Avocado Fruit Pulp Transcriptomes in the after-Ripening Process
Avocado is an important tropical fruit whose after-ripening process is still poorly understood. The fatty acid, phenolics, flavonoids, and tannins were analyzed in ‘Lisa’ avocado (Persea americana Mill. ‘Lisa’) fruit pulp during after-ripening. The transcriptome was analyzed to screen for transcripts associated with the aforementioned after-ripening parameters. The results showed that there were no significant differences in the total fatty acid content among the preclimacteric, climacteric, and postclimacteric stages. Nevertheless, the concentrations of C18:3 (α-linolenic acid) were significantly higher in the climacteric and postclimacteric stages than the preclimacteric stage. RNAseq generated 235,082 transcripts and 151,545 unigenes. In addition, 4,324 DEGs were produced among the three stages. KEGG analysis of the DEGs suggested the pathways about “α-linolenic acid metabolism, unsaturated fatty acid biosynthesis”, “fatty acid degradation”, “linoleic acid metabolism and fatty acid biosynthesis”, “linoleic acid metabolism and fatty acid elongation”, and “fatty acid elongation” may all contribute to the C18:3 variations in ‘Lisa’ avocado fruit pulp. Several transcription factors, including the ethylene-related transcription factors, such as NAC, MYB, bHLH, and WRKY, were also identified in the DEGs database. This study generated transcript data and screened the transcription factors involved in the avocado after-ripening process. This information could be used to control after-ripening in avocado and maintain fruit quality during storage.
Bora PS, Narain N, Rocha RVM, Paulo MQ (2001). Characterization of the oils from the pulp and seeds of avocado (cultivar: Fuerte) fruits. Grasas y Aceites 52:171-174.
Djami-Tchatchou AT, Straker CJ, Allie F (2012). 454 Sequencing for the identification of genes differentially expressed in avocado fruit (cultivar: Fuerte) infected by Colletotrichum gloeosporioides. Journal of Phytopathology 160(9):449-460.
Djeridane A, Yousfi M, Nadjemi B, Boutassouna D, Stocker P, Vidal N (2006). Antioxidant activity of some Algerian medicinal plants extracts containing phenolic compounds. Food Chemistry 97(4):654-660.
Dreher ML, Davenport AJ (2013). Hass avocado composition and potential health effects. Critical Reviews in Food Science and Nutrition 53(7):738-750.
Elitzur T, Vrebalov J, Giovannoni JJ, Goldschmidt EE, Friedman H (2010). The regulation of MADS-box gene expression during ripening of banana and their regulatory interaction with ethylene. Journal of Experimental Botany 61(5):1523-1535.
Elitzur T, Yakir E, Quansah L, Zhangjun F, Vrebalov JT, Khayat E, … Friedman H (2016). Banana MaMADS transcription factors are necessary for fruit ripening and molecular tools to promote shelf-life and food security. Plant Physiology 171(1):380-391.
Gapper NE, McQuinn RP, Giovannoni JJ (2013). Molecular and genetic regulation of fruit ripening. Plant Molecular Biology 82(6):575-591.
Garber M, Grabherr MG, Guttman M, Trapnell C (2011). Computational methods for transcriptome annotation and quantification using RNA-seq. Nature Methods 8(6):469-477.
Gaydou EM, Lozano Y, Ratovohery J (1987). Triglyceride and fatty acid compositions in the mesocarp of Persea americana during fruit development. Phytochemistry 26(6):1595-1597.
Giovannoni JJ (2007). Fruit ripening mutants yield insights into ripening control. Current Opinion in Plant Biology 10(3):283-289.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, … Regev A (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29(7):644-652.
Handa Y, Nishide H, Takeda N, Suzuki Y, Kawaguchi M, Saito K (2015). RNA-seq transcriptional profiling of an arbuscular mycorrhiza provides insights into regulated and coordinated gene expression in Lotus japonicus and Rhizophagus irregularis. Plant and Cell Physiology 56(8):1490-1511.
Hara A, Radin NS (1978). Lipid extraction of tissues with a low-toxicity solvent. Analytical Biochemistry 90(1):420-426.
Ibarra-Laclette E, Méndez-Bravo A, Pérez-Torres CA, Albert VA, Mockaitis K, Kilaru A, … Herrera-Estrella L (2015). Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids. BMC Genomics 16(1):599.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, … Yamanishi Y (2008). KEGG for linking genomes to life and the environment. Nucleic Acids Research 36(Suppl 1):D480-D484.
Katalinic V, Milos M, Kulisic T, Jukic M (2006). Screening of 70 medicinal plant extracts for antioxidant capacity and total phenols. Food Chemistry 94(4):550-557.
Kilaru A, Cao X, Dabbs PB, Sung HJ, Rahman MM, Thrower N, … Ohlrogge JB (2015). Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea americana mesocarp. BMC Plant Biology 15(1):203.
Li B, Dewey C (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12(1):323.
Mahomed W, Van den Berg N (2011). EST sequencing and gene expression profiling of defence-related genes from Persea americana infected with Phytophthora cinnamomi. BMC Plant Biology 11(1):167.
Manning K, Tör M, Poole M, Hong Y, Thompson AJ, King GJ, … Seymour GB (2006). A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nature Genetics 38(8):948-952.
Mao X, Cai T, Olyarchuk JG, Wei L (2005). Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21(19):3787-3793.
Ozdemir F, Topuz A (2004). Changes in dry matter, oil content and fatty acids composition of avocado during harvesting time and post-harvesting ripening period. Food Chemistry 86(1):79-83.
Reeksting BJ, Coetzer N, Mahomed W, Engelbrecht J, Van den Berg N (2014). De novo sequencing, assembly, and analysis of the root transcriptome of Persea americana (Mill.) in response to Phytophthora cinnamomi and flooding. PLoS ONE 9(2):e86399.
Shan W, Kuang J, Chen L, Xie H, Peng H, Xiao Y, … Lu W (2012). Molecular characterization of banana NAC transcription factors and their interactions with ethylene signalling component EIL during fruit ripening. Journal of Experimental Botany 63(14):5171-5187.
Shu B, Li WC, Liu LQ, Wei YZ, Shi SY (2016). Transcriptomes of arbuscular mycorrhizal fungi and litchi host interaction after tree girdling. Frontiers in Microbiology 7(636):408.
Singleton VL, Rossi JA (1965). Colorimetry of total phenolics with phosphomolybdic-phosphotungstic acid reagents. American Journal of Enology and Viticulture 16(3):144-158.
Storey JD (2003). The positive false discovery rate: a Bayesian interpretation and the q-value. The Annals of Statistics 31(6):2013-2035.
Villa-Rodriguez J, Molina-Corral J, Ayala-Zavala F, Olivas G, Gonzalez-Aguilar G (2011). Effect of maturity stage on the content of fatty acids and antioxidant activity of ‘Hass’ avocado. Food Research International 44(5):1231-1237.
Vrebalov J, Ruezinsky D, Padmanabhan V, White R, Medrano D, Drake R, … Giovannoni J (2002). A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296(5566):343-346.
Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, … Tong W (2014). The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nature Biotechnology 32(9):926-932.
Werman MJ, Neeman I (1987). Avocado oil production and chemical characteristics. Journal of the American Oil Chemists' Society 64(2):229-232.
Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology 11(2):R14.
Zhang L, Zhang DS, Liu KD (2015). Environment analysis and policy for development of avocado industry in Hainan. Chinese Journal of Agricultural Resources and Regional Planning 36(4):78-84.
Open Access Journal:
The journal allows the author(s) to retain publishing rights without restriction. Users are allowed to read, download, copy, distribute, print, search, or link to the full texts of the articles, or use them for any other lawful purpose, without asking prior permission from the publisher or the author.