Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins

PLoS Genetics

Volumn 3, Issue 10, 2007, Pages 1848-1861

  Jones Rhoades, Matthew W ^a   Borevitz, Justin O ^a   Preuss, Daphne ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b Chromatin Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; COMPLEMENTARY DNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MYB98; UNCLASSIFIED DRUG;

ARABIDOPSIS; ARTICLE; DEVELOPMENTAL GENETICS; DNA SEQUENCE; DOWN REGULATION; EMBRYO DEVELOPMENT; FEMALE GAMETOPHYTE; FERTILIZATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENETIC CODE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HIGH THROUGHPUT SCREENING; MICROARRAY ANALYSIS; MULTIGENE FAMILY; NONHUMAN; PLANT DEVELOPMENT; PLANT GENETICS; PLANT REPRODUCTION; PROTEIN DOMAIN; PROTEIN SECRETION; SIGNAL TRANSDUCTION; WILD TYPE;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; DIPLOIDY; DNA, COMPLEMENTARY; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME; GENOME, PLANT; PLANT PROTEINS; POLLEN; POLLEN TUBE; SIGNAL TRANSDUCTION;

ARABIDOPSIS; MAGNOLIOPHYTA;

EID: 35948958253     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0030171     Document Type: Article

References (48)

1. Drews GN, Yadegari R (2002) Development and function of the angiosperm female gametophyte. Annu Rev Genet 36: 99-124.
2. Yadegari R, Drews GN (2004) Female gametophyte development. Plant Cell 16 Suppl: S133-S141.
3. Christensen CA, King JK, Jordan JR, Drews GN (1997) Megagametogenesis in Arabidopsis wild type and the Gf mutant. Sex Plant Reprod 10: 49-64.
4. Christensen CA, Subramanian S, Drews GN (1998) Identification of gametophytic mutations affecting female gametophyte development in Arabidopsis. Dev Biol 202: 136-151.
5. Gross-Hardt R, Kagi C, Baumann N, Moore JM, Baskar R, et al. (2007) LACHESIS restricts gametic cell fate in the female gametophyte of Arabidopsis. PLoS Biol 5: e47. doi:10.1371/journal.pbio.0050047
6. Huck N, Moore JM, Federer M, Grossniklaus U (2003) The Arabidopsis mutant feronia disrupts the female gametophytic control of pollen tube reception. Development 130: 2149-2159.
7. Pagnussat GC, Yu HJ, Ngo QA, Rajani S, Mayalagu S, et al. (2005) Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis. Development 132: 603-614.
8. Schneitz K, Hulskamp M, Kopczak SD, Pruitt RE (1997) Dissection of sexual organ ontogenesis: a genetic analysis of ovule development in Arabidopsis thaliana. Development 124: 1367-1376.
9. Shimizu KK, Okada K (2000) Attractive and repulsive interactions between female and male gametophytes in Arabidopsis pollen tube guidance. Development 127: 4511-4518.
10. Ray SM, Park SS, Ray A (1997) Pollen tube guidance by the female gametophyte. Development 124: 2489-2498.
11. Kasahara RD, Portereiko MF, Sandaklie-Nikolova L, Rabiger DS, Drews GN (2005) MYB98 is required for pollen tube guidance and synergid cell differentiation in Arabidopsis. Plant Cell 17: 2981-2992.
12. Higashiyama T (2002) The synergid cell: attractor and acceptor of the pollen tube for double fertilization. J Plant Res 115: 149-160.
13. Higashiyama T, Yabe S, Sasaki N, Nishimura Y, Miyagishima S, et al. (2001) Pollen tube attraction by the synergid cell. Science 293: 1480-1483.
14. Christensen CA, Gorsich SW, Brown RH, Jones LG, Brown J, et al. (2002) Mitochondrial GFA2 is required for synergid cell death in Arabidopsis. Plant Cell 14: 2215-2232.
15. Rotman N, Rozier F, Boavida L, Dumas C, Berger F, et al. (2003) Female control of male gamete delivery during fertilization in Arabidopsis thaliana. Curr Biol 13: 432-436.
16. Chaudhury AM, Ming L, Miller C, Craig S, Dennis ES, et al. (1997) Fertilization-independent seed development in Arabidopsis thaliana. Proc Natl Acad Sci U S A 94: 4223-4228.
17. Grossniklaus U, Vielle-Calzada JP, Hoeppner MA, Gagliano WB (1998) Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science 280: 446-450.
18. Ohad N, Yadegari R, Margossian L, Hannon M, Michaeli D, et al. (1999) Mutations in FIE, a WD polycomb group gene, allow endosperm development without fertilization. Plant Cell 11: 407-416.
19. Portereiko MF, Lloyd A, Steffen JG, Punwani JA, Otsuga D, et al. (2006) AGL80 is required for central cell and endosperm development in Arabidopsis. Plant Cell 18: 1862-1872.
20. Bhatt AM, Lister C, Page T, Fransz P, Findlay K, et al. (1999) The DIF1 gene of Arabidopsis is required for meiotic chromosome segregation and belongs to the REC8/RAD21 cohesin gene family. Plant J 19: 463-472.
21. Bhatt AM, Page T, Lawson EJ, Lister C, Dean C (1996) Use of Ac as an insertional mutagen in Arabidopsis. Plant J 9: 935-945.
22. Steffen J, Kang I, Macfarlane J, Drews G (2007) Identification of genes expressed in the Arabidopsis female gametophyte. Plant J 51: 281-292.
23. Yu HJ, Hogan P, Sundaresan V (2005) Analysis of the female gametophyte transcriptome of Arabidopsis by comparative expression profiling. Plant Physiol 139: 1853-1869.
24. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
25. The Arabidopsis Genome Consortium (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
26. Charlesworth D, Vekemans X, Castric V, Glemin S (2005) Plant selfincompatability systems: a molecular evolutionary perspective. New Phytologist 168: 61-69.
27. Pelegrini PB, Franco OL (2005) Plant gamma-thionins: novel insights on the mechanism of action of a multi-functional class of defense proteins. Int J Biochem Cell Biol 37: 2239-2253.
28. Thomma BP, Cammue BP, Thevissen K (2002) Plant defensins. Planta 216: 193-202.
29. Redman JC, Haas BJ, Tanimoto G, Town CD (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J 38: 545-561.
30. Silverstein K, Moskal W, Wu H, Underwood B, Graham M, et al. (2007) Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. Plant J 51: 262-280.
31. Silverstein KA, Graham MA, Paape TD, VandenBosch KA (2005) Genome organization of more than 300 defensin-like genes in Arabidopsis. Plant Physiol 138: 600-610.
32. Balasubramanian S, Schneitz K (2000) NOZZLE regulates proximal-distal pattern formation, cell proliferation and early sporogenesis during ovule development in Arabidopsis thaliana. Development 127: 4227-4238.
33. Balasubramanian S, Schneitz K (2002) NOZZLE links proximal-distal and adaxial-abaxial pattern formation during ovule development in Arabidopsis thaliana. Development 129: 4291-4300.
34. Schiefthaler U, Balasubramanian S, Sieber P, Chevalier D, Wisman E, et al. (1999) Molecular analysis of NOZZLE, a gene involved in pattern formation and early sporogenesis during sex organ development in Arabidopsis thaliana. Proc Natl Acad Sci U S A 96: 11664-11669.
35. Yang WC, Ye D, Xu J, Sundaresan V (1999) The SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein. Genes Dev 13: 2108-2117.
36. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
37. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, et al. (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506.
38. Swanson R, Clark T, Preuss D (2005) Expression profiling of Arabidopsis stigma tissue identifies stigma-specific genes. Sex Plant Reprod 18: 163-171.
39. Thomas SG, Franklin-Tong VE (2004) Self-incompatibility triggers programmed cell death in Papaver pollen. Nature 429: 305-309.
40. Vrinten PL, Nakamura T, Kasha KJ (1999) Characterization of cDNAs expressed in the early stages of microspore embryogenesis in barley (Hordeum vulgare) L. Plant Mol Biol 41: 455-463.
41. Sprunck S, Baumann U, Edwards K, Langridge P, Dresselhaus T (2005) The transcript composition of egg cells changes significantly following fertilization in wheat (Triticum aestivum L.). Plant J 41: 660-672.
42. Kent WJ (2002) blat-the BLAST-like alignment tool. Genome Res 12: 656-664.
43. Zhang M, Gish W (2006) Improved spliced alignment from an information theoretic approach. Bioinformatics 22: 13-20.
44. Hanada K, Zhang X, Borevitz JO, Li WH, Shiu SH (2007) A large number of novel coding small ORFs in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res 17: 632-640.
45. Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20: 307-315.
46. Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, et al. (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13: 513-523.
47. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783-795.
48. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735-743.