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Comparative de novo transcriptome analysis and metabolic pathway studies of Citrus paradisi flavedo from naive stage to ripened stage

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Abstract

Grapefruit (Citrus pardisi) is a popular citrus fruit that is a cross between a sweet orange and pummelo. This research article focuses on an in silico approach for comparative analysis of C. paradisi green flavedo (GF) and ethylene treated flavedo (ETF) transcriptome data. Our pathway analysis provides comprehensive information of genes playing significant role in different stages of ripening in fruit. De novo assembly was carried out using six different assemblers namely GS assembler, SeqMan NGEN, Velvet/Oases, CLC, iAssembler and Cortex followed by subsequent meta-assembly, annotation and pathway analysis. We conclude that de novo transcriptome assembly using meta-assembly approach is used to increase assembly quality in comparison to single assembler.

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References

  1. Barry Cornelius S, Giovannoni James J (2007) Ethylene and fruit ripening. J Plant Growth Regul 26:143–159

    Google Scholar 

  2. Jain M (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18(1):53–63

    Article  PubMed Central  PubMed  Google Scholar 

  3. Moriya Y, Itoh M, Okuda S, Yoshizawa A, Kaneshia M (2007) KASS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:182–185

    Article  Google Scholar 

  4. Zerbino DR, Birney E (2008) Velvet: algorithm for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M (2011) Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genom 12:317

    Article  Google Scholar 

  7. Kumar S, Blaxter ML (2010) Comparing de novo assemblers for 454 transcriptome data. BMC Genom 11:571

    Article  Google Scholar 

  8. Altschul SF, Gish W, Miller W, Myres EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  9. Ribeiroa MHL, Rabaca M (2011) Cross-linked enzyme aggregates of naringinase: novel biocatalysts for naringin hydrolysis. Enzyme Res. 2011:851272

    Google Scholar 

  10. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO:a universal tool for annotation, visulization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  11. Wang XW, Liu SS (2010) De novo charecterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genom 11:400

    Article  Google Scholar 

  12. Shi CY, Yang H, Wei CL (2011) Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genom 12:131

    Article  CAS  Google Scholar 

  13. Parani M (2011) De novo assembly and transcriptome analysis of five major tissue s of Jatropha curcus L. using GS FLX titanium platform of 454 pyrosequencing. BMC Genom 12:191

    Article  Google Scholar 

  14. Kelebek H (2010) Sugars, organic acids, phenolic compositions and antioxidant activity of Grapefruit (Citrus paradisi) cultivars grown in Turkey. Ind Crops Prod 32(3):269–274

    Article  Google Scholar 

  15. Huberman M, Zehavi U, Stein WD, Etxeberria E, Goren R (2005) In vitro sugar uptake by grapefruit (Citrus paradisi) juice-sac cells. Funct Plant Biol 32(4):357–366

    Article  CAS  Google Scholar 

  16. Prasanna V, Prabha TN, Tharanathan RN (2007) Fruit ripening phenomena–an overview. Crit Rev Food Sci Nutr 47(1):1–19

    Article  CAS  PubMed  Google Scholar 

  17. Donascimento J, Júnior AV, Bassinello P, Cordenunsi B, Mainardi J, Purgatto E, Lajolo F (2006) Beta-amylase expression and starch degradation during banana ripening. Postharvest Biol Technol 40(1):41–47

    Article  Google Scholar 

  18. Herrera M, Rodrigo J, Gil L (2007) Ethylene stimulates emission of terpenoids and aliphatic esters in citrus fruits. Adv Plant Ethyl Res 4:257–259

    Article  Google Scholar 

  19. Terpenes, Terpenoids and Cannabis, http://berkeleypatientscare.com/2010/10/08/terpenes-terpenoids-and-cannabis/

  20. Rodrigo MJ, Zacarias L (2007) Effect of postharvest ethylene treatment on carotenoid accumulation and the expression of carotenoid biosynthetic genes in the flavedo of orange(Citrus sinensis L. Osbeck) fruit. Postharvest Biol Technol 43:14–22

    Article  CAS  Google Scholar 

  21. Lafuente MT, Sala JM (2002) Abscisic acid levels and the influence of ethylene, humidity and storage temperature on the incidence of postharvest rindstaning of ‘Navelina’ orange (Citrus sinensis L. Osbeck) fruit. Postharvest Biol Technol 25(1):49–57

    Article  CAS  Google Scholar 

  22. Eo J, Lee BY (2009) Effects of ethylene, abscisic acid and auxin on fruit abscission in water dropwort (Oenanthe stolonifera DC.). Sci Hortic 123(2):224–227

    Article  CAS  Google Scholar 

  23. Alós E, Cercós M, Rodrigo MJ, Zacarías L, Talón M (2006) Regulation of color break in citrus fruits. Changes in pigment profiling and gene expression induced by gibberellins and nitrate, two ripening retardants. J Agric Food Che 54(13):4888–4895

    Article  Google Scholar 

  24. Brisker HE, Goldschmidt EE, Goren R (1976) Ethylene-induced Formation of ABA in Citrus Peel as Related to Chloroplast Transformations. Plant Physiol 58:377–379

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Ogata YN (2006) Flavonoid composition of fruit tissues of citrus species. Biosci Biotechnol Biochem 70(1):178–192

    Article  Google Scholar 

  26. Ness RW, Siol M, Barrett SCH (2011) De novo sequemce assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants. BMC Genom 12:298

    Article  CAS  Google Scholar 

  27. Mansell RL (1985) Naringin Levels in Citrus Tissues. Plant Physiol 77:903–908

    Article  PubMed Central  PubMed  Google Scholar 

  28. Ververidis F, Trantas E, Douglas C, Vollmer G, Kretzschmar G, Panopoulos N (2007) Biotechnology of flavonoids and other phenylpropanoid-derived natural products. Part I: chemical diversity, impacts on plant biology and human health. Biotechnol J 2(10):1214–1234

    Article  CAS  PubMed  Google Scholar 

  29. Giorgio E, Parrinello N, Caccamese S, Rosini C (2004) Non-empirical assignment of the absolute configuration of (−)-naringenin, by coupling the exciton analysis of the circular dichroism spectrum and the ab initio calculation of the optical rotatory power. Org Biomol Chem 2:3602–3607

    Article  CAS  PubMed  Google Scholar 

  30. Menichinia F, Loizzoa MR, Bonesia M, Confortia F, Lucab DD, Stattia GA, Cindioc DE, Menichinia F, Tundis R (2011) Phytochemical profile, antioxidant, anti-inflammatory and hypoglycemic potential of hydroalcoholic extracts from Citrus medica L. cv Diamante flowers, leaves and fruits at two maturity stages. Food Chem Toxicol 49(7):1549–1555

    Article  Google Scholar 

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Acknowledgments

We acknowledge UC-COE, for providing us transcriptome data of C. paradisi flavedo by mean of NCBI Sequence Read Archive. We also acknowledge Xcelris Labs Ltd. management for infrastructure and support.

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Authors and Affiliations

  1. Department of Genomics, Xcelris Genomics Research Centre, Ahmadabad, India

    Maulik Patel, Toral Manvar, Sachin Apurwa, Arpita Ghosh, Tanushree Tiwari & Surendra K. Chikara

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  1. Maulik Patel
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  2. Toral Manvar
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  3. Sachin Apurwa
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  4. Arpita Ghosh
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  5. Tanushree Tiwari
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  6. Surendra K. Chikara
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Correspondence to Surendra K. Chikara.

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Patel, M., Manvar, T., Apurwa, S. et al. Comparative de novo transcriptome analysis and metabolic pathway studies of Citrus paradisi flavedo from naive stage to ripened stage. Mol Biol Rep 41, 3071–3080 (2014). https://doi.org/10.1007/s11033-014-3166-x

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  • DOI: https://doi.org/10.1007/s11033-014-3166-x

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