De novo sequencing, assembly, and analysis of the Taxodium 'Zhongshansa' roots and shoots transcriptome in response to short-term waterlogging

BMC Plant Biology

Volumn 14, Issue 1, 2014, Pages

  Qi, Baiyan ^a,b   Yang, Ying ^a   Yin, Yunlong ^b   Xu, Meng ^a   Li, Huogen ^a  

^a NANJING FORESTRY UNIVERSITY   (China)

^b INSTITUTE OF BOTANY   (China)

Author keywords

qRT PCR; Stress; Taxodium; Transcriptome; Waterlogging

Indexed keywords

TAXODIUM;

OXYGEN; TRANSCRIPTOME; WATER;

FLOODING; GENE EXPRESSION PROFILING; METABOLISM; MOLECULAR GENETICS; PHYSIOLOGY; PLANT; PLANT GENE; PLANT ROOT; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; TAXODIUM;

FLOODS; GENE EXPRESSION PROFILING; GENES, PLANT; MOLECULAR SEQUENCE ANNOTATION; OXYGEN; PLANT ROOTS; PLANT SHOOTS; REAL-TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, RNA; TAXODIUM; TRANSCRIPTOME; WATER;

EID: 84905731156     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/s12870-014-0201-y     Document Type: Article

References (51)

1. Denny GC, Arnold MA. Taxonomy and nomenclature of baldcypress, pondcypress, and montezuma cypress: One, two, or three species?. Horttechnology 2007, 17(1):125-127.
2. Zheng W. SYLVA SINICA, Volume 1 1983, China Forestry Publishing House, Beijing.
3. Allen JA, Pezeshki SR, Chambers JL. Interaction of flooding and salinity stress on baldcypress (Taxodium distichum). Tree Physiol 1996, 16(1-2):307-313. 14871777.
4. Hua J, Yin Y, Zhou D, Yu C, Xu J. Effects of soil water conditions on growth and physiology of Taxodium 'Zhongshanshan 406'. J Ecol Rural Environ 2011, 6:10. In Chinese.
5. Christianson JA, Llewellyn DJ, Dennis ES, Wilson IW. Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L). Plant Cell Physiol 2010, 51(1):21-37. 19923201.
6. Sachs MM, Subbaiah CC, Saab IN. Anaerobic gene expression and flooding tolerance in maize. J Exp Bot 1996, 47(1):1-15.
7. Ellis MH, Dennis ES, Peacock WJ. Arabidopsis roots and shoots have different mechanisms for hypoxic stress tolerance. Plant Physiol 1999, 119(1):57-64. 9880346.
8. Dennis ES, Dolferus R, Ellis M, Rahman M, Wu Y, Hoeren FU, Grover A, Ismond KP, Good AG, Peacock WJ. Molecular strategies for improving waterlogging tolerance in plants. J Exp Bot 2000, 51(342):89-97. 10938799.
9. Klok EJ, Wilson IW, Wilson D, Chapman SC, Ewing RM, Somerville SC, Peacock WJ, Dolferus R, Dennis ES. Expression profile analysis of the low-oxygen response in Arabidopsis root cultures. Plant Cell 2002, 14(10):2481-2494. 12368499.
10. Chang WW, Huang L, Shen M, Webster C, Burlingame AL, Roberts JK. Patterns of protein synthesis and tolerance of anoxia in root tips of maize seedlings acclimated to a low-oxygen environment, and identification of proteins by mass spectrometry. Plant Physiol 2000, 122(2):295-318. 10677424.
11. Kreuzwieser JUR, Hauberg J, Howell KA, Carroll A, Rennenberg H, Millar AH, Whelan J. Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia. Plant Physiol 2009, 149(1):461-473. 19005089.
12. Sachs MM, Freeling M, Okimoto R. The anaerobic proteins of maize. Cell 1980, 20(3):761-767. 7418006.
13. Geigenberger P. Response of plant metabolism to too little oxygen. Curr Opin Plant Biol 2003, 6(3):247-256. 12753974.
14. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18(9):1509-1517. 18550803.
15. Pang T, Ye C, Xia X, Yin W. De novo sequencing and transcriptome analysis of the desert shrub, Ammopiptanthus mongolicus, during cold acclimation using Illumina/Solexa. BMC Genomics 2013, 14(1):488. 23865740.
16. Fan X, Wang J, Yang N, Dong Y, Liu L, Wang F, Wang N, Chen H, Liu W, Sun Y, Wu J, Li H. Gene expression profiling of soybean leaves and roots under salt, saline-alkali and drought stress by high-throughput Illumina sequencing. Gene 2013, 512(2):392-402. 23063936.
17. Postnikova OA, Shao J, Nemchinov LG. Analysis of the alfalfa root transcriptome in response to salinity stress. Plant Cell Physiol 2013, 54(7):1041-1055. 23592587.
18. Dong C, Li C, Yan X, Huang S, Huang J, Wang L, Guo R, Lu G, Zhang X, Fang X, Wei W. Gene expression profiling of Sinapis alba leaves under drought stress and rewatering growth conditions with Illumina deep sequencing. Mol Biol Rep 2012, 39(5):5851-5857. 22207172.
19. Zhai L, Liu Z, Zou X, Jiang Y, Qiu F, Zheng Y, Zhang Z. Genome-wide identification and analysis of microRNA responding to long-term waterlogging in crown roots of maize seedlings. Physiol Plant 2013, 147(2):181-193. 22607471.
20. Qi X, Xu X, Lin X, Zhang W, Chen X. Identification of differentially expressed genes in cucumber (<i > Cucumis sativus L.) root under waterlogging stress by digital gene expression profile. Genomics 2012, 99(3):160-168. 22240004.
21. Wang L, Zhang Y, Qi X, Li D, Wei W, Zhang X. Global gene expression responses to waterlogging in roots of sesame (Sesamum indicum L.). Acta Physiol Plant 2012, 34(6):2241-2249.
22. Lee Y, Kim K, Jang Y, Hwang J, Lee D, Choi I. Global gene expression responses to waterlogging in leaves of rape seedlings. Plant Cell Rep 2014, 33(2):289-299. 24384821.
23. Lv J, Liu P, Wang Y, Gao B, Chen P, Li J. Transcriptome analysis of portunus trituberculatus in response to salinity stress provides insights into the molecular basis of osmoregulation. PLoS One 2013, 8(12):e82155. 24312639.
24. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhinke A, Dj Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhinke A, Dj Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29(7):644-652. 21572440.
25. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011, 12(1):323. 21816040.
26. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26(1):139-140. 19910308.
27. Storey JD. The positive false discovery rate: a Bayesian interpretation and the q-value. Ann Stat 2003, 31(6):2013-2035.
28. Young MD, Wakefield MJ, Smyth GK, Oshlack A: Method gene ontology analysis for RNA-seq: accounting for selection bias.Genome Biol 2010. PubMed..
29. Mao X, Cai T, Olyarchuk JG, Wei L. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 2005, 21(19):3787-3793. 15817693.
30. Mustroph A, Zanetti ME, Jang CJ, Holtan HE, Repetti PP, Galbraith DW, Girke T, Bailey-Serres J. Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc Natl Acad Sci 2009, 106(44):18843-18848. 19843695.
31. Kennedy RA, Rumpho ME, Fox TC. Anaerobic metabolism in plants. Plant Physiol 1992, 100(1):1-6. 16652929.
32. Hsu F, Chou M, Peng H, Chou S, Shih M. Insights into hypoxic systemic responses based on analyses of transcriptional regulation in Arabidopsis. PLoS One 2011, 6(12):e28888. 22194941.
33. Mustroph A, Lee SC, Oosumi T, Zanetti ME, Yang H, Ma K, Yaghoubi-Masihi A, Fukao T, Bailey-Serres J. Cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses. Plant Physiol 2010, 152(3):1484-1500. 20097791.
34. Lin KR, Weng C, Lo H, Chen J. Study of the root antioxidative system of tomatoes and eggplants under waterlogged conditions. Plant Sci 2004, 167(2):355-365.
35. Perez-Ramos IM, Maranon T. Effects of waterlogging on seed germination of three Mediterranean oak species: ecological implications. Acta Oecologica 2009, 35(3):422-428.
36. Kato C, Ohshima N, Kamada H, Satoh S. Enhancement of the inhibitory activity for greening in xylem sap of squash root with waterlogging. Plant Physiol Bioch 2001, 39(6):513-519.
37. Blokhina O, Virolainen E, Fagerstedt KV. Antioxidants, oxidative damage and oxygen deprivation stress: a review. Ann Bot-London 2003, 91(2):179-194.
38. Foyer CH, Souriau NEG, Perret S, Lelandais M, Kunert K, Pruvost C, Jouanin L. Overexpression of glutathione reductase but not glutathione synthetase leads to increases in antioxidant capacity and resistance to photoinhibition in poplar trees. Plant Physiol 1995, 109(3):1047-1057. 8552710.
39. Tan W, Liu J, Dai T, Jing Q, Cao W, Jiang D. Alterations in photosynthesis and antioxidant enzyme activity in winter wheat subjected to post-anthesis water-logging. Photosynthetica 2008, 46(1):21-27.
40. Ahmed S, Nawata E, Hosokawa M, Domae Y, Sakuratani T. Alterations in photosynthesis and some antioxidant enzymatic activities of mungbean subjected to waterlogging. Plant Sci 2002, 163(1):117-123.
41. Arbona V, Hossain Z, Lo´pez-Climent MF, Pe´rez-Clemente RM, Go´mez-Cadenas A. Antioxidant enzymatic activity is linked to waterlogging stress tolerance in citrus. Physiol Plantarum 2008, 132(4):452-466.
42. Geigenberger P, Fernie AR, Gibon Y, Christ M, Stitt M. Metabolic activity decreases as an adaptive response to low internal oxygen in growing potato tubers. Biol Chem 2000, 381(8):723-740. 11030430.
43. Narsai R, Rocha M, Geigenberger P, Whelan J, Van Dongen JT. Comparative analysis between plant species of transcriptional and metabolic responses to hypoxia. New Phytol 2011, 190(2):472-487. 21244431.
44. Christianson JA, Llewellyn DJ, Dennis ES, Wilson IW. Comparisons of early transcriptome responses to low-oxygen environments in three dicotyledonous plant species. Plant Signal Behav 2010, 5(8):1006-1009. 20724824.
45. Iordachescu M, Imai R. Trehalose biosynthesis in response to abiotic stresses. J Integr Plant Biol 2008, 50(10):1223-1229. 19017109.
46. Eastmond PJ, Li Y, Graham IA. Is trehalose-6-phosphate a regulator of sugar metabolism in plants?. J Exp Bot 2003, 54(382):533-537. 12508064.
47. Eastmond PJ, Graham IA. Trehalose metabolism: a regulatory role for trehalose-6-phosphate?. Curr Opin Plant Biol 2003, 6(3):231-235. 12753972.
48. Narsai R, Whelan J. How unique is the low oxygen response? An analysis of the anaerobic response during germination and comparison with abiotic stress in rice and Arabidopsis. Front Plant Sci 2013, 4:349. 24101922.
49. Parent C, Vecoeur MEL CE, Capelli N, Dat JF. Contrasting growth and adaptive responses of two oak species to flooding stress: role of non-symbiotic haemoglobin. Plant Cell Environ 2011, 34(7):1113-1126. 21410709.
50. Sasidharan R, Mustroph A, Boonman A, Akman M, Ammerlaan AM, Breit T, Schranz ME, Voesenek LA, Van Tienderen PH. Root transcript profiling of two rorippa species reveals gene clusters associated with extreme submergence tolerance. Plant Physiol 2013, 163(3):1277-1292. 24077074.
51. Sairam RK, Kumutha D, Ezhilmathi K. Waterlogging tolerance: nonsymbiotic haemoglobin-nitric oxide homeostasis and antioxidants. Curr Sci 2009, 96(5):674-682.