A. De Novo sequencing and transcriptome analysis for Tetramorium bicarinatum: a comprehensive venom gland transcriptome analysis from an ant species. BMC Genomics 2014; 15:987. [PMID: 25407482 PMCID: PMC4256838 DOI: 10.1186/1471-2164-15-987] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 09/09/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Arthropod venoms are invaluable sources of bioactive substances with biotechnological application. The limited availability of some venoms, such as those from ants, has restricted the knowledge about the composition and the potential that these biomolecules could represent. In order to provide a global insight on the transcripts expressed in the venom gland of the Brazilian ant species Tetramorium bicarinatum and to unveil the potential of its products, high-throughput approach using Illumina technology has been applied to analyze the genes expressed in active venom glands of this ant species. RESULTS A total of 212,371,758 pairs of quality-filtered, 100-base-pair Illumina reads were obtained. The de novo assemblies yielded 36,042 contigs for which 27,873 have at least one predicted ORF among which 59.77% produce significant hits in the available databases. The investigation of the reads mapping toxin class revealed a high diversification with the major part consistent with the classical hymenopteran venom protein signature represented by venom allergen (33.3%), followed by a diverse toxin-expression profile including several distinct isoforms of phospholipase A1 and A2, venom serine protease, hyaluronidase, protease inhibitor and secapin. Moreover, our results revealed for the first time the presence of toxin-like peptides that have been previously identified from unrelated venomous animals such as waprin-like (snakes) and agatoxins (spiders and conus).The non-toxin transcripts were mainly represented by contigs involved in protein folding and translation, consistent with the protein-secretory function of the venom gland tissue. Finally, about 40% of the generated contigs have no hits in the databases with 25% of the predicted peptides bearing signal peptide emphasizing the potential of the investigation of these sequences as source of new molecules. Among these contigs, six putative novel peptides that show homologies with previously identified antimicrobial peptides were identified. CONCLUSIONS To the best of our knowledge, this work reports the first large-scale analysis of genes transcribed by the venomous gland of the ant species T. bicarinatum and helps with the identification of Hymenoptera toxin arsenal. In addition, results from this study demonstrate that de novo transcriptome assembly allows useful venom gene expression analysis in a species lacking a genome sequence database.
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Affiliation(s)
| | | | | | | | | | - Angélique Vétillard
- Venoms and Biological Activities Laboratory, EA 4357, PRES-University of Toulouse, Jean-François Champollion University Center, Albi, France.
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50
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Teixeira RT, Fortes AM, Pinheiro C, Pereira H. Comparison of good- and bad-quality cork: application of high-throughput sequencing of phellogenic tissue. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4887-905. [PMID: 24958897 DOI: 10.1093/jxb/eru252] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cork is one of the most valuable non-wood forest products and plays an important role in Mediterranean economies. The production of high-quality cork is dependent on both genome and environment, posing constraints on the industry because an ever-growing amount of bad-quality cork (BQC) development has been observed. In order to identify genes responsible for production of cork of superior quality we performed a comparative analysis using the 454 pyrosequencing approach on phellogenic tissue of good- and bad-quality samples. The transcriptional profiling showed a high number of genes differentially expressed (8.48%) from which 78.8% displayed annotation. Genes more highly represented in BQC are involved in DNA synthesis, RNA processing, proteolysis, and transcription factors related to the abiotic stress response. Putative stomatal/lenticular-associated genes which may be responsible for the disadvantageous higher number of lenticular channels in BQC are also more highly represented. BQC also showed an elevated content of free phenolics. On the other hand, good-quality cork (GQC) can be distinguished by highly expressed genes encoding heat-shock proteins. Together the results provide valuable new information about the molecular events leading to cork formation and provide putative biomarkers associated with cork quality that can be useful in breeding programmes.
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Affiliation(s)
- Rita Teresa Teixeira
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade Técnica de Lisboa, 1349-017, Portugal
| | - Ana Margarida Fortes
- Center for Biodiversity, Functional and Integrative Genomics (BioFIG); Science Faculty, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Carla Pinheiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Helena Pereira
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade Técnica de Lisboa, 1349-017, Portugal
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