Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on Linkage groups I and III

Journal of Eukaryotic Microbiology

Volumn 50, Issue 3, 2003, Pages 145-155

  Li, Jin Billy ^a   Lin, Shaoping ^b   Jia, Honggui ^b   Wu, Hongmin ^b   Roe, Bruce A ^b   Kulp, David ^c   Stormo, Gary D ^a   Dutcher, Susan K ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF OKLAHOMA   (United States)

^c Thermo Fisher Scientific   (United States)

Author keywords

Alga; Gene prediction; GreenGenie; Repetitive elements

Indexed keywords

GENOME;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CHLAMYDOMONAS REINHARDTII; DNA, PROTOZOAN; GENOME; LINKAGE (GENETICS); MOLECULAR SEQUENCE DATA; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA, TRANSFER; SEQUENCE ALIGNMENT;

ALGAE; CHLAMYDOMONAS; CHLAMYDOMONAS REINHARDTII; CHLOROPHYTA; EUKARYOTA;

EID: 0037790948     PISSN: 10665234     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1550-7408.2003.tb00109.x     Document Type: Article

References (50)

1. Adams, M. D., Celniker, S. E., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., George, R. A., Lewis, S. E., Richards, S., Ashburner, M., Henderson, S. N., Sutton, G. G., Wortman, J. R., Yandell, M. D., Zhang, Q., Chen, L. X., Brandon, R. C., Rogers, Y. H., Blazej, R. G., Champe, M., Pfeiffer, B. D., Wan, K. H., Doyle, C., Baxter, E. G., Helt, G., Nelson, C. R., Gabor, G. L., Abril, J. F., Agbayani, A., An, H. J., Andrews-Pfannkoch, C., Baldwin, D., Ballew, R. M., Basu, A., Baxendale, J., Bayraktaroglu, L., Beasley, E. M., Beeson, K. Y., Benos, P. V., Berman, B. P., Bhandari, D., Bolshakov, S., Borkova, D., Botchan, M. R., Bouck, J., Brokstein, P., Brottier, P., Burtis, K. C., Busam, D. A., Butler, H., Cadieu, E., Center, A., Chandra, I., Cherry, J. M., Cawley, S., Dahlke, C., Davenport, L. B., Davies, P., de Pablos, B., Delcher, A., Deng, Z., Mays, A. D., Dew, I., Dietz, S. M., Dodson, K., Doup, L. E., Downes, M., Dugan-Rocha, S., Dunkov, B. C., Dunn, P., Durbin, K. J., Evangelista, C. C., Ferraz, C., Ferriera, S., Fleischmann, W., Fosler, C., Gabrielian, A. E., Garg, N. S., Gelbart, W. M., Glasser, K., Glodek, A., Gong, F., Gorrell, J. H., Gu, Z., Guan, P., Harris, M., Harris, N. L., Harvey, D., Heiman, T. J., Hernandez, J. R., Houck, J., Hostin, D., Houston, K. A., Howland, T. J., Wei, M. H., Ibegwam, C., Jalali, M., Kalush, F., Karpen, G. H., Ke, Z., Kennison, J. A., Ketchum, K. A., Kimmel, B. E., Kodira, C. D., Kraft, C., Kravitz, S., Kulp, D., Lai, Z., Lasko, P., Lei, Y., Levitsky, A. A., Li, J., Li, Z., Liang, Y., Lin, X., Liu, X., Mattei, B., McIntosh, T. C., McLeod, M. P., McPherson, D., Merkulov, G., Milshina, N. V., Mobarry, C., Morris, J., Moshrefi, A., Mount, S. M., Moy, M., Murphy, B., Murphy, L., Muzny, D. M., Nelson, D. L., Nelson, D. R., Nelson, K. A., Nixon, K., Nusskern, D. R., Pacleb, J. M., Palazzolo, M., Pittman, G. S., Pan, S., Pollard, J., Puri, V., Reese, M. G., Reinert, K., Remington, K., Saunders, R. D., Scheeler, F., Shen, H., Shue, B. C., Siden-Kiamos, I., Simpson, M., Skupski, M. P., Smith, T., Spier, E., Spradling, A. C., Stapleton, M., Strong, R., Sun, E., Svirskas, R., Tector, C., Turner, R., Venter, E., Wang, A. H., Wang, X., Wang, Z. Y., Wassarman, D. A., Weinstock, G. M., Weissenbach, J., Williams, S. M., Woodage, T., Worley, K. C., Wu, D., Yang, S., Yao, Q. A., Ye, J., Yeh, R. F., Zaveri, J. S., Zhan, M., Zhang, G., Zhao, Q., Zheng, L., Zheng, X. H., Zhong, F. N., Zhong, W., Zhou, X., Zhu, S., Zhu, X., Smith, H. O., Gibbs, R. A., Myers, E. W., Rubin, G. M. & Venter, J. C. 2000. The genome sequence of Drosophila melanogaster. Science, 287:2185-2195.
2. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408:796-815.
3. Bodenteich, A., Chissoe, S., Wang, Y. F. & Roe, B. A. 1993. Shotgun cloning as the strategy of choice to generate templates for high-throughput dideoxynucleotide sequencing. In: Venter, J. C. (ed.), Automated DNA Sequencing and Analysis Techniques. Academic Press, London. p. 42-50.
4. Burge, C. & Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268:78-94.
5. Chissoe, S. L., Bodenteich, A., Wang, Y. F., Wang, Y. P., Burian, D., Clifton, S. W., Crabtree, J., Freeman, A., Iyer, K., Jian, L., Ma, Y., McLaury, H. J., Pan, H. Q., Sharan, O., Toth, S., Wong, Z., Zhang, G., Heisterkamp, N., Groffen, J. & Roe, B. A. 1995. Sequence and analysis of the human ABL gene, the BCR gene, and regions involved in the Philadelphia chromosomal translocation. Genomics, 27:67-82.
6. The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science, 282:2012-2018.
7. Dame, G., Gloeckner, G. & Beck, C. F. 2002. Knock-out of a putative transporter results in altered blue-light signalling in Chlamydomonas. Plant J., 31:577-587.
8. Day, A. 1995. A transposon-like sequence with short terminal inverted repeats in the nuclear genome of Chlamydomonas reinhardtii. Plant Mol. Biol., 28:437-442.
9. Day, A. & Rochaix, J. D. 1989. Characterization of transcribed dispersed repetitive DNAs in the nuclear genome of the green alga Chlamydomonas reinhardtii. Curr. Genet., 16:165-176.
10. Day, A., Schirmer-Rahire, M., Kuchka, M. R., Mayfield, S. P. & Rochaix, J. D. 1988. A transposon with an unusual arrangement of long terminal repeats in the green alga Chlamydomonas reinhardtii. EMBO J., 7:1917-1927.
11. Dinant, M., Baurain, D., Coosemans, N., Joris, B. & Matagne, R. F. 2001. Characterization of two genes encoding the mitochondrial alternative oxidase in Chlamydomonas reinhardtii. Curr. Genet., 39:101-108.
12. Dutcher, S. K. 2000. Chlamydomonas reinhardtii: Biological rationale for genomics. J. Eukaryot. Microbiol., 47:340-349.
13. Dutcher, S. K., Morrissette, N. S., Preble, A. M., Rackley, C. & Stanga, J. 2002. Epsilon-tubulin is an essential component of the centriole. Mol. Biol. Cell, 13:3859-3869.
14. Emanuelsson, O., Nielsen, H. & von Heijne, G. 1999. ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci., 8:978-84.
15. Emanuelsson, O., Nielsen, H., Brunak, S. & von Heijne, G. 2000. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol., 300:1005-1016.
16. Ewing, B. & Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8:186-194.
17. Ewing, B. & Green, P. 2000. Analysis of expressed sequence tags indicates 35,000 human genes. Nat Genet., 25:232-234.
18. Ewing, B., Hillier, L., Wendl, M. C. & Green, P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res., 8:175-185.
19. Ferris, P. J. 1989. Characterization of a Chlamydomonas transposon, Gulliver, resembling those in higher plants. Genetics, 122:363-377.
20. Ferris, P. J. & Goodenough, U. W. 1994. The mating-type locus of Chlamydomonas reinhardtii contains highly rearranged DNA sequences. Cell, 76:1135-1145.
21. Ferris, P. J., Armbrust, E. V. & Goodenough, U. W. 2002. Genetic structure of the mating-type locus of Chlamydomonas reinhardtii. Genetics, 160:181-200.
22. Ferris, P. J., Woessner, J. P., Waffenschmidt, S., Kilz, S., Drees, J. & Goodenough, U. W. 2001. Glycosylated polyproline II rods with kinks as a structural motif in plant hydroxyproline-rich glycoproteins. Biochemistry, 40:2978-2987.
23. Florea, L., Hartzell, G., Zhang, Z., Rubin, G. M. & Miller, W. 1998. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8:967-974.
24. 2 availability. Proc. Natl. Acad. Sci. USA, 98:5347-5352.
25. Gish, W. http://blast.wustl.edu/; 1996-2000. WU-BLAST
26. Gordon, D., Abajian, C. & Green, P. 1998. Consed: A graphical tool for sequence finishing. Genome Res., 8:195-202.
27. Gowans, C. S. 1965. Tetrad analysis. Taiwania, 11:1-19.
28. Graham, J. E., Spanier, J. G. & Jarvik, J. W. 1995. Isolation and characterization of Pioneer1, a novel Chlamydomonas transposable element. Curr. Genet., 28:429-436.
29. Gross, C. H., Ranum, L. P., & Lefebvre, P. A. 1988. Extensive restriction fragment length polymorphisms in a new isolate of Chlamydomonas reinhardtii. Curr. Genet., 13:503-508.
30. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature, 409:860-921.
31. Kan, Z., Rouchka, E., Gish, W. & States, D. 2001. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res., 11:875-888.
32. Kindle, K. L. 1990. High frequency transformation of Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA, 87:1228-1232.
33. Kulp, D., Haussler, D., Reese, M. G. & Eeckman, F. H. 1996. A generalized Hidden Markov Model for the recognition of human genes in DNA. ISMB-96, St. Louis, MO, AAAI/MIT Press.
34. Lefebvre, P. A. & Silflow, C. D. 1999. Chlamydomonas: the cell and its genomes. Genetics. 151:9-14.
35. Life Technologies European Patent Number WO09946400, and protocols available at URLs: http://www.genome.ou.edu/protocol_enhancing_PCR. html and http://www.genome.ou.edu/seq_very-difficult-regions.html
36. Lowe, T. M. & 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. Lukashin, A. & Borodovsky, M. 1998. GeneMark. hmm: new solutions for gene finding. Nucleic Acids Res., 26:1107-1115.
38. Marra, M. A., Kucaba, T. A., Dietrich, N. L., Green, E. D., Brownstein, B., Wilson, R. K., McDonald, K. M., Hillier, L. W., McPherson, J. D. & Waterston, R. H. 1997. High throughput fingerprint analysis of large-insert clones. Genome Res., 7:1072-1084.
39. Mathe, C., Sagot, M.-F., Schiex, T. & Rouze, P. 2002. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res., 30:4103-4117.
40. Moseley, J. L., Page, M. D., Alder, N. P., Eriksson, M., Quinn, J., Soto, F., Theg, S. M., Hippler, M. & Merchant, S. 2002. Reciprocal expression of two candidate di-iron enzymes affecting photosystem I and light-harvesting complex accumulation. Plant Cell, 14:673-688.
41. Pan, H. Q., Wang, Y. P., Chissoe, S. L., Bodenteich, A., Wang, Z., Iyer, K., Clifton, S. W., Crabtree, J. S. & Roe, B. A. 1994. The complete nucleotide sequence of the SacBII domain of the P1 pAD10-SacBII cloning vector and three cosmid cloning vectors: pTCF, svPHEP, and LAWRIST16. Genet. Anal. Tech. Appl., 11:181-186.
42. Proschold, T., Marin, B., Schlosser, U. G. & Melkonian, M. 2001. Molecular phylogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov. Protist, 152:265-300.
43. Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajahdream, M.-A. & Barrell, B. 2000. Artemis: sequence visualisation and annotation. Bioinformatics, 16:944-945.
44. Sager, R. & Ishida, R. 1963. Chloroplast DNA in Chlamydomonas. Proc. Natl. Acad. Sci. USA, 50:725-730.
45. Sambrook, J., Fritsch, E. F. & Maniatis, T. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
46. Schroda, M., Vallon, O., Whitelegge, J. P., Beck, C. F. & Wollman, F. A. 2001. The chloroplastic GrpE homolog of Chlamydomonas: two isoforms generated by differential splicing. Plant Cell, 13:2823-2839.
47. Sineshchekov, O. A., Jung, K. H. & Spudich, J. L. 2002. Two rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA, 99:8689-8694.
48. Uchida, H., Suzuki, L., Anai, T., Doi, K., Takano, H., Yamashita, H., Oka, T., Kawano, S., Tomizawa, K. I., Kawazu, T., Kuroiwa, H. & Kuroiwa, T. 1999. A pair of invertedly repeated genes in Chlamydomonas reinhardtii encodes a zygote-specific protein whose expression is UV-sensitive. Curr. Genet., 36:232-240.
49. Vysotskaia V. S., Curtis, D. E., Voinov, A. V., Kathir, P., Silflow, C. D. & Lefebvre, P. A. 2001. Development and characterization of genome-wide single nucleotide polymorphism markers in the green alga Chlamydomonas reinhardtii. Plant Physiol., 127:386-389.
50. Wang, S. C., Schnell, R. A. & Lefebvre, P. A. 1998. Isolation and characterization of a new transposable element in Chlamydomonas reinhardtii. Plant Mol. Biol., 38:681-687.