Ribosomal DNA is differentially amplified across life-cycle stages in the foraminifer Allogromia laticollaris strain CSH

Journal of Foraminiferal Research

Volumn 42, Issue 2, 2012, Pages 151-155

  Parfrey, Laura Wegener ^a,b,c   Grant, Jessica ^b   Katz, Laura A ^a,b  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

^b SMITH COLLEGE   (United States)

^c UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENTHIC FORAMINIFERA; DNA; GENETIC DIFFERENTIATION; GENOMICS; HYPOTHESIS TESTING; LIFE CYCLE; POLYMERASE CHAIN REACTION; PROTEIN; QUANTITATIVE ANALYSIS;

ALLOGROMIA; ALLOGROMIA LATICOLLARIS; EUKARYOTA; FORAMINIFERA; RHIZARIA;

EID: 84863834982     PISSN: 00961191     EISSN: None     Source Type: Journal    
DOI: 10.2113/gsjfr.42.2.151     Document Type: Article

References (33)

1. ARNOLD, Z. M., 1955, Life history and cytology of the foraminiferan Allogromia laticollaris: University of California Publications in Zoology, v. 61, p. 167-252.
2. BAGCHI, A., BHATTACHARYA, A., and BHATTACHARYA, S., 1999, Lack of a chromosomal copy of the circular rDNA plasmid of Entamoeba histolytica: International Journal For Parasitology, v. 29, p. 1775-1783.
3. COHEN, S., and SEGAL, D., 2009, Extrachromosomal circular DNA in eukaryotes: possible involvement in the plasticity of tandem repeats: Cytogenetic And Genome Research, v. 124, p. 327-338.
4. CULLIS, C. A., 2005, Mechanisms and control of rapid genomic changes in flax: Annals of Botany, v. 95, p. 201-206.
5. DAHLGREN, L., 1964, On nuclear cytology and reproduction in the monothalamous Foraminifera Ovammina opaca Dahlgren: Zoologiska Bidrag frân Uppsala, v. 36, p. 315-334.
6. ERENPREISA, J., and CRAGG, M. S., 2007, Cancer: a matter of life cycle?: Cell Biology International, v. 31, p. 1507-1510.
7. FLAKOWSKI, J., BOLIVAR, L, FAHRNI, J., and PAWLOWSKI, J., 2005, Actin phylogeny of foraminifera: Journal of Foraminiferal Research, v. 35, p. 93-102.
8. FøYN, B., 1936, Über die Kernverhaltnisse der Foraminifere Myxotheca arenilega Schaudinn: Archiv Fur Protistenkunde, v. 87, p. 272-295.
9. GOLDSTEIN, S. T., 1997, Gametogenesis and the antiquity of reproductive pattern in the Foraminiferida: Journal of Foraminiferal Research, v. 27, p. 319-328.
10. -, 1999, Foraminifera: A biological overview, in Sen Gupta, B. K. (ed.), Modern Foraminifera: Kluwer Press, Dordrecht, p. 37-56.
11. GUY, R. A., PAYMENT, P., KRULL, U. J., and HORGEN, P. A., 2003, Real-time PCR for quantification of Giardia and Cryptosporidium in environmental water samples and sewage: Applied and Environmental Microbiology, v. 69, p. 5178-5185.
12. HABURA, A., HOU, Y., REILLY, A. A., and BOWSER, S. S., 2011, Highthroughput sequencing of Astrammina rara: sampling the giant genome of a giant foraminiferan protist: BMC Genomics, v. 12, p. 1-11.
13. HENIKOFF, S., 2005, Rapid changes in plant genomes: Plant Cell, v. 17, p. 2852-2855.
14. HOSPODSKY, D., YAMAMOTO, N., and PECCIA, J., 2010, Accuracy, precision, and method detection limits of quantitative PCR for airborne bacteria and fungi: Applied and Environmental Microbiology, v. 76, p. 7004-7012.
15. KABIR, S., RAJENDRAN, N., AMEMIYA, T., and ITOH, K., 2003, Quantitative measurement of fungal DNA extracted by three different methods using real-time polymerase chain reaction: Journal of Bioscience and Bioengineering, v. 96, p. 337-343.
16. KONDRASHOV, A. S., 1997, Evolutionary genetics of life cycles: Annual Review of Ecology and Systematics, v. 28, p. 391-435.
17. LEE, J. J., and MCENERY, M. E., 1970, Autogamy in Allogromia laticollaris (Foraminifera): Journal of Protozoology, v. 17, p. 184-195.
18. -, -, and RUBIN, H., 1969, Quantitative Studies on Growth of Allogromia laticollaris (Foraminifera): Journal of Protozoology, v. 16, p. 377-395.
19. LI, M., WANG, I. X., LI, Y., BRUZEL, A., RICHARDS, A. L., TOUNG, J. M., and CHEUNG, V. G., 2011, Widespread RNA and DNA sequence differences in the human transcriptome: Science, v. 333, p. 53-58.
20. MCENERY, M. E., and LEE, J. J., 1976, Allogromia laticollaris: a Foraminiferan with an unusual apogamic metagenic life cycle: Journal of Protozoology, v. 23, p. 94-108.
21. MCGRATH, C. L., and KATZ, L. A., 2004, Genome diversity in microbial eukaryotes: Trends in Ecology and Evolution, v. 19, p. 32-38.
22. MUKHERJEE, C., MAJUMDER, S., and LOHIA, A., 2009, Inter-cellular variation in DNA content of Entamoeba histolytica originates from temporal and spatial uncoupling of cytokinesis from the nuclear cycle: PLoS Neglected Tropical Diseases, v. 3, p. e409.
23. MUMY, K. L., and FINDLAY, R. H., 2004, Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR: Journal of Microbiological Methods, v. 57, p. 259-268.
24. PARFREY, L. W., and KATZ, L. A., 2010a, Dynamic genomes of eukaryotes and the maintenance of genomic integrity: Microbe Magazine, v. 5, p. 156-163.
25. -, and -, 2010b, Genome dynamics are influenced by food source in Allogromia laticollaris strain CSH (Foraminifera): Genome Biology and Evolution, v. 2, p. 678-685.
26. -, LAHR, D. J. G., and KATZ, L. A., 2008, The dynamic nature of eukaryotic genomes: Molecular Biology and Evolution, v. 25, p. 787-794.
27. PAWLOWSKI, J., 2000, Introduction to the molecular systematics of Foraminifera: Micropaleontology, v. 46, p. 1-12.
28. RAIKOV, I. B., 1982, The Protozoan Nucleus: Morphology and Evolution: Springer-Verlag, Vienna, 474 p.
29. REDON, R., ISHIKAWA, S., FITCH, K. R., FEUK, L., PERRY, G. H., ANDREWS, T. D., FIEGLER, H., SHAPERO, M. H., CARSON, A. R., CHEN, W. W., CHO, E. K., DALLAIRE, S., FREEMAN, J. L., GONZALEZ, J. R., GRATACOS, M., HUANG, J., KALAITZOPOULOS, D., KOMURA, D., MACDONALD, J. R., MARSHALL, C R., MEI, R., MONTGOMERY, L., NISHIMURA, K., OKAMURA, K., SHEN, F., SOMERVILLE, M. J., TCHINDA, J., VALSESIA, A., WOODWARK, C., YANG, F. T., ZHANG, J. J., ZERJAL, T., ZHANG, J., ARMENGOL, L., CONRAD, D. F., ESTIVILL, X., TYLER-SMITH, C., CARTER, N. P., ABURATANI, H., LEE, C., JONES, K. W., SCHERER, S. W., and HURLES, M. E., 2006, Global variation in copy number in the human genome: Nature, v. 444, p. 444-454.
30. STORCHOVA, Z., and PELLMAN, D., 2004, From polyploidy to aneuploidy, genome instability and cancer: Nature Reviews Molecular Cell Biology, v. 5, p. 45-54.
31. YOON, H. S., GRANT, J., TEKLE, Y. I., WU, M., CHAON, B. C., COLE, J. C., LOGSDON, J. M., PATTERSON, D. J., BHATTACHARYA, D., and KATZ, L. A., 2008, Broadly sampled multigene trees of eukaryotes: BMC Evolutionary Biology, v. 8, p. 14.
32. ZHOU, J., BRUNS, M., and TIEDJE, J. M., 1996, DNA recovery from soils of diverse composition: Applied and Environmental Microbiology, v. 62, p. 316-322.
33. ZUFALL, R. A., ROBINSON, T., and KATZ, L. A., 2005, Evolution of developmentally regulated genome rearrangements in eukaryotes: Journal of Experimental Zoology Part B-Molecular and Developmental Evolution, v. 304B, p. 448-455.