The sacred lotus genome provides insights into the evolution of flowering plants

Plant Journal

Volumn 76, Issue 4, 2013, Pages 557-567

  Wang, Yun ^a   Fan, Guangyi ^b,c   Liu, Yiman ^a   Sun, Fengming ^b,c   Shi, Chengcheng ^b,c   Liu, Xin ^b   Peng, Jing ^a   Chen, Wenbin ^b   Huang, Xinfang ^a   Cheng, Shifeng ^b   Liu, Yuping ^a   Liang, Xinming ^b   Zhu, Honglian ^a   Bian, Chao ^b   Zhong, Lan ^a   Lv, Tian ^b   Dong, Hongxia ^a   Liu, Weiqing ^b   Zhong, Xiao ^b   Chen, Jing ^b   Quan, Zhiwu ^b   Wang, Zhihong ^a   Tan, Benzhong ^d   Lin, Chufa ^d   Mu, Feng ^c   Xu, Xun ^b   Ding, Yi ^e   Guo, An Yuan ^f   Wang, Jun ^b,g,h   Ke, Weidong ^a   more..

^a Wuhan Vegetable Research Institute   (China)

^b BGI SHENZHEN   (China)

^c BGI Wuhan   (China)

^d Wuhan Academy of Agricultural Science and Technology   (China)

^e WUHAN UNIVERSITY   (China)

^f HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^g UNIVERSITY OF COPENHAGEN   (Denmark)

^h KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

whole genome duplication; basal eudicots; sacred lotus (Nelumbo nucifera) genome; seed dormancy and development; starch synthesis

Indexed keywords

EUDICOTS; GENOME DUPLICATION; NELUMBO NUCIFERA; SEED DORMANCY; STARCH SYNTHESIS;

PLANTS (BOTANY); STARCH;

GENES;

MAGNOLIOPHYTA; NELUMBO NUCIFERA;

STARCH;

AMINO ACID SEQUENCE; ARTICLE; BASAL EUDICOTS; BIOSYNTHESIS; DNA SEQUENCE; DORMANCY; EVOLUTION; GENETIC SELECTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MOLECULAR GENETICS; NELUMBO; PLANT GENOME; PLANT SEED; SACRED LOTUS (NELUMBO NUCIFERA) GENOME; SEED DORMANCY AND DEVELOPMENT; STARCH SYNTHESIS; Γ WHOLE GENOME DUPLICATION;

BASAL EUDICOTS; SACRED LOTUS (NELUMBO NUCIFERA) GENOME; SEED DORMANCY AND DEVELOPMENT; STARCH SYNTHESIS; Γ WHOLE GENOME DUPLICATION;

AMINO ACID SEQUENCE; BIOLOGICAL EVOLUTION; GENOME, PLANT; MOLECULAR SEQUENCE DATA; NELUMBO; PLANT DORMANCY; SEEDS; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA; STARCH;

EID: 84886778146     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12313     Document Type: Article

References (64)

1. Angiosperm Phylogeny Group. (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 161, 105-121.
2. Ashburner, M., Ball, C.A., Blake, J.A., et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25-29.
3. Bairoch, A., and, Apweiler, R., (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45-48.
4. Bao, Z., and, Eddy, S.R., (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12, 1269-1276.
5. Benson, G., (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580.
6. Berg, M., Rogers, R., Muralla, R., and, Meinke, D., (2005) Requirement of aminoacyl-tRNA synthetases for gametogenesis and embryo development in Arabidopsis. Plant J. 44, 866-878.
7. Birney, E., Clamp, M., and, Durbin, R., (2004) GeneWise and Genomewise. Genome Res. 14, 988-995.
8. Bowers, J.E., Chapman, B.A., Rong, J., and, Paterson, A.H., (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433-438.
9. Cevallos-Ferriz, S.R.S., and, Stockey, S.A., (1989) Permineralized fruits and seeds from the Princeton chert (Middle Eocene) of British Columbia: Nymphaeaceae. Bot. Gaz. 150, 207-217.
10. Chaudhuri, P., and, Marron, J.S., (1999) SiZer for exploration of structures in curves. J. Am. Stat. Assoc. 94, 807-823.
11. Chu, P., Chen, H., Zhou, Y., Li, Y., Ding, Y., Jiang, L., Tsang, E.W., Wu, K., and, Huang, S., (2012) Proteomic and functional analyses of Nelumbo nucifera annexins involved in seed thermotolerance and germination vigor. Planta, 235, 1271-1288.
12. Collinson, M.E., (1980) Recent and tertiary seeds of the Nymphaeaceae sensu lato with a revision of Brasenia ovula (Brong.) Reid and Chandler. Ann. Bot. 46, 603-632.
13. Delmer, D.P., and, Potikha, T.S., (1997) Structures and functions of annexins in plants. Cell. Mol. Life Sci. 53, 546-553.
14. Diao, Y., Chen, L., Yang, G., Zhou, M., Song, Y., Hu, Z., and, Lin, J.Y., (2006) Nuclear DNA C-values in 12 species in Nymphaeales. Caryologia 59, 25-30.
15. Ding, Y., Cheng, H., and, Song, S., (2008) Changes in extreme high-temperature tolerance and activities of antioxidant enzymes of sacred lotus seeds. Sci. China Ser. C Life Sci. 51, 842-853.
16. Edgar, R.C., (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
17. Elsik, C.G., Mackey, A.J., Reese, J.T., Milshina, N.V., Roos, D.S., and, Weinstock, G.M., (2007) Creating a honey bee consensus gene set. Genome Biol. 8, R13.
18. Finkelstein, R., Reeves, W., Ariizumi, T., and, Steber, C., (2008) Molecular aspects of seed dormancy. Annu. Rev. Plant Biol. 59, 387-415.
19. Fisher, D.K., Gao, M., Kim, K.N., Boyer, C.D., and, Guiltinan, M.J., (1996) Allelic analysis of the Maize amylose-extender locus suggests that independent genes encode starch-branching enzymes IIa and IIb. Plant Physiol. 110, 611-619.
20. Gandolfo, M.A., Nixon, K.C., and, Crepet, W.L., (2004) Cretaceous flowers of Nymphaeaceae and implications for complex insect entrapment pollination mechanisms in early Angiosperms. Proc. Natl Acad. Sci. USA, 101, 8056-8060.
21. 2+ signalling to membrane dynamics. Nat. Rev. Mol. Cell Biol. 6, 449-461.
22. Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., and, Bateman, A., (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33, D121-D124.
23. Hedges, S.B., Dudley, J., and, Kumar, S., (2006) TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22, 2971-2972.
24. Hu, T.T., Pattyn, P., Bakker, E.G., et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43, 476-481.
25. Hu, J., Pan, L., Liu, H., Wang, S., Wu, Z., Ke, W., and, Ding, Y., (2012) Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers. Mol. Biol. Rep. 39, 3637-3647.
26. Huelsenbeck, J.P., and, Ronquist, F., (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754-755.
27. Jaillon, O., Aury, J.M., Noel, B., et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449, 463-467.
28. Jami, S.K., Clark, G.B., Turlapati, S.A., (2008) Ectopic expression of an annexin from Brassica juncea confers tolerance to abiotic and biotic stress treatments in transgenic tobacco. Plant Physiol. Biochem. 46, 1019-1030.
29. Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., and, Walichiewicz, J., (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467.
30. Kanehisa, M., and, Goto, S., (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30.
31. Kashiwada, Y., Aoshima, A., Ikeshiro, Y., et al. (2005) Anti-HIV benzylisoquinoline alkaloids and flavonoids from the leaves of Nelumbo nucifera, and structure-activity correlations with related alkaloids. Bioorg. Med. Chem. 13, 443-448.
32. Li, J.K., and, Huang, S.Q., (2009) Flower thermoregulation facilitates fertilization in Asian sacred lotus. Ann. Bot. 103, 1159-1163.
33. Li, L., Stoeckert, C.J. Jr, and, Roos, D.S., (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189.
34. Li, R., Fan, W., Tian, G., et al. (2010a) The sequence and de novo assembly of the giant panda genome. Nature, 463, 311-317.
35. Li, R., Zhu, H., Ruan, J., et al. (2010b) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272.
36. Lowe, T.M., and, Eddy, S.R., (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964.
37. Mukherjee, P.K., Mukherjee, D., Maji, A.K., Rai, S., and, Heinrich, M., (2009) The sacred lotus (Nelumbo nucifera)-phytochemical and therapeutic profile. J. Pharm. Pharmacol. 61, 407-422.
38. Muller, J., (1981) Fossil pollen records of extant angiosperms. Bot. Rev. 47, 1-142.
39. Nawrocki, E.P., Kolbe, D.L., and, Eddy, S.R., (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
40. Ohkoshi, E., Miyazaki, H., Shindo, K., Watanabe, H., Yoshida, A., and, Yajima, H., (2007) Constituents from the leaves of Nelumbo nucifera stimulate lipolysis in the white adipose tissue of mice. Planta Med. 73, 1255-1259.
41. Ono, Y., Hattori, E., Fukaya, Y., Imai, S., and, Ohizumi, Y., (2006) Anti-obesity effect of Nelumbo nucifera leaves extract in mice and rats. J. Ethnopharmacol. 106, 238-244.
42. Pan, L., Quan, Z., Li, S., Liu, H., Huang, X., Ke, W., and, Ding, Y., (2007) Isolation and characterization of microsatellite markers in the sacred lotus (Nelumbo nucifera Gaertn.). Mol. Ecol. Resour. 7, 1054-1056.
43. Pan, L., Xia, Q., Quan, Z., Liu, H., Ke, W., and, Ding, Y., (2010) Development of novel EST-SSRs from sacred lotus (Nelumbo nucifera Gaertn) and their utilization for the genetic diversity analysis of N. nucifera. J. Hered. 101, 71-82.
44. Price, A.L., Jones, N.C., and, Pevzner, P.A., (2005) De novo identification of repeat families in large genomes. Bioinformatics, 21, i351-i358.
45. Salamov, A.A., and, Solovyev, V.V., (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516-522.
46. SanMiguel, P., Gaut, B.S., Tikhonov, A., Nakajima, Y., and, Bennetzen, J.L., (1998) The paleontology of intergene retrotransposons of maize. Nat. Genet. 20, 43-45.
47. Schmutz, J., Cannon, S.B., Schlueter, J., et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature, 463, 178-183.
48. Seymour, R.S., (1998) Physiological temperature regulation by flowers of the sacred lotus. Philos. Trans. R. Soc. Lond. B Biol. Sci. 353, 935-943.
49. Shen-Miller, J., Schopf, J.W., Harbottle, G., Cao, R.J., Ouyang, S., Zhou, K.S., Southon, J.R., and, Liu, G.H., (2002) Long-living lotus: germination and soil γ-irradiation of centuries-old fruits, and cultivation, growth, and phenotypic abnormalities of offspring. Am. J. Bot. 89, 236-247.
50. Shimada, H., Tada, Y., Kawasaki, T., and, Fujimura, T., (1993) Antisense regulation of the rice waxy gene expression using a PCR-amplified fragment of the rice genome reduce the amylose content in grain starch. Theor. Appl. Genet. 86, 665-672.
51. Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., and, Morgenstern, B., (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435-W439.
52. Takaha, T., Yanase, M., Okada, S., and, Smith, S.M., (1993) Disproportionating enzyme (4-alpha-glucanotransferase; EC 2.4.1.25) of potato. Purification, molecular cloning, and potential role in starch metabolism. J. Biol. Chem. 268, 1391-1396.
53. Tang, H., Bowers, J.E., Wang, X., Ming, R., Alam, M., and, Paterson, A.H., (2008) Synteny and collinearity in plant genomes. Science, 320, 486-488.
54. Trapnell, C., Pachter, L., and, Salzberg, S.L., (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
55. Trapnell, C., Williams, B.A., Pertea, G., et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515.
56. Tzafrir, I., Dickerman, A., Brazhnik, O., et al. (2003) The Arabidopsis SeedGenes project. Nucleic Acids Res. 31, 90-93.
57. Van de Peer, Y., (2004) Computational approaches to unveiling ancient genome duplications. Nat. Rev. Genet. 5, 752-763.
58. Vekemans, D., Proost, S., Vanneste, K., Coenen, H., Viaene, T., Ruelens, P., Maere, S., Van de Peer, Y., and, Geuten, K., (2012) Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-Box gene and species diversification. Mol. Biol. Evol. 29, 3793-3806.
59. Watling, J.R., Robinson, S.A., and, Seymour, R.S., (2006) Contribution of the alternative pathway to respiration during thermogenesis in flowers of the sacred lotus. Plant Physiol. 140, 1367-1373.
60. Xu, Z., and, Wang, H., (2007) LTR-FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265-W268.
61. Xu, X., Pan, S., Cheng, S., et al. (2011) Genome sequence and analysis of the tuber crop potato. Nature, 475, 189-195.
62. Yang, Z., (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591.
63. Yang, Z., Wong, W.S.W., and, Nielsen, R., (2005) Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22, 1107-1118.
64. Zdobnov, E.M., and, Apweiler, R., (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847-848.