57 research outputs found
Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data
Background: Identification of biological specimens is a major requirement for
a range of applications. Reference-free methods analyse unprocessed sequencing
data without relying on prior knowledge, but generally do not scale to
arbitrarily large genomes and arbitrarily large phylogenetic distances.
Results: We present Cnidaria, a practical tool for clustering genomic and
transcriptomic data with no limitation on genome size or phylogenetic
distances. We successfully simultaneously clustered 169 genomic and
transcriptomic datasets from 4 kingdoms, achieving 100% identification accuracy
at supra-species level and 78% accuracy for species level. Discussion: CNIDARIA
allows for fast, resource-efficient comparison and identification of both raw
and assembled genome and transcriptome data. This can help answer both
fundamental (e.g. in phylogeny, ecological diversity analysis) and practical
questions (e.g. sequencing quality control, primer design).Comment: 47 pages, 13 figure
MBW complexes impinge on anthocyanidin reductase gene regulation for proanthocyanidin biosynthesis in persimmon fruit
[EN] MBW protein complexes containing MYB, bHLH and WD40 repeat factors are known transcriptional regulators of secondary metabolites production such as proanthocyanidins and anthocyanins, and developmental processes such as trichome formation in many plant species. DkMYB2 and DkMYB4 (MYB-type), DkMYC1 (bHLH-type) and DkWDR1 (WD40-type) factors have been proposed by different authors to take part of persimmon MBW complexes for proanthocyanidin accumulation in immature fruit, leading to its characteristic astringent flavour with important agronomical and ecological effects. We have confirmed the nuclear localization of these proteins and their mutual physical interaction by bimolecular fluorescence complementation analysis. In addition, transient expression of DkMYB2, DkMYB4 and DkMYC1 cooperatively increase the expression of a persimmon anthocyanidin reductase gene (ANR), involved in the biosynthesis of cis-flavan-3-ols, the structural units of proanthocyanidin compounds. Collectively, these data support the presence of MBW complexes in persimmon fruit and suggest their coordinated participation in ANR regulation for proanthocyanidin production.This work was funded by the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-FEDER (grant no. RF2013-00043-C02-02 and RTA2017-00011-C03-01). FG-M was funded by a fellowship co-financed by the Generalitat Valenciana and European Social Fund (2014 2020) (grant no. ACIF/2016/115).Gil Muñoz, F.; Sanchez Navarro, JA.; Besada Ferreiro, CM.; Salvador Perez, AA.; Badenes Catala, M.; Naval Merino, MDM.; Rios Garcia, G. (2020). MBW complexes impinge on anthocyanidin reductase gene regulation for proanthocyanidin biosynthesis in persimmon fruit. Scientific Reports. 10:1-11. https://doi.org/10.1038/s41598-020-60635-wS11110Dixon, R. A., Xie, D.-Y. & Sharma, S. B. Proanthocyanidins–a final frontier in flavonoid research? New Phytol. 165, 9–28 (2005).Yonemori, K. & Matsushima, J. Property of development of the tannin cells in non-astringent type fruits of Japanese persimmon (Diospyros kaki) and its relationship to natural deastringency. J. Jpn. Soc. Hortic. Sci. 54, 201–208 (1985).Salvador, A. et al. Physiological and structural changes during ripening and deastringency treatment of persimmon fruit cv. ‘Rojo Brillante’. Postharvest Biol. Tec. 46, 181–188 (2007).Bernays, E. A., Driver, G. C. & Bilgener, M. Herbivores and plant tannins. In Advances in Ecological Research (eds. Begon, M., Fitter, A. H., Ford, E. D. & MacFadyen, A.) 19, 263–302 (Academic Press, 1989).Tessmer, M. A. et al. Microstructural changes while persimmon fruits mature and ripen. Comparison between astringent and non-astringent cultivars. Postharvest Biol. Tec. 120, 52–60 (2016).Nishiyama, S. et al. Characterization of a gene regulatory network underlying astringency loss in persimmon fruit. Planta 247, 733–743 (2018).Sugiura, A., Yonemori, K., Harada, H. & Tomama, T. Changes of ethanol and acetaldehyde contents in Japanese persimmon fruits and their relation to natural deastringency. Studies from Inst. Hort. Kyoto Univ. 9, 41–47 (1979).Sugiura, A. & Tomana, T. Relationships of ethanol production by seeds of different types of Japanese persimmons and their tannin content. HortSci. 18, 319–321 (1983).Ben-Arie, R. & Sonego, L. Temperature affects astringency removal and recurrence in persimmon. J. Food Sci. 58, 1397–1400 (1993).Matsuo, T. & Itoo, S. A model experiment for de-astringency of persimmon fruit with high carbon dioxide treatment: in vitro gelation of kaki-tannin by reacting with acetaldehyde. Agr. Biol. Chem. Tokyo 46, 683–689 (1982).Pesis, E. & Ben-Arie, R. Involvement of acetaldehyde and ethanol accumulation during induced deastringency of persimmon fruits. J. Food Sci. 49, 896–899 (1984).Kanzaki, S., Yonemori, K., Sugiura, A., Sato, A. & Yamada, M. Identification of molecular markers linked to the trait of natural astringency loss of Japanese persimmon (Diospyros kaki) fruit. J. Am. Soc. Hortic. Sci. 126, 51–55 (2001).Yamada, M. & Sato, A. Segregation for fruit astringency type in progenies derived from crosses of ‘Nishimurawase’×pollination constant non-astringent genotypes in oriental persimmon (Diospyros kaki Thunb.). Sci. Hortic.-Amsterdam 92, 107–111 (2002).Besada, C. et al. Chloride stress triggers maturation and negatively affects the postharvest quality of persimmon fruit. Involvement of calyx ethylene production. Plant Physiol. Biochem. 100, 105–112 (2016).Lepiniec, L. et al. Genetics and biochemistry of seed flavonoids. Annu. Rev. Plant Biol. 57, 405–430 (2006).Tanner, G. J. et al. Proanthocyanidin biosynthesis in plants. Purification of legume leucoanthocyanidin reductase and molecular cloning of its cDNA. J. Biol. Chem. 278, 31647–31656 (2003).Xie, D.-Y., Sharma, S. B., Paiva, N. L., Ferreira, D. & Dixon, R. A. Role of anthocyanidin reductase, encoded by BANYULS in plant flavonoid biosynthesis. Science 299, 396–399 (2003).Ikegami, A., Eguchi, S., Kitajima, A., Inoue, K. & Yonemori, K. Identification of genes involved in proanthocyanidin biosynthesis of persimmon (Diospyros kaki) fruit. Plant Science 172, 1037–1047 (2007).Akagi, T. et al. Expression balances of structural genes in shikimate and flavonoid biosynthesis cause a difference in proanthocyanidin accumulation in persimmon (Diospyros kaki Thunb.) fruit. Planta 230, 899–915 (2009).Baudry, A. et al. TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant J. 39, 366–380 (2004).Xu, W. et al. Complexity and robustness of the flavonoid transcriptional regulatory network revealed by comprehensive analyses of MYB-bHLH-WDR complexes and their targets in Arabidopsis seed. New Phytol. 202, 132–144 (2014).Xu, W., Dubos, C. & Lepiniec, L. Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends Plant Sci. 20, 176–185 (2015).Hichri, I. et al. The basic helix-loop-helix transcription factor MYC1 is involved in the regulation of the flavonoid biosynthesis pathway in grapevine. Mol. Plant 3, 509–523 (2010).Schaart, J. G. et al. Identification and characterization of MYB-bHLH-WD40 regulatory complexes controlling proanthocyanidin biosynthesis in strawberry (Fragaria × ananassa) fruits. New Phytol. 197, 454–467 (2013).Gesell, A., Yoshida, K., Tran, L. T. & Constabel, C. P. Characterization of an apple TT2-type R2R3 MYB transcription factor functionally similar to the poplar proanthocyanidin regulator PtMYB134. Planta 240, 497–511 (2014).Naval, M. et al. A WD40-repeat protein from persimmon interacts with the regulators of proanthocyanidin biosynthesis DkMYB2 and DkMYB4. Tree Genet. Genomes 12, 13 (2016).Akagi, T. et al. DkMyb4 is a Myb transcription factor involved in proanthocyanidin biosynthesis in persimmon fruit. Plant Physiol. 151, 2028–2045 (2009).Akagi, T., Ikegami, A. & Yonemori, K. DkMyb2 wound-induced transcription factor of persimmon (Diospyros kaki Thunb.), contributes to proanthocyanidin regulation. Planta 232, 1045–1059 (2010).Su, F., Hu, J., Zhang, Q. & Luo, Z. Isolation and characterization of a basic Helix–Loop–Helix transcription factor gene potentially involved in proanthocyanidin biosynthesis regulation in persimmon (Diospyros kaki Thunb.). Sci. Hortic.-Amsterdam 136, 115–121 (2012).Hribal, J., Zavrtanik, M., Simćić, M. & Vidrih, R. Changes during storing and astringency removal of persimmon fruit Diospyros kaki L. Acta Aliment. Hung. 29, 123–136 (2000).Nesi, N., Jond, C., Debeaujon, I., Caboche, M. & Lepiniec, L. The Arabidopsis TT2 gene encodes an R2R3 MYB domain protein that acts as a key determinant for proanthocyanidin accumulation in developing seed. Plant Cell 13, 2099–2114 (2001).Zhao, M., Morohashi, K., Hatlestad, G., Grotewold, E. & Lloyd, A. The TTG1-bHLH-MYB complex controls trichome cell fate and patterning through direct targeting of regulatory loci. Development 135, 1991–1999 (2008).Weill, U. et al. Assessment of GFP tag position on protein localization and growth Fitness in yeast. J. Mol. Biol. 431, 636–641 (2019).Wang, P. et al. A sucrose-induced MYB (SIMYB) transcription factor promoting proanthocyanidin accumulation in the tea plant (Camellia sinensis). J. Agric. Food Chem. 67, 1418–1428 (2019).Baudry, A., Caboche, M. & Lepiniec, L. TT8 controls its own expression in a feedback regulation involving TTG1 and homologous MYB and bHLH factors, allowing a strong and cell-specific accumulation of flavonoids in Arabidopsis thaliana. Plant J. 46, 768–779 (2006).Albert, N. W. et al. A conserved network of transcriptional activators and repressors regulates anthocyanin pigmentation in eudicots. Plant Cell 26, 962–980 (2014).Bellini, E. Cultural practices for persimmon production. In Options Méditerranéennes. Série A: Séminaires Méditerranéens (CIHEAM) (eds. Bellini, E. & Giordani, E.) 51. 39–52 (CIHEAM-IAMZ, 2002).Taira, S. Astringency in Persimmon. In Fruit Analysis (eds. Linskens, H. F. & Jackson, J. F.) 97–110 (Springer Berlin Heidelberg, 1995).Arnal, L. & Rio, M. A. D. Quality of persimmon fruit cv. Rojo brillante during storage at different temperatures. Span. J. Agric. Res. 2, 243–247 (2004).Akagi, T., Henry, I. M., Tao, R. & Comai, L. A Y-chromosome–encoded small RNA acts as a sex determinant in persimmons. Science 346, 646–650 (2014).Doyle, J. J. & Doyle, J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19, 11–15 (1987).Herranz, M. C., Sanchez-Navarro, J. A., Aparicio, F. & Pallás, V. Simultaneous detection of six stone fruit viruses by non-isotopic molecular hybridization using a unique riboprobe or ‘polyprobe’. J. Virol. Methods 124, 49–55 (2005).Leastro, M. O., Pallás, V., Resende, R. O. & Sánchez-Navarro, J. A. The movement proteins (NSm) of distinct tospoviruses peripherally associate with cellular membranes and interact with homologous and heterologous NSm and nucleocapsid proteins. Virology 478, 39–49 (2015).Knoester, M. et al. Ethylene-insensitive tobacco lacks nonhost resistance against soil-borne fungi. Proc. Natl. Acad. Sci. USA 95, 1933–1937 (1998).Hellens, R. P., Edwards, E. A., Leyland, N. R., Bean, S. & Mullineaux, P. M. pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation. Plant Mol. Biol. 42, 819–832 (2000).Hamilton, C. M., Frary, A., Lewis, C. & Tanksley, S. D. Stable transfer of intact high molecular weight DNA into plant chromosomes. Proc. Natl. Acad. Sci. USA 93, 9975–9979 (1996).Genovés, A., Pallás, V. & Navarro, J. A. Contribution of topology determinants of a viral movement protein to its membrane association, intracellular traffic, and viral cell-to-cell movement. J. Virol. 85, 7797–7809 (2011).Aparicio, F., Sánchez-Navarro, J. A. & Pallás, V. In vitro and in vivo mapping of the Prunus necrotic ringspot virus coat protein C-terminal dimerization domain by bimolecular fluorescence complementation. J. Gen. Virol. 87, 1745–1750 (2006).Laemmli, U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685 (1970).Gambino, G., Perrone, I. & Gribaudo, I. A Rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochem. Anal. 19, 520–525 (2008)
Arabidopsis BIRD Zinc Finger Proteins Jointly Stabilize Tissue Boundaries by Confining the Cell Fate Regulator SHORT-ROOT and Contributing to Fate Specification
Arabidopsis RETINOBLASTOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control
The rapidly proliferating cells in plant meristems must be protected from genome damage. Here, we show that the regulatory role of the Arabidopsis RETINOBLASTOMA RELATED (RBR) in cell proliferation can be separated from a novel function in safeguarding genome integrity. Upon DNA damage, RBR and its binding partner E2FA are recruited to heterochromatic γH2AX-labelled DNA damage foci in an ATM- and ATR-dependent manner. These γH2AX-labelled DNA lesions are more dispersedly occupied by the conserved repair protein, AtBRCA1, which can also co-localise with RBR foci. RBR and AtBRCA1 physically interact in vitro and in planta. Genetic interaction between the RBR-silenced amiRBR and Atbrca1 mutants suggests that RBR and AtBRCA1 may function together in maintaining genome integrity. Together with E2FA, RBR is directly involved in the transcriptional DNA damage response as well as in the cell death pathway that is independent of SOG1, the plant functional analogue of p53. Thus, plant homologs and analogues of major mammalian tumour suppressor proteins form a regulatory network that coordinates cell proliferation with cell and genome integrity
Ciencias de la Biología y Agronomía
Este volumen I contiene 17 capítulos arbitrados que se ocupan de estos asuntos en Tópicos Selectos de Ciencias de la Biología y Agronomía, elegidos de entre las contribuciones, reunimos algunos investigadores y estudiantes. Se presenta un Estudio Comparativo de los Recursos Hidrológico-Forestales de la Microcuenca de la Laguna de Epatlan, Pue. (1993 a 2014); la Situación Actual de la Mancha de Asfalto en Maíz (Zea mays L.) en los Municipios de Jiquipilas y Ocozocoautla, Chiapas, México; las poblaciones sobresalientes de maíz de la raza Zapalote Chico, en la Región Istmeña de Oaxaca; Se indica el índice de área foliar de cultivo de Chile Poblano mediante dos métodos en condiciones protegidas; Esquivel, Urzúa y Ramírez exploran el efecto de la biofertilización con Azospirillum en el crecimiento y producción de Jitomate; esbozan su artículo sobre la determinación del nivel de Heterosis en híbridos de Maíz para la Comarca Lagunera; una investigación sobre la estabilización de semilla de Solanum lycopersicum durante el almacenamiento y estimulación de la germinación; acotan sobre el CTAB como una nueva opción para la detección de Huanglongbing en cítricos, plantean su evaluación sobre el aluminio y cómo afecta la vida de florero de Heliconia psittacorum; indican sobre el impacto del H-564C, como un híbrido de maíz con alta calidad de proteina para el trópico húmedo de México; presetan su investigación sobre la producción de Piña Cayena Lisa y MD2 (Ananas comosus L.) en condiciones de Loma Bonita, en Oaxaca; acotan sobre el efecto de coberteras como control biológico por conservación contra áfidos en Nogal Pecanero; esbozan sobre la caracterización de cuatro genotipos de Frijol Negro en Martínez de la Torre, Veracruz, México; presentan una caracterización hidroecológica de la microcuenca de Arroyo Prieto, Yuriría, Gto., y alternativas para su restauración ambiental; presentan su investigación sobre el efecto del hongo Beauveria bassiana sobre solubilización de fosfatos y la disponibilidad de fósforo en el suelo; plantean su investigación sobre la Germinación y regeneración in vitro de Epidendrum falcatum LINDL; esbozan su artículo sobre genotipos de frijol negro y su tolerancia a sequía terminal en Veracruz, México
Probing the roles of LRR RLK genes in Arabidopsis thaliana roots using a custom T-DNA insertion set
Leucine-rich repeat receptor-like protein kinases (LRR RLKs) represent the largest group of Arabidopsis RLKs with approximately 235 members. A minority of these LRR RLKs have been assigned to diverse roles in development, pathogen resistance and hormone perception. Using a reverse genetics approach, a collection of homozygous T-DNA insertion lines for 69 root expressed LRR RLK genes was screened for root developmental defects and altered response after exposure to environmental, hormonal/chemical and abiotic stress. The obtained data demonstrate that LRR RLKs play a role in a wide variety of signal transduction pathways related to hormone and abiotic stress responses. The described collection of T-DNA insertion mutants provides a valuable tool for future research into the function of LRR RLK genes
Estudios de Caso sobre Ciencias Agropecuarias y Rurales en el siglo XXI.
Libro científico sobre estudios de casos en el medio agropecuario y ruralCon el advenimiento del siglo XXI y el avance de los procesos de globalización, el medio rural presenta diversos cambios económicos, sociales, políticos y culturales. Lo anterior significa que el campo es un objeto de estudio altamente dinámico, complejo e inasible. las ciencias agropecuarias y rurales, en la actualidad, requieren de un abordaje sistémico e interdisciplinario que den cuenta de la heterogeneidad de situaciones y contextos que enfrenta el campo mexicano. La presente obra agrupa 18 estudios de caso, que capturan algunas fotografías de las diversas problemáticas de la ruralidad mexicana, con lo cual se pretende dar cuenta tanto de los objetivos de estudio como de la perspectiva teórico metodológico desde que estos son abordados. lo anterior tiene que ver con el hecho de que las ciencias agropecuarias y rurales manifiestan un alto grado de observación empírica, motivo por el que los estudios de caso se convierten en la perspectiva metodológica idónea que permite ir y venir de la realidad a la teoría y viceversa para la construcción de objetos de estudio. En este volumen se aborda una gran diversidad de casos, que sintetizan la heterogeneidad de enfoques y perspectivas mediante las cuales los fenómenos agropecuarios y rurales han sido abordados en el Instituto de Ciencias Agropecuarias y Rurales de la Universidad Autónoma del Estado de México, en los últimos 30 años
Prioritization of candidate genes in QTL regions based on associations between traits and biological processes
- …