De novo transcriptome analysis of Liriodendron chinense petals and leaves by Illumina sequencing

Gene

Volumn 534, Issue 2, 2014, Pages 155-162

  Yang, Ying ^a   Xu, Meng ^a   Luo, Qunfeng ^a   Wang, Jie ^a   Li, Huogen ^a  

^a NANJING FORESTRY UNIVERSITY   (China)

Author keywords

Carotenoids biosynthesis; Endangered; Gene expression differences; Unigenes

Indexed keywords

CAROTENOID; TRANSCRIPTOME; VEGETABLE PROTEIN;

AMINO ACID METABOLISM; ARTICLE; BIOSYNTHESIS; CARBOHYDRATE METABOLISM; CONTROLLED STUDY; DNA BASE COMPOSITION; DOWN REGULATION; ENDANGERED SPECIES; ENERGY METABOLISM; ESSENTIAL GENE; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC VARIABILITY; ILLUMINA SEQUENCING; LIRIODENDRON; LIRIODENDRON CHINENSE; NONHUMAN; OXIDATIVE PHOSPHORYLATION; PETAL; PHOTOSYSTEM II; PLANT GENE; PLANT LEAF; PRIORITY JOURNAL; PROTEIN METABOLISM; SEQUENCE ANALYSIS; UPREGULATION;

LIRIODENDRON; LIRIODENDRON CHINENSE; MAGNOLIOPHYTA;

ABA; CAPSANTHIN/CAPSORUBIN SYNTHASE; CAROTENOID ISOMERASE; CAROTENOIDS BIOSYNTHESIS; CCS; CLUSTERS OF ORTHOLOGOUS GROUPS OF PROTEINS; COG; CRTISO; DEGS; DIFFERENTIALLY EXPRESSED GENES; ENDANGERED; FBP2; FLORAL BINDING PROTEIN 2; GENE EXPRESSION DIFFERENCES; GENE ONTOLOGY; GERANYLGERANYL PYROPHOSPHATE SYNTHASE; GGPP; GO; KEGG ORTHOLOG DATABASE; KO; LCY; LYCOPENE CYCLASES; MYB-RELATED PROTEIN 340; MYB340; NEXT-GENERATION SEQUENCING; NGS; NON-REDUNDANT NUCLEOTIDE SEQUENCES; NON-REDUNDANT PROTEIN DATABASE; NR; NT; PDS; PHYTOCHROME KINASE SUBSTRATE 1; PHYTOENE DESATURASE; PHYTOENE SYNTHASE; PHYTOHORMONES ABSCISIC ACID; PKS1; PSY; UNIGENES; VDE; VIOLAXANTHIN DE-EPOXIDASE; Z-ISO; ZDS; ZEAXANTHIN EPOXIDASE; ZEP; Ζ-CAROTENE DESATURASE; Ζ-CAROTENE ISOMERASE;

CAROTENOIDS; DOWN-REGULATION; FLOWERS; GENE EXPRESSION PROFILING; GENES, PLANT; LIRIODENDRON; METABOLIC NETWORKS AND PATHWAYS; PLANT LEAVES; PLANT PROTEINS; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME; UP-REGULATION;

EID: 84890442816     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.10.073     Document Type: Article

References (61)

1. Anders S., Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010, 11(10):R106. 10.1186/gb-2010-11-10-r106.
2. Angenent G.C., Busscher M., Franken J., Mol J.N., van Tunen A.J. Differential expression of two MADS box genes in wild-type and mutant petunia flowers. Plant Cell 1992, 4(8):983-993.
3. Bedell J., Korf I., Yandell M. BLAST 2003, O'Reilly.
4. Chaudhary N., Nijhawan A., Khurana J.P., Khurana P. Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis. Mol. Genet. Genomics 2010, 283(1):13-33.
5. Chew B.P., Park J.S. Carotenoid action on the immune response. J. Nutr. 2004, 134:257S-261S.
6. Cunningham F.X. Regulation of carotenoid synthesis and accumulation in plants. Pure Appl. Chem. 2002, 74:1409-1417.
7. De Donato M., Peters S.O., Mitchell S.E., Hussain T., Imumorin I.G. Genotyping-by-sequencing (GBS): a novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing. PLoS One 2013, 8(5):e62137. 10.1371/journal.pone.0062137.
8. Dong H., et al. The Arabidopsis spontaneous cell death1 gene, encoding a zeta-carotene desaturase essential for carotenoid biosynthesis, is involved in chloroplast development, photoprotection and retrograde signalling. Cell Res. 2007, 17(5):458-470.
9. Fambrini M., Michelotti V., Pugliesi C. Orange, yellow and white-cream: inheritance of carotenoid-based colour in sunflower pollen. Plant Biol. (Stuttg) 2010, 12(1):197-205.
10. Fang Y.M. Geographical distribution and spatial pattern of Liriondendron Chinese (Hemsl.). Sarg. J. Nanjing For. Univ. 1994, 18(2):13-18. (in Chinese with English abstract).
11. Fraser P.D., Bramley P.M. The biosynthesis and nutritional uses of carotenoids. Prog. Lipid Res. 2004, 43:228-265.
12. Fu L.G., Jin J.M. Red list of endangered plants in China 1992, Science Press, Beijing, China, (in Chinese).
13. Gamble T., Simons A.M., Colli G.R., Vitt L.J. Tertiary climate change and the diversification of the Amazonian gecko genus Gonatodes (Sphaerodactylidae, Squamata). Mol. Phylogenet. Evol. 2008, 46(1):269-277.
14. Giovannucci E. Lycopene and prostate cancer risk: methodological considerations in the epidemiologic literature. Pure Appl. Chem. 2002, 74:1427-1434.
15. Giuliano G., Tavazza R., Diretto G., Beyer P., Taylor M.A. Metabolic engineering of carotenoid biosynthesis in plants. Trends Biotechnol. 2008, 26:139-145.
16. Götz S., et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008, 36:3420-3435.
17. Grabherr M.G., et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29:644-652.
18. Ha S.H., Kim J.B., Park J.S., Lee S.W., Cho K.J. A comparison of the carotenoid accumulation in Capsicum varieties that show different ripening colours: deletion of the capsanthin-capsorubin synthase gene is not a prerequisite for the formation of a yellow pepper. J. Exp. Bot. 2007, 58(12):3135-3144.
19. Haas B.J., et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 2013, 8(8):1494-1512.
20. Hao R.M., He S.A., Tang S.J., Wu S.P. Geographical distribution of Liriodendron Chinese in China and its significance. J. Plant Resour. Environ. 1995, 4:1-6. (in Chinese).
21. He S.A., Hao R.M. Study on the natural population dynamics and the endangering habital of Liriodendron Chinese in China. Acta Phytoecol. Sin. 1999, 23(1):87-95. (in Chinese with English abstract).
22. Howitt C.A., et al. Alternative splicing, activation of cryptic exons and amino acid substitutions in carotenoid biosynthetic genes are associated with lutein accumulation in wheat endosperm. Funct. Integr. Genomics 2009, 9(3):363-376.
23. Huang H.H., et al. De novo characterization of the Chinese fir (Cunninghamia lanceolata) transcriptome and analysis of candidate genes involved in cellulose and lignin biosynthesis. BMC Genomics 2012, 21(13):648. 10.1186/1471-2164-13-648.
24. Isaacson T., Ohad I., Beyer P., Hirschberg J. Analysis in vitro of the enzyme CRTISO establishes a poly-cis-carotenoid biosynthesis pathway in plants. Plant Physiol. 2004, 136(4):4246-4255.
25. Jin H., Do J., Moon D., Noh E.W., Kim W., Kwon M. EST analysis of functional genes associated with cell wall biosynthesis and modification in the secondary xylem of the yellow poplar (Liriodendron tulipifera) stem during early stage of tension wood formation. Planta 2011, 234(5):959-977.
26. Kanehisa M., et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006, 34:D354-D357.
27. Kanehisa M., et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008, 36:D480-D484.
28. Lang Y.Q., Yanagawa S., Sasanuma T., Sasakuma T. Orange fruit colour in Capsicum due to deletion of capsanthin-capsorubin synthase gene. Breed. Sci. 2004, 54:33-39.
29. Lariguet P., et al. Phytochrome kinase substrate 1 is a phototropin 1 binding protein required for phototropism. Proc. Natl. Acad. Sci. U. S. A. 2006, 103(26):10134-10139.
30. Lefebvre V., Kuntz M., Camara B., Palloix A. The capsanthin-capsorubin synthase gene: a candidate gene for the y locus controlling the red fruit colour in pepper. Plant Mol. Biol. 1998, 36:785-789.
31. Lemmon E.M., Lemmon A.R., Cannatella D.C. Geological and climatic forces driving speciation in the continentally distributed trilling chorus frogs (Pseudacris). Evolution 2007, 61(9):2086-2103.
32. Li B., Dewey C.N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinforma 2011, 10.1186/1471-2105-12-323.
33. Li B., Gu W.C., Xia L.F., Li X.Q., Gan S.X. Genetic variation and provenance selection of Chinese Tuliptree. For. Res. 2001, 14(3):237-244. (in Chinese with English abstract).
34. Li H.G., Chen L., Liang C.Y., Huang M.R. A case study on provenance testing of tulip tree (Liriodendron spp). Chin. For. Sci. Technol. 2005, 19(5):13-16.
35. Li F., Murillo C., Wurtzel E.T. Maize Y9 encodes a product essential for 15-cis-zeta-carotene isomerization. Plant Physiol. 2007, 144(2):1181-1189.
36. Li F., Vallabhaneni R., Wurtzel E.T. PSY3, a new member of the phytoene synthase gene family conserved in the Poaceae and regulator of abiotic stress-induced root carotenogenesis. Plant Physiol. 2008, 146(3):1333-1345.
37. Liang H., et al. Development of a BAC library for yellow-poplar (Liriodendron tulipifera) and the identification of genes associated with flower development and lignin biosynthesis. Tree Genet. Genomes 2007, 3:215-225.
38. Liang H., et al. An EST Database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron. Tree Genet. Genomes 2008, 4:419-433.
39. Liang H., et al. Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron. Tree Genet. Genomes 2011, 7:941-954.
40. Liu L., et al. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012, 2012:251364.
41. Mann V., Pecker I., Hirschberg J. Cloning and characterization of the gene for phytoene desaturase (Pds) from tomato (Lycopersicon esculentum). Plant Mol. Biol. 1994, 24(3):429-434.
42. Mao X., Cai T., Olyarchuk J.G., Wei L. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 2005, 21:3787-3793.
43. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5:621-628.
44. Moyano E., Martínez-Garcia J.F., Martin C. Apparent redundancy in myb gene function provides gearing for the control of flavonoid biosynthesis in antirrhinum flowers. Plant Cell 1996, 8(9):1519-1532.
45. Nathan P.H., Christopher S.C., Thomas F.V., Ben L., Randall J.B., Michael J.D. Phylogeny and biogeography of Tsuga (Pinaceae) inferred from nuclear ribosomal ITS and chloroplast DNA sequence data. Syst. Bot. 2008, 33(3):478-789.
46. Nie Z.L., Sun H., Beardsley P.M., Olmstead R.G., Wen J. Evolution of biogeographic disjunction between eastern Asia and eastern North America in Phryma (Phrymaceae). Am. J. Bot. 2006, 93(9):1343-1356.
47. Petrini I., et al. Whole genome and transcriptome sequencing of a b3 thymoma. PLoS One 2013, 8(4):e60572. 10.1371/journal.pone.
48. Popovsky S., Paran I. Molecular genetics of the y locus in pepper: its relation to capsanthin-capsorubin synthase and to fruit color. Theor. Appl. Genet. 2000, 101:86-89.
49. Soltis D.E., Soltis P.S., Chase M.W., Endress P. Phylogeny, Evolution, and Classification of Flowering Plants 2005, Sinauer Associates, Sunderland, MA.
50. Stigliani A.L., Giorio G., D'Ambrosio C. Characterization of P450 carotenoid beta- and epsilon-hydroxylases of tomato and transcriptional regulation of xanthophyll biosynthesis in root, leaf, petal and fruit. Plant Cell Physiol. 2011, 52(5):851-865.
51. Storey J.D., Tibshirani R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U. S. A. 2003, 100(16):9440-9445.
52. Tian L., Musetti V., Kim J., Magallanes-Lundback M., DellaPenna D. The Arabidopsis LUT1 locus encodes a member of the cytochrome p450 family that is required for carotenoid epsilon-ring hydroxylation activity. Proc. Natl. Acad. Sci. 2004, 101(1):402-407.
53. Wang L., Feng Z., Wang X., Wang X., Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 2010, 26(1):136-138.
54. Wang X.W., Luan J.B., Li J.M., Bao Y.Y., Zhang C.X., Liu S.S. De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 2010, 11:400.
55. Wang S., et al. Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Plant Cell Rep. 2012, 31(8):1437-1447.
56. Welsch R., Wüst F., Bär C., Al-Babili S., Beyer P. A third phytoene synthase is devoted to abiotic stress-induced abscisic acid formation in rice and defines functional diversification of phytoene synthase genes. Plant Physiol. 2008, 147(1):367-380.
57. Wen Z.X., Wu Z.Y. Pollen ultrastructure of Liriodendron and its systematic significance. Acta Bot. Yunnanica 1993, 15(2):163-166. (in Chinese with English abstract).
58. Wu C.Y., Wang H.S. Chinese physical geography: phytogeography (I) 1983, Science Press, Beijing, (in Chinese).
59. Xie C., Li B., Xu Y., Ji D., Chen C. Characterization of the global transcriptome for Pyropia haitanensis (Bangiales, Rhodophyta) and development of cSSR markers. BMC Genomics 2013, 16(14):107.
60. Young M.D., Wakefield M.J., Smyth G.K., Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010, 11(2):R14.
61. Zhai R., et al. Transcriptome analysis of rice root heterosis by RNA-Seq. BMC Genomics 2013, 16(14):19.