The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
Tóm tắt
Từ khóa
Tài liệu tham khảo
Gonsalves, D. Control of papaya ringspot virus in papaya: a case study. Annu. Rev. Phytopathol. 36, 415–437 (1998)
The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana . Nature 408, 796–815 (2000)
International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature 436, 793–800 (2005)
Tuskan, G. A. et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596–1604 (2006)
Jaillon, C. O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463–467 (2007)
Arumuganathan, K. & Earle, E. D. Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208–218 (1991)
Fitch, M. M. M., Manshardt, R. M., Gonsalves, D., Slightom, J. L. & Sanford, J. C. Virus resistant papaya plants derived from tissues bombarded with the coat protein gene of papaya ringspot virus. Bio/technology 10, 1466–1472 (1992)
Liu, Z. et al. A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature 427, 348–352 (2004)
Wikström, N., Savolainen, V. & Chase, M. W. Evolution of the angiosperms: calibrating the family tree. Proc. R. Soc. Lond. B 268, 2211–2220 (2001)
Storey, W. B. Papaya. in Outlines of Perennial Crop Breeding in the Tropics (eds Ferwerda, F. P. and Wit, F.) 389–408 (H. Veenman & Zonen, Wageningen, 1969)
Li, L. et al. Genome-wide transcription analyses in rice using tiling microarrays. Nature Genet. 38, 124–129 (2006)
Lander, E. S. & Waterman, M. S. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2, 231–239 (1988)
Hanada, K., Zhang, X., Borevitz, J. O., Li, W.-H. & Shiu, S.-H. A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res. 17, 632–640 (2007)
Bowers, J. E., Chapman, B. A., Rong, J. & Paterson, A. H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433–438 (2003)
Schranz, M. E. & Mitchell-Olds, T. Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. Plant Cell 18, 1152–1165 (2006)
Lyons, E. & Freeling, M. How to usefully compare homologous plant genes and chromosomes as DNA sequence. Plant J. 53, 661–673 (2008)
Thomas, B. C., Rapaka, L., Lyons, E., Pedersen, B. & Freeling, M. Arabidopsis intragenomic conserved noncoding sequence. Proc. Natl Acad. Sci. USA 104, 3348–3353 (2007)
Wall, P. K. et al. PlantTribes: a gene and gene family resource for comparative genomics in plants. Nucleic Acids Res. 36, D970–D976 (2008)
Meyers, B. C., Morgante, M. & Michelmore, R. W. TIR-X and TIR-NBS proteins: two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes. Plant J. 32, 77–92 (2002)
Zhou, T. et al. Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol. Genet. Genomics 271, 402–415 (2004)
Fry, S. C. Primary cell wall metabolism: tracking the careers of wall polymers in living plant cells. New Phytol. 161, 641–675 (2004)
Ehlting, J. et al. Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation. Plant J. 42, 618–640 (2005)
Zhou, L. L. & Paull, R. E. Sucrose metabolism during papaya (Carica papaya) fruit growth and ripening. J. Am. Soc. Hortic. Sci. 126, 351–357 (2001)
Paull, R. E. & Chen, N. J. Postharvest variation in cell wall-degrading enzymes of papaya (Carica papaya L.) during fruit ripening. Plant Physiol. 72, 382–385 (1983)
Richardt, S., Lang, D., Reski, R., Frank, W. & Rensing, S. A. PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. Plant Physiol. 143, 1452–1466 (2007)
Yu, Q. et al. Low X/Y divergence of four pairs of papaya sex-liked genes. Plant J. 53, 124–132 (2008)
Yu, Q. et al. Chromosomal location and gene paucity of the male specific region on papaya Y chromosome. Mol. Genet. Genomics 278, 177–185 (2007)
Sawasaki, T., Takahashi, M., Goshima, N. & Morikawa, H. Structures of transgene loci in transgenic Arabidopsis plants obtained by particle bombardment: junction regions can bind to nuclear matrices. Gene 218, 27–35 (1998)
Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004)
Jaffe, D. B. et al. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 13, 91–96 (2003)
Chou, H. H. & Holmes, M. H. DNA sequence quality trimming and vector removal. Bioinformatics 17, 1093–1104 (2001)
Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker (Release Open-3.1.3, 2006)
Price, A. L., Jones, N. C. & Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21 (suppl.). i351–i358 (2005)
Haas, B. J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003)
Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19 (suppl.). ii215–ii225 (2003)
Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20, 2878–2879 (2004)
Salamov, A. A. & Solovyev, V. V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516–522 (2000)
Burge, C. & Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78–94 (1997)
Korf, I., Flicek, P., Duan, D. & Brent, M. R. Integrating genomic homology into gene structure prediction. Bioinformatics 17 (suppl. 1). S140–S148 (2001)
Huang, X., Adams, M. D., Zhou, H. & Kerlavage, A. R. A tool for analyzing and annotating genomic sequences. Genomics 46, 37–45 (1997)
Finn, R. D. et al. Pfam: clans, web tools and services. Nucleic Acids Res. 34 (Database issue). D247–D251 (2006)
Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7.1–R7.19 (2008)
Quevillon, E. et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116–W120 (2005)
Attwood, T. K. et al. PRINTS and its automatic supplement, prePRINTs. Nucleic Acids Res. 31, 400–402 (2003)
Bru, C. et al. The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res. 33 (Database issue). D212–D215 (2005)
Letunic, I. et al. SMART 5: domains in the context of genomes and networks. Nucleic Acids Res. 34 (Database issue). D257–D260 (2006)
Edgar, R. C. & Myers, E. W. PILER: Identification and classification of genomic repeats. Bioinformatics 21 (suppl.). i152–i158 (2005)