Published March 31, 2020 | Version v1
Journal article Restricted

Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress

  • 1. ∗ & Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, PR China & ∗ & Southwestern Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement, Ministry of Agriculture, Chengdu, Sichuan, 610066, PR China

Description

Liu, Jia, Deng, Jia Lin, Tian, Yun (2020): Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress. Phytochemistry (112226) 171: 1-10, DOI: 10.1016/j.phytochem.2019.112226, URL: http://dx.doi.org/10.1016/j.phytochem.2019.112226

Files

Restricted

The record is publicly accessible, but files are restricted to users with access.

Linked records

Additional details

Identifiers

LSID
urn:lsid:plazi.org:pub:FF86FFDB9D369869FFB89D3AFFF70910

References

  • Akman, M., Carlson, J.E., Holsinger, K.E., Latimer, A.M., 2016. Transcriptome sequencing reveals population differentiation in gene expression linked to functional traits and environmental gradients in the South African shrub Protea repens. New Phytol. 210, 295-309.
  • Ana, C., Stefan, G.T., Juan Miguel, G.G., Javier, T., Manuel, T., Montserrat, R., 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676.
  • Antolin, M.C., Yoller, J., Sanchez-Diaz, M., 1995. Effects of temporary drought on nitratefed and nitrogen-fixing alfalfa plants. Plant Sci. 107, 159-165.
  • Bowler, C., Montagu, M.V., Inze, D., 1992. Superoxide dismutase and stress tolerance. Annu. Rev. Plant Biol. 43, 83-116.
  • Castrodiez, P., Puyravaud, J.P., Cornelissen, J.H.C., 2000. Leaf structure and anatomy as related to leaf mass per area variation in seedlings of a wide range of woody plant species and types. Oecologia 124, 476-486.
  • Chen, L., Yu, S., Li, S., Zhang, L., Zou, C., Yu, D., 2012. The role of WRKY transcription factors in plant abiotic stresses ☆. Biochim. Biophys. Acta 1819, 120-128.
  • Du, X.L., Zhang, X.F., Nie, H., Liu, M.L., Cheng, J.L., 2016. Transcript profiling analysis reveals crucial genes regulating main metabolism during adventitious root formation in cuttings of Morus alba L. Plant Growth Regul. 79, 251-262.
  • Flexas, J., Medrano, H., 2002. Drought-inhibition of photosynthesis in C-3 plants: stomatal and non-stomatal limitations revisited. Ann Bot-London 89, 183-189.
  • Giannopolitis, C.N., Ries, S.K., 1977. Superoxide dismutases: I. Occurrence in higher plants. Plant Physiol. 59, 309-314.
  • Gomes, F.P., Oliva, M.A., Mielke, M.S., Almeida, A.A.F., Aquino, L.A., 2010. Osmotic adjustment, proline accumulation and cell membrane stability in leaves of Cocos nucifera submitted to drought stress. Sci Hortic-Amsterdam 126, 379-384.
  • Gorka, E., Sa D, L., Juan Jose, I., Manuel, S.D., Jean-Christophe, A., 2010. Biomass partitioning, morphology and water status of four alfalfa genotypes submitted to progressive drought and subsequent recovery. J. Plant Physiol. 167, 114-120.
  • Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Xian, A., Lin, F., Raychowdhury, R., Zeng, Q., 2011. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat. Biotechnol. 29, 644-652.
  • Griffiths, H., Maj, P., 2002. Plant responses to water stress - Preface. Ann Bot-London 89, 801-802.
  • Grimplet, J., Romieu, C., Audergon, J.M., Marty, I., Albagnac, G., Lambert, P., Bouchet, J.P., Terrier, N., 2010. Transcriptomic study of apricot fruit (Prunus armeniaca) ripening among 13006 expressed sequence tags. Physiol Plant. Physiol Plantarum 125, 281-292.
  • Guo, Y., Jia, L.I., 2002. Changes of fatty acid composition of membrane lipid, ethylene release and lipoxygenase activity in leaves of apricot under drought stress. J. Zhejiang Agric. Univ. 28, 513-517.
  • Hao, Z.B., Cang, J., Xu, Z., 2004. Plant Physiology Experiment. Harbin Institute of Technology Press, Harbin, China.
  • Hsiao, T.C., Acevedo, E., Fereres, E., Henderson, D.W., 1976. Water stress, growth, and osmotic adjustment. Philos. Trans. R. Soc. Lond. 273, 479-500.
  • Huber, S.C., Moreland, D.E., 1981. Co-transport of potassium and sugars across the plasmalemma of mesophyll protoplasts. Plant Physiol. 67, 163-169.
  • Huie, L., Weijie, Y., Yaru, F., Shaoke, L., Qiqiang, G., 2015. De novo assembly and discovery of genes that are involved in drought tolerance in Tibetan Sophora moorcroftiana. PLoS One 10, e111054.
  • Irigoyen, J.J., Emerich, D.W., Sanchez-Diaz, M., 2010. Alfalfa leaf senescence induced by drought stress: photosynthesis, hydrogen peroxide metabolism, lipid peroxidation and ethylene evolution. Physiol Plantarum 84, 67-72.
  • Ismail, M.R., Davies, W.J., 1998. Root restriction affects leaf growth and stomatal response: the role of xylem sap ABA. Sci Hortic-Amsterdam 74, 268.
  • Ismail, M.R., Davies, W.J., Awad, M.H., 2002. Leaf growth and stomatal sensitivity to ABA in droughted pepper plants. Sci Hortic-Amsterdam 96, 313-327.
  • Jaleel, C.A., Manivannan, P., Kishorekumar, A., Sankar, B., Gopi, R., Somasundaram, R., Panneerselvam, R., 2007. Alterations in osmoregulation, antioxidant enzymes and indole alkaloid levels in Catharanthus roseus exposed to water deficit. Colloids Surfaces B Biointerfaces 59, 150-157.
  • Kramer, P.J., 2010. Changing concepts regarding plant water relations. Plant Cell Environ. 11, 565-568.
  • Leafe, E.L., Jones, M.B., Stiles, W., 1980. Physiological Effects of Water Stress on Perennial Ryegrass in the Field. XIII International Grassland Congress, Lolium perenne. German Democratic Republic, Leipzig.
  • Li, B., Dewey, C.N., 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinf.
  • Li, F., Huang, Z., Lun, S., 2000. A Study on Rules of Spatiao-Temporal Change and Water Use Efficiency of Corn. Acta Botanica Boreali-Occidentalia Sinica 20 (6), 1010-1015.
  • Li, H.S., Sun, Q., Zhao, S.J., Zhang, W.H., 2000b. Principles and Techniques of Plant Physiological Biochemical Experiment. Higher Education, Beijing, pp. 195-197.
  • Liu, T., Zhu, S., Tang, Q., Yu, Y., Tang, S., 2013. Identification of drought stress-responsive transcription factors in ramie (Boehmeria nivea L. Gaud). BMC Plant Biol. 13, 130.
  • Lopes, M.S., Sefc, K.M., Laimer, M., Machado, A.D.C., 2010. Identification of microsatellite loci in apricot. Mol Ecol Resour 2, 24-26.
  • Machlis, L., Torrey, J.G., 1956. Plants in action. A laboratory manual of plant physiology. Plants in action. A laboratory manual of plant physiology.
  • Melendreras, A.T., Galego, R., Pastor, A.P., Sanchez, M.D.C.R., 1999. Gas exchange and water relations of young apricot plants under drought conditions. J Agr Sci- Cambridge 132, 445-452.
  • Miyashita, K., Tanakamaru, S., Maitani, T., Kimura, K., 2005. Recovery responses of photosynthesis, transpiration, and stomatal conductance in kidney bean following drought stress. Environ. Exp. Bot. 53, 205-214.
  • Mohammadkhani, N., Heidari, R., 2008. Drought-induced accumulation of soluble sugars and proline in two maize varieties. World Appl. Sci. J. 3, 448-453.
  • Moliterni, V.M.C., Paris, R., Onofri, C., Orru, L., Cattivelli, L., Pacifico, D., Avanzato, C., Ferrarini, A., Delledonne, M., Mandolino, G., 2015. Early transcriptional changes in Beta vulgaris in response to low temperature. Planta 242, 187-201.
  • Nagarjun, V., Poelstra, J.W., Axel, K., Wolf, J.B.W., 2013. Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Mol. Ecol. 22, 620-634.
  • Ober, E.S., Bloa, M.L., Clark, C.J.A., Royal, A., Jaggard, K.W., Pidgeon, J.D., 2005. Evaluation of physiological traits as indirect selection criteria for drought tolerance in sugar beet. Field Crop. Res. 91, 231-249.
  • Olsson, M., 1995. Alterations in lipid composition, lipid peroxidation and anti-oxidative protection during senescence in drought stressed plants and non drought stressed plants of Pisum sativum. Plant Physiol. Biochem. 33, 547-553.
  • O'Rourke, J.A., S Samuel, Y., Miller, S.S., Bruna, B., Junqi, L., Ariel, R., Zoltan, B., Claudia, U.S., Jin, T.Z., Deborah, A., 2013. An RNA-Seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants. Plant Physiol. 161, 705-724.
  • Pan, R.C., Zheng, X.N., Wen, Z.Q., 1994. Change OF water physiology OF cymbidium sinense during soil drought period. Acta Bot. Yunnanica 16, 379-384.
  • Pertea, G., Huang, X., Liang, F., Antonescu, V., Sultana, R., Karamycheva, S., Lee, Y., White, J., Cheung, F., Parvizi, B., 2003. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19, 651-652.
  • Ron, M., Sandy, V., Martin, G., Frank, V.B., 2004. Reactive oxygen gene network of plants. Trends Plant Sci. 9, 498.
  • Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninci, P., Hayashizaki, Y., Shinozaki, K., 2001. Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13, 61-72.
  • Sheffer, K.M., Dunn, J.H., Minner, D.D., 1987. Summer drought response and rooting depth of three cool-season turfgrasses. Hortscience.
  • Shen, B., Jensen, R.G., Bohnert, H.J., 1997. Increased resistance to oxidative stress in transgenic plants by targeting mannitol biosynthesis to chloroplasts. Plant Physiol. 113, 1177-1183.
  • Shinozaki, K., Yamaguchishinozaki, K., 2007. Gene networks involved in drought stress response and tolerance. J. Exp. Bot. 58, 221.
  • Singh, H., Deshmukh, R.K., Singh, A., Singh, A.K., Gaikwad, K., Sharma, T.R., Mohapatra, T., Singh, N.K., 2010. Highly variable SSR markers suitable for rice genotyping using agarose gels. Mol Breeding 25, 359-364.
  • Strain, H.H., Svec, W.A., 1966. 2 - extraction, separation, estimation, and isolation of the chlorophylls *. Chlorophylls 21-66.
  • Sturgeon, A., Stull, J.W., Costa, M.C., Weese, J.S., 2013. Metagenomic analysis of the canine oral cavity as revealed by high-throughput pyrosequencing of the 16S rRNA gene. Vet. Microbiol. 162, 891-898.
  • Sui, N., Li, M., Liu, X.Y., Wang, N., Fang, W., Meng, Q.W., 2007. Response of xanthophyll cycle and chloroplastic antioxidant enzymes to chilling stress in tomato over-expressing glycerol-3-phosphate acyltransferase gene. Photosynthetica 45, 447-454.
  • Tim, D.M., Evi, M., Micha, L.V., Simon, D., Geert, T., Jean-Pierre, R., Sarah, D.K., Pierre, D., Gerben, M., Wim, V.C., 2013. Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing. PLoS One 8, e59068.
  • Upham, B.L., Jahnke, L.S., 1986. Photooxidative reactions in chloroplast thylakoids. Evidence for a Fenton-type reaction promoted by superoxide or ascorbate. Photosynth. Res. 8, 235-247.
  • Wang, B., Guo, G., Wang, C., Lin, Y., Wang, X., Zhao, M., Guo, Y., He, M., Zhang, Y., Pan, L., 2010. Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res. 38, 5075-5087.
  • Wu, S., Hu, C., Tan, Q., Nie, Z., Sun, X., 2014. Effects of molybdenum on water utilization, antioxidative defense system and osmotic-adjustment ability in winter wheat (Triticumaestivum) under drought stress. Plant Physiol. Biochem. 83, 365-374.
  • Xin, Z.X., Kai, H.L., Quan, Z.X., Zhou, L., Yan, P., 2014. Effects of heat acclimation on photosynthesis, antioxidant enzyme activities, and gene expression in orchardgrass under heat stress. Molecules 19, 13564-13576.
  • Xiong, L., Schumaker, K.S., Zhu, J.K., 2002. Cell signaling during cold, drought, and salt stress. PLANT CELL 14, S165.
  • Yi It, D., Yi It, N., Mavi, A., 2009. Antioxidant and antimicrobial activities of bitter and sweet apricot (Prunus armeniaca L.) kernels. Braz. J. Med. Biol. Res. 42, 346-352.
  • Zhang, G., Guo, G.X., Zhang, Y., Li, Q., Li, R., Zhuang, R., Lu, Z., He, Z., Fang, X., Chen, L., 2010. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res. 20, 646-654.
  • Zhang, J., Luo, W., Zhao, Y., Xu, Y., Song, S., Chong, K., 2016. Comparative metabolomic analysis reveals a reactive oxygen species- dominated dynamic model underlying chilling environment adaptation and tolerance in rice. New Phytol. 211, 1295-1310.
  • Zhang, N.H., Qi, Z., 2005. Effect of calcium on alleviation of decreased photosynthetic ability in salt-stressed maize leaves. Acta Phytoecol. Sin. 29, 324-330.
  • Zhang, N., Liu, B., Ma, C., Zhang, G., Chang, J., Si, H., Wang, D., 2014. Transcriptome characterization and sequencing-based identification of drought-responsive genes in potato. Mol. Biol. Rep. 41, 505-517.
  • Zhang, Z., Pang, T., Li, Q., Zhang, L., Li, L., Liu, J., 2015. Transcriptome sequencing and characterization for Kappaphycus alvarezii. Eur. J. Phycol. 50, 400-407.
  • Zhu, Y., Liu, Q., Xu, W., Zhang, J., Wang, X., Nie, G., Yao, L., Wang, H., Lin, C., 2019. De novo assembly and discovery of genes that involved in drought tolerance in the common vetch. Int. J. Mol. Sci. 20, 328.
  • Zhu, Y., Wang, X., Huang, L., Lin, C., Zhang, X., Xu, W., Peng, J., Li, Z., Yan, H., Luo, F., 2017. Transcriptomic identification of drought-related genes and SSR markers in Sudan grass based on RNA-seq. Front. Plant Sci. 8, 687.