Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome

<p>Abstract</p> <p>Background</p> <p>The carnivorous plant <it>Utricularia gibba </it>(bladderwort) is remarkable in having a minute genome, which at ca. 80 megabases is approximately half that of <it>Arabidopsis</it>. Bladderworts show an incredible diversity of forms surrounding a defined theme: tiny, bladder-like suction traps on terrestrial, epiphytic, or aquatic plants with a diversity of unusual vegetative forms. <it>Utricularia </it>plants, which are rootless, are also anomalous in physiological features (respiration and carbon distribution), and highly enhanced molecular evolutionary rates in chloroplast, mitochondrial and nuclear ribosomal sequences. Despite great interest in the genus, no genomic resources exist for <it>Utricularia</it>, and the substitution rate increase has received limited study.</p> <p>Results</p> <p>Here we describe the sequencing and analysis of the <it>Utricularia gibba </it>transcriptome. Three different organs were surveyed, the traps, the vegetative shoot bodies, and the inflorescence stems. We also examined the bladderwort transcriptome under diverse stress conditions. We detail aspects of functional classification, tissue similarity, nitrogen and phosphorus metabolism, respiration, DNA repair, and detoxification of reactive oxygen species (ROS). Long contigs of plastid and mitochondrial genomes, as well as sequences for 100 individual nuclear genes, were compared with those of other plants to better establish information on molecular evolutionary rates.</p> <p>Conclusion</p> <p>The <it>Utricularia </it>transcriptome provides a detailed genomic window into processes occurring in a carnivorous plant. It contains a deep representation of the complex metabolic pathways that characterize a putative minimal plant genome, permitting its use as a source of genomic information to explore the structural, functional, and evolutionary diversity of the genus. Vegetative shoots and traps are the most similar organs by functional classification of their transcriptome, the traps expressing hydrolytic enzymes for prey digestion that were previously thought to be encoded by bacteria. Supporting physiological data, global gene expression analysis shows that traps significantly over-express genes involved in respiration and that phosphate uptake might occur mainly in traps, whereas nitrogen uptake could in part take place in vegetative parts. Expression of DNA repair and ROS detoxification enzymes may be indicative of a response to increased respiration. Finally, evidence from the bladderwort transcriptome, direct measurement of ROS <it>in situ</it>, and cross-species comparisons of organellar genomes and multiple nuclear genes supports the hypothesis that increased nucleotide substitution rates throughout the plant may be due to the mutagenic action of amplified ROS production.</p

Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba

The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compared the U. gibba genome with that of four other eudicot species, defining a total of 17,324 gene families (orthogroups). These families were further classified as either 1) lineage-specific expanded/contracted or 2) stable in size. The U. gibba-expanded families are generically related to three main phenotypic features: 1) trap physiology, 2) key plant morphogenetic/developmental pathways, and 3) response to environmental stimuli, including adaptations to life in aquatic environments. Further scans for signatures of protein functional specialization permitted identification of seven candidate genes with amino acid changes putatively fixed by positive Darwinian selection in the U. gibba lineage. The Arabidopsis orthologs of these genes (AXR, UMAMIT41, IGS, TAR2, SOL1, DEG9, and DEG10) are involved in diverse plant biological functions potentially relevant for U. gibba phenotypic diversification, including 1) auxin metabolism and signal transduction, 2) flowering induction and floral meristem transition, 3) root development, and 4) peptidases. Taken together, our results suggest numerous candidate genes and gene families as interesting targets for further experimental confirmation of their functional and adaptive roles in the U. gibba's unique lifestyle and highly specialized body plan

Deep Sequencing of the Mexican Avocado Transcriptome, an Ancient Angiosperm with a High Content of Fatty Acids

Background: Avocado (Persea americana) is an economically important tropical fruit considered to be a good source of fatty acids. Despite its importance, the molecular and cellular characterization of biochemical and developmental processes in avocado is limited due to the lack of transcriptome and genomic information. Results: The transcriptomes of seeds, roots, stems, leaves, aerial buds and flowers were determined using different sequencing platforms. Additionally, the transcriptomes of three different stages of fruit ripening (pre-climacteric, climacteric and post-climacteric) were also analyzed. The analysis of the RNAseqatlas presented here reveals strong differences in gene expression patterns between different organs, especially between root and flower, but also reveals similarities among the gene expression patterns in other organs, such as stem, leaves and aerial buds (vegetative organs) or seed and fruit (storage organs). Important regulators, functional categories, and differentially expressed genes involved in avocado fruit ripening were identified. Additionally, to demonstrate the utility of the avocado gene expression atlas, we investigated the expression patterns of genes implicated in fatty acid metabolism and fruit ripening. Conclusions: A description of transcriptomic changes occurring during fruit ripening was obtained in Mexican avocado, contributing to a dynamic view of the expression patterns of genes involved in fatty acid biosynthesis and the fruit ripening process

Genome Sequence of the Deltaproteobacterial Strain NaphS2 and Analysis of Differential Gene Expression during Anaerobic Growth on Naphthalene

Anaerobic polycyclic hydrocarbon (PAH) degradation coupled to sulfate reduction may be an important mechanism for in situ remediation of contaminated sediments. Steps involved in the anaerobic degradation of 2-methylnaphthalene have been described in the sulfate reducing strains NaphS3, NaphS6 and N47. Evidence from N47 suggests that naphthalene degradation involves 2-methylnaphthalene as an intermediate, whereas evidence in NaphS2, NaphS3 and NaphS6 suggests a mechanism for naphthalene degradation that does not involve 2-methylnaphthalene. To further characterize pathways involved in naphthalene degradation in NaphS2, the draft genome was sequenced, and gene and protein expression examined.Draft genome sequencing, gene expression analysis, and proteomic analysis revealed that NaphS2 degrades naphthoyl-CoA in a manner analogous to benzoyl-CoA degradation. Genes including the previously characterized NmsA, thought to encode an enzyme necessary for 2-methylnaphthalene metabolism, were not upregulated during growth of NaphS2 on naphthalene, nor were the corresponding protein products. NaphS2 may possess a non-classical dearomatizing enzyme for benzoate degradation, similar to one previously characterized in Geobacter metallireducens. Identification of genes involved in toluene degradation in NaphS2 led us to determine that NaphS2 degrades toluene, a previously unreported capacity. The genome sequence also suggests that NaphS2 may degrade other monoaromatic compounds.This study demonstrates that steps leading to the degradation of 2-naphthoyl-CoA are conserved between NaphS2 and N47, however while NaphS2 possesses the capacity to degrade 2-methylnaphthalene, naphthalene degradation likely does not proceed via 2-methylnaphthalene. Instead, carboxylation or another form of activation may serve as the first step in naphthalene degradation. Degradation of toluene and 2-methylnaphthalene, and the presence of at least one bss-like and bbs-like gene cluster in this organism, suggests that NaphS2 degrades both compounds via parallel mechanisms. Elucidation of the key genes necessary for anaerobic naphthalene degradation may provide the ability to track naphthalene degradation through in situ transcript monitoring

Alkamides Activate Jasmonic Acid Biosynthesis and Signaling Pathways and Confer Resistance to Botrytis cinerea in Arabidopsis thaliana

Alkamides are fatty acid amides of wide distribution in plants, structurally related to N-acyl-L-homoserine lactones (AHLs) from Gram-negative bacteria and to N- acylethanolamines (NAEs) from plants and mammals. Global analysis of gene expression changes in Arabidopsis thaliana in response to N-isobutyl decanamide, the most highly active alkamide identified to date, revealed an overrepresentation of defense-responsive transcriptional networks. In particular, genes encoding enzymes for jasmonic acid (JA) biosynthesis increased their expression, which occurred in parallel with JA, nitric oxide (NO) and H2O2 accumulation. The activity of the alkamide to confer resistance against the necrotizing fungus Botrytis cinerea was tested by inoculating Arabidopsis detached leaves with conidiospores and evaluating disease symptoms and fungal proliferation. N-isobutyl decanamide application significantly reduced necrosis caused by the pathogen and inhibited fungal proliferation. Arabidopsis mutants jar1 and coi1 altered in JA signaling and a MAP kinase mutant (mpk6), unlike salicylic acid- (SA) related mutant eds16/sid2-1, were unable to defend from fungal attack even when N-isobutyl decanamide was supplied, indicating that alkamides could modulate some necrotrophic-associated defense responses through JA-dependent and MPK6-regulated signaling pathways. Our results suggest a role of alkamides in plant immunity induction

Identificación y caracterización de Aeromonas sp patógenas aisladas de truchas arcoíris (Oncorhynchus mykiss) clínicamente enfermas cultivadas en piscigranjas del Perú

The present research aimed at the biochemical characterization and molecular identification of pathogenic strains of Aeromonas sp, isolated from juvenile rainbow trout with clinical signs compatible with aeromoniasis in six fish farms in Junín (2), Pasco (2), Cajamarca (1) and Ancash (1), Peru. In total, 60 juvenile trout of 4-5 months were selected, with suggestive signs of outbreaks of aeromoniasis between 2017 and 2018. Euthanasia and necropsy were performed and the external and internal lesions present were recorded. Bacterial isolation of spleen and anterior kidney samples was carried out on TSA and GSP agar for 24-48 hours at 25 °C, bacterial colonies were characterized by biochemical tests and identified by conventional PCR using specific primers of the 16S rRNA gene (Aeromonas spp.), fstA (A. salmonicida) and gyrB (A. hydrophila), and sequencing was performed and confirmed by BLAST analysis (NCBI). The external lesions were melanosis, necrotic and haemorrhagic fins, skin ulcers and abdominal distention. Internal lesions were hepatomegaly, splenomegaly, and petechial haemorrhage in the liver, pyloric cecum, and peritoneal fat. Twelve strains were isolated in GSP (7 from Junín and 5 from Cajamarca), characterized as Aeromonas spp, being negative in the Pasco and Ancash samples. The biochemical tests determined four strains as Aeromonas salmonicida and eight as mobile Aeromonas sp, differing by motility and indole tests. Molecular identification by PCR determined four A. salmonicida strains from Junín, one A. hydrophila strain from Cajamarca and seven Aeromonas spp mobile strains (3 from Junín and 4 from Cajamarca) that were negative to the PCR of A. salmonicida and A. hydrophila. BLAST analysis (NCBI) confirmed the strains A. salmonicida and Aeromonas spp (98-100% identity). Furthermore, the Cajamarca strain (identified as A. hydrophila by biochemistry) presented 95.65% identity with A. hydrophila subspecies dhakensis. In conclusion, Aeromonas salmonicida, A. hydrophila subspecies dhakensis and other pathogenic mobile Aeromonas produce symptoms associated with aeromoniasis in juvenile rainbow trout in the Junín and Cajamarca fish farms. It is the first time that A. hydrophila subsp. dhakensis is detected in the country.La investigación tuvo como objetivo la caracterización bioquímica e identificación molecular de cepas patógenas de Aeromonas sp aisladas de truchas arcoíris juveniles con signología compatible a aeromoniasis, cultivadas en seis piscigranjas de los departamentos de Junín (2), Pasco (2), Cajamarca (1) y Ancash (1), Perú. Se seleccionaron 60 truchas juveniles de 4-5 meses, con signología sugerente de brotes de aeromoniasis entre 2017 y 2018. Se realizó la eutanasia y necropsia y se registraron las lesiones externas e internas presentes. Se efectuó el aislamiento bacteriano de muestras de bazo y riñón anterior en agar TSA y GSP por 24-48 horas a 25 °C, se caracterizaron las colonias bacterianas mediante pruebas bioquímicas y se identificaron por PCR convencional utilizando cebadores específicos del gen ARNr 16S (Aeromonas spp.), fstA (A. salmonicida) y gyrB (A. hydrophila). Además, se realizó la secuenciación y se confirmó por análisis BLAST (NCBI). Las lesiones externas registradas fueron melanosis, aletas necróticas y hemorrágicas, úlceras en la piel y distensión abdominal. Las lesiones internas fueron hepatomegalia, esplenomegalia y hemorragia petequial en hígado, ciegos pilóricos y grasa peritoneal. Se aislaron 12 cepas en GSP (7 de Junín y 5 de Cajamarca), caracterizadas como Aeromonas spp, siendo negativas en las muestras de Pasco y Ancash. Las pruebas bioquímicas determinaron cuatro cepas como Aeromonas salmonicida y ocho como Aeromonas sp móviles, diferenciándose por pruebas de motilidad e indol. La identificación molecular por PCR determinó cuatro cepas A. salmonicida procedentes de Junín, una cepa A. hydrophila de Cajamarca y siete cepas móviles Aeromonas spp (3 de Junín y 4 de Cajamarca) que fueron negativas a la PCR de A. salmonicida y A. hydrophila. El análisis BLAST (NCBI) confirmó las cepas A. salmonicida y Aeromonas spp (identidad de 98-100%); además, la cepa de Cajamarca (identificada como A. hydrophila por bioquímica) presentó identidad de 95.65% con A. hydrophila subespecie dhakensis. En conclusión, Aeromonas salmonicida, A. hydrophila subespecie dhakensis y otras Aeromonas móviles patógenas causan signología asociada a aeromoniasis en truchas arcoiris juveniles en las piscigranjas de Junín y Cajamarca. Es la primera vez que se detecta A. hydrophila subsp. dhakensis en el país.

Insights into bear evolution from a Pleistocene polar bear genome

The polar bear (Ursus maritimus) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population history, including evidence for ancient admixture between polar bears and brown bears (Ursus arctos). Here, we extend our earlier studies of a 130,000- to 115,000-y-old polar bear from the Svalbard Archipelago using a 10x coverage genome sequence and 10 new genomes of polar and brown bears from contemporary zones of overlap in northern Alaska. We demonstrate a dramatic decline in effective population size for this ancient polar bear's lineage, followed by a modest increase just before its demise. A slightly higher genetic diversity in the ancient polar bear suggests a severe genetic erosion over a prolonged bottleneck in modern polar bears. Statistical fitting of data to alternative admixture graph scenarios favors at least one ancient introgression event from brown bears into the ancestor of polar bears, possibly dating back over 150,000 y. Gene flow was likely bidirectional, but allelic transfer from brown into polar bear is the strongest detected signal, which contrasts with other published work. These findings may have implications for our understanding of climate change impacts: Polar bears, a specialist Arctic lineage, may not only have undergone severe genetic bottlenecks but also been the recipient of generalist, boreal genetic variants from brown bears during critical phases of Northern Hemisphere glacial oscillations.Peer reviewe

Genetic analysis indicate superiority of perfomance of cape goosberry (Physalis peruviana L.) hybrids

The use of hybrids as a new type of cape gooseberry (Physalis peruviana L.) cultivars could improve yield in this crop, but little or no information is available on hybrid perfomance. We studied several vegetative characters, yield, fruit weight and fruit shape, soluble solids content (SSC), titratable acidity (TA) and ascorbic acid content (AAC) in three hybrids of cape gooseberry and their parents grown outdoors and in a glasshouse. The highest yields were obtained with hybrids, specially in a glasshouse. Interaction dominance environment for yield was very important; a higher dominance effect was detected in the glasshouse, than that observed outdoors. Quality characters were highly affected by the environment and showed variable results for the different families. For fruit composition traits, the additive and additive environment interactions were most important. Broad-sense heritability for all characters was high to medium (0.48-0.91), indicating that a high response to selection would be expected. Hybrids can improve cape gooseberry yield without impairing fruit quality.Leiva-Brondo, M.; Prohens Tomás, J.; Nuez Viñals, F. (2001). Genetic analysis indicate superiority of perfomance of cape goosberry (Physalis peruviana L.) hybrids. Journal of New Seeds. 3(3):71-84. doi:10.1300/J153v03n03_04718433Abak, K., Güler, H. Y., Sari, N., & Paksoy, M. (1994). EARLINESS AND YIELD OF PHYSALIS (P. IXOCARPA BROT. AND P. PERUVIANA L.) IN GREENHOUSE, LOW TUNNEL AND OPEN FIELD. Acta Horticulturae, (366), 301-306. doi:10.17660/actahortic.1994.366.37Kang, M. S. (1997). Using Genotype-by-Environment Interaction for Crop Cultivar Development. Advances in Agronomy Volume 62, 199-252. doi:10.1016/s0065-2113(08)60569-6Klinac, D. J. (1986). Cape gooseberry (Physalis peruviana) production systems. New Zealand Journal of Experimental Agriculture, 14(4), 425-430. doi:10.1080/03015521.1986.10423060Mather, K., & Jinks, J. L. (1977). Introduction to Biometrical Genetics. doi:10.1007/978-94-009-5787-9Mazer, S. J., & Schick, C. T. (1991). Constancy of population parameters for life history and floral traits in Raphanus sativus L. I. Norms of reaction and the nature of genotype by environment interactions. Heredity, 67(2), 143-156. doi:10.1038/hdy.1991.74Nyquist, W. E., & Baker, R. J. (1991). Estimation of heritability and prediction of selection response in plant populations. Critical Reviews in Plant Sciences, 10(3), 235-322. doi:10.1080/07352689109382313Pearcy, R. W. (1990). Sunflecks and Photosynthesis in Plant Canopies. Annual Review of Plant Physiology and Plant Molecular Biology, 41(1), 421-453. doi:10.1146/annurev.pp.41.060190.002225Péron, J. Y., Demaure, E., & Hannetel, C. (1989). POSSIBILITIES OF TROPICAL SOLANACEAE AND CUCURBITACEAE INTRODUCTION IN FRANCE. Acta Horticulturae, (242), 179-186. doi:10.17660/actahortic.1989.242.24Proctor, F. J. (1990). THE EUROPEAN COMMUNITY MARKET FOR TROPICAL FRUIT AND FACTORS LIMITING GROWTH. Acta Horticulturae, (269), 29-40. doi:10.17660/actahortic.1990.269.

Tomato: a crop species amenable to improvement by cellular and molecular methods

Tomato is a crop plant with a relatively small DNA content per haploid genome and a well developed genetics. Plant regeneration from explants and protoplasts is feasable which led to the development of efficient transformation procedures. In view of the current data, the isolation of useful mutants at the cellular level probably will be of limited value in the genetic improvement of tomato. Protoplast fusion may lead to novel combinations of organelle and nuclear DNA (cybrids), whereas this technique also provides a means of introducing genetic information from alien species into tomato. Important developments have come from molecular approaches. Following the construction of an RFLP map, these RFLP markers can be used in tomato to tag quantitative traits bred in from related species. Both RFLP's and transposons are in the process of being used to clone desired genes for which no gene products are known. Cloned genes can be introduced and potentially improve specific properties of tomato especially those controlled by single genes. Recent results suggest that, in principle, phenotypic mutants can be created for cloned and characterized genes and will prove their value in further improving the cultivated tomato.