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Terminal Bias Patterns in Protein Coding Sequences of Phytophthora Sojae

Sarkar, Chandra, SARKAR
http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1499444381524856

Abstract Details

2017, Master of Science (MS), Bowling Green State University, Biological Sciences.
Phytophthora sojae is an economically important plant pathogen of the soybean. It belongs to the oomycetes group of organisms and has a hemi-biotrophic lifestyle. Previous attempts to design primers for certain genes in P. sojae posed a challenge as GC content in the N-terminal was higher than the C-terminals. To test the hypothesis that there was a general N-terminal GC bias across all protein coding sequences, we used a sliding window of 6 codons along the two terminals, calculating the positional bias of the sequences. The GC% at the N-terminals showed high elevation when compared to the mean across the sequences. The highest deviation being at around 50 bp for P. sojae. It gradually fell off but remained slightly higher even after 300bp. In comparison, the C-terminals showed the lowest GC% at 4-25bp and at 60 bp it reached the mean quicker than the N-terminals and maintained it further along. This pattern of positional GC bias was also observed in P. ramorum, P. infestans, P. parasitica, P. capsici and P. cinnamomi. While G/C rich based codons have increased presence at the N-terminals compared to the global usage, they showed reduced presence at the C-terminals. Further examination of certain protein coding sequences, such as signal peptide containing sequences and subsets of effector proteins in P. sojae, conformed to the global bias patterns at the terminals. In the RXLR effector sequences, the terminal bias shows altered codon usage frequencies in the 5’-ends, relative to the global codon usage bias. Other plant pathogenic fungi examined, did not show such significant bias in their terminals nor did the oomycete Albugo spp. Hyalonoperonospora arabidopsis and Pythium ultimum however, showed similar GC pattern only in the N-terminals. Our studies show that, the positional GC bias potentially is a factor which shapes codon preferences at the terminals of coding sequences.
Paul Morris, Professor (Advisor)
Zhaohui Xu, Associate Professor (Committee Member)
Robert Huber, Professor (Committee Member)
209 p.
Biology
oomycetes; Phytophthora; codon bias; terminal bias; RXLR

Recommended Citations

Citations

  • Sarkar, SARKAR, C. (2017). Terminal Bias Patterns in Protein Coding Sequences of Phytophthora Sojae [Master's thesis, Bowling Green State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1499444381524856

    APA Style (7th edition)

  • Sarkar, SARKAR, Chandra. Terminal Bias Patterns in Protein Coding Sequences of Phytophthora Sojae. 2017. Bowling Green State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1499444381524856.

    MLA Style (8th edition)

  • Sarkar, SARKAR, Chandra. "Terminal Bias Patterns in Protein Coding Sequences of Phytophthora Sojae." Master's thesis, Bowling Green State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1499444381524856

    Chicago Manual of Style (17th edition)

bgsu1499444381524856
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This open access ETD is published by Bowling Green State University and OhioLINK.