Transcript free energy positively correlates with codon usage bias in mitochondrial genes of Calypogeia species (Calypogeiaceae, Marchantiophyta)

Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Sudipa DasSupriyo Chakraborty

Abstract

The present study attempts to focus on the pattern of codon usage bias (CUB) in mitochondrial genes among four species of Calypogeia viz. C. arguta, C. integristipula, C. neogaea and C. suecica along with the factors influencing their CUB as no work was reported yet. The four taxa exhibit noticeable difference in their morphological features, habitat preference and growth forms. To understand the patterns of codon usage in Calypogeia mitochondrial genomes, we used bioinformatic tools to analyze the mitochondrial protein-coding sequences of four Calypogeia. In our current study, the mean nucleobase T was the highest while G was the lowest in all four species. The overall GC content was higher than AT content i.e. genes were AT rich. The CUB was low in mitochondrial genes of C. arguta, C. integristipula, C. neogaea and C. suecica, respectively as revealed from low synonymous codon usage order (SCUO) values. Heat map study revealed that most of the GC and AT ending codons showed positive correlations between codon usage and GC3. From the neutrality plot, the slope of the regression line indicated that natural selection might have played a major role over mutation pressure in shaping the CUB of mitochondrial genes in these four tax...Continue Reading

References

Jan 25, 1989·Nucleic Acids Research·E E MurrayM Eberle
Apr 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·N Sueoka
Nov 25, 1993·Nucleic Acids Research·S L Fennoy, J Bailey-Serres
Oct 1, 1996·Current Opinion in Biotechnology·C Kurland, J Gallant
Mar 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SantaLucia
Mar 5, 1999·Science·M W GrayB F Lang
Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·L Duret, D Mouchiroud
Oct 4, 2000·Nature Genetics·E R Tillier, R A Collins
Feb 28, 2003·Virus Research·Gareth M Jenkins, Edward C Holmes
Mar 5, 2003·Proceedings. Biological Sciences·Paul D N HebertJeremy R deWaard
Dec 17, 2003·Genes & Genetic Systems·Akira Kawabe, Naohiko T Miyashita
Apr 12, 2005·PLoS Biology·Kenneth R Chien
Apr 19, 2005·Archives of Virology·H ZhouP Clifford
Jan 1, 1990·Plant Physiology·W H Campbell, G Gowri
Nov 5, 2010·PloS One·Gareth A PalidworXuhua Xia
Dec 5, 2013·PloS One·Zhicheng ZhangDingzhen Dai
Mar 26, 2015·PloS One·Tarikul Huda Mazumder, Supriyo Chakraborty
May 7, 2015·BMC Genomics·Xian JiaJingchen Sun
Oct 6, 2016·Scientific Reports·Tianhua HeJohn Manning
Oct 26, 2016·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Arif UddinSupriyo Chakraborty
Jul 3, 2017·Mitochondrion·Arif UddinSupriyo Chakraborty

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