Analysis of dinucleotide frequency and codon usage in the phylum Apicomplexa

Gene
J EllisA M Johnson

Abstract

Dinucleotide frequency (DiF) and codon usage (cu) were analysed in gene sequences from four parasitic protozoa, Babesia bovis, Theileria parva, Toxoplasma gondii and Eimeria tenella, of the phylum Apicomplexa. In keeping with the 'genome hypothesis', cu was found to be non-random and species specific in these organisms, although cu among members of the same subclass was found to be very similar. Several low-usage (lu) codons were identified, and the usage of lu codons appears to be related to the taxonomic position of the organisms under study. A comparison of the observed/expected DiF ratios obtained from gene coding regions revealed a low frequency of the TA and CG dinucleotides in all organisms studied. A comparison of these DiF ratios with those found in rRNA-encoding genes and in introns, showed that in the parasites, B. bovis and Th. parva (representing the piroplasms), the low frequency of dinucleotides appeared to be the result of coding pressure alone. In T. gondii and E. tenella (representing the coccidia), however, coding pressure could not completely explain differences in DiF.

References

Aug 1, 1992·Molecular and Biochemical Parasitology·H A BaylisR Hall
Aug 1, 1992·Molecular and Biochemical Parasitology·J EllisA M Johnson
Jan 1, 1992·Molecular and Biochemical Parasitology·P N OssorioJ C Boothroyd
Feb 1, 1990·Molecular and Biochemical Parasitology·K P IamsA J Musoke
Dec 1, 1991·Molecular and Biochemical Parasitology·F M TomleyJ J Kok
May 1, 1991·Experimental Parasitology·Y PollackJ Golenser
Jan 1, 1991·Journal of Molecular Evolution·M Long, J H Gillespie
Apr 25, 1991·Nucleic Acids Research·K WadaT Ikemura
Nov 1, 1990·Molecular and Biochemical Parasitology·J B PrinceJ S Remington
Apr 1, 1989·Molecular and Biochemical Parasitology·J B PrinceS D Sharma
Oct 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·M F Cesbron-DelauwJ P Lecocq
Jan 15, 1988·Molecular and Biochemical Parasitology·D Snary, M A Smith
Aug 15, 1986·European Journal of Biochemistry·J T Wong, R Cedergren
Jan 1, 1988·Molecular and Biochemical Parasitology·A Saul, D Battistutta
Jun 1, 1988·Molecular and Biochemical Parasitology·S D Nagel, J C Boothroyd
Jan 10, 1986·Nucleic Acids Research·R Staden
Jan 11, 1984·Nucleic Acids Research·J DevereuxO Smithies
Mar 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·J C Shepherd
Jan 10, 1981·Nucleic Acids Research·R GranthamR Mercier
Jan 1, 1991·Parasitology Today·J Ellis, F Tomley

❮ Previous
Next ❯

Citations

Jul 12, 2002·Cell Motility and the Cytoskeleton·A E LewJ C Pinder
Feb 1, 1996·Molecular and Biochemical Parasitology·G Zhu, J S Keithly
Nov 25, 1996·Molecular and Biochemical Parasitology·C Odberg-FerragutJ F Dubremetz
Mar 25, 2000·International Journal for Parasitology·V NeneA Irvin
Jun 6, 2000·Molecular and Biochemical Parasitology·G WidmerS Tzipori
Oct 8, 1998·Molecular and Biochemical Parasitology·V NeneR Bishop
Dec 7, 2011·Algorithms for Molecular Biology : AMB·Tahir MehmoodLars Snipen
Jan 1, 1995·Parasitology·J T Ellis, D A Morrison
Mar 21, 1998·Experimental Parasitology·J G WaterkeynM W Lightowlers
Jan 27, 1999·Biochemical and Biophysical Research Communications·M Biñas, A M Johnson
Jul 23, 1999·Infection and Immunity·C LiuM S Abrahamsen

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.