BCAWT: Automated tool for codon usage bias analysis for molecular evolution

Anwar, Ali Mostafa

doi:10.21105/joss.01500

Cited by 8 publications

(9 citation statements)

References 7 publications

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“…In the neutrality plot, a significant correlation ( P <0.05) between GC12 and GC3, and the slope of the regression line near 1.0 indicate that the mutational pressure plays a more important role than natural selection in shaping the codon usage [ 45 ]. The vhcub [ 46 ] was used to draw ENC-GC3 plots, while BCAWT [ 47 ] was employed to draw GC12-GC3 plots and PR2 plots.…”

Section: Methodsmentioning

confidence: 99%

Cryptosporidium felis differs from other Cryptosporidium spp. in codon usage

Guo

Roellig

et al. 2021

Microbial Genomics

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Cryptosporidium spp. are important enteric pathogens in a wide range of vertebrates including humans. Previous comparative analysis revealed conservation in genome composition, gene content, and gene organization among Cryptosporidium spp., with a progressive reductive evolution in metabolic pathways and invasion-related proteins. In this study, we sequenced the genome of zoonotic pathogen Cryptosporidium felis and conducted a comparative genomic analysis. While most intestinal Cryptosporidium species have similar genomic characteristics and almost complete genome synteny, fewer protein-coding genes and some sequence inversions and translocations were found in the C. felis genome. The C. felis genome exhibits much higher GC content (39.6 %) than other Cryptosporidium species (24.3–32.9 %), especially at the third codon position (GC3) of protein-coding genes. Thus, C. felis has a different codon usage, which increases the use of less energy costly amino acids (Gly and Ala) encoded by GC-rich codons. While the tRNA usage is conserved among Cryptosporidium species, consistent with its higher GC content, C. felis uses a unique tRNA for GTG for valine instead of GTA in other Cryptosporidium species. Both mutational pressures and natural selection are associated with the evolution of the codon usage in Cryptosporidium spp., while natural selection seems to drive the codon usage in C. felis. Other unique features of the C. felis genome include the loss of the entire traditional and alternative electron transport systems and several invasion-related proteins. Thus, the preference for the use of some less energy costly amino acids in C. felis may lead to a more harmonious parasite–host interaction, and the strengthened host-adaptation is reflected by the further reductive evolution of metabolism and host invasion-related proteins.

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Section: Methodsmentioning

confidence: 99%

Cryptosporidium felis differs from other Cryptosporidium spp. in codon usage

Guo

Roellig

et al. 2021

Microbial Genomics

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“…Principal component analysis (PCA) of the RSCU values was conducted using TBtools [45]. Parity rule 2 (PR2) [72], the effective number of codons against the GC content at the third codon position (ENC-GC3) [73], and neutrality (GC12-GC3) plots [74] were calculated using vhcub (https://cran.r-project.org/web/packages/ vhcub/) [75] and BCAWT (https://github.com/AliYoussef96/BCAW-Tool) [76] to analyse the evolutionary pressures for codon usages in Cryptosporidium spp. In the PR2 analysis, an even distribution of purines (A and G) and pyrimidines (T and C) in the coordinates is an indication of having no mutational pressure and natural selection for codon usage.…”

Section: Analysis Of Codon and Amino Acid Usagesmentioning

confidence: 99%

High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species

Roellig

et al. 2023

Microbial Genomics

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Cryptosporidium canis is a zoonotic species causing cryptosporidiosis in humans in addition to its natural hosts dogs and other fur animals. To understand the genetic basis for host adaptation, we sequenced the genomes of C. canis from dogs, minks, and foxes and conducted a comparative genomics analysis. While the genomes of C. canis have similar gene contents and organisations, they (~41.0 %) and C. felis (39.6 %) have GC content much higher than other Cryptosporidium spp. (24.3–32.9 %) sequenced to date. The high GC content is mostly restricted to subtelomeric regions of the eight chromosomes. Most of these GC-balanced genes encode Cryptosporidium-specific proteins that have intrinsically disordered regions and are involved in host-parasite interactions. Natural selection appears to play a more important role in the evolution of codon usage in GC-balanced C. canis, and most of the GC-balanced genes have undergone positive selection. While the identity in whole genome sequences between the mink- and dog-derived isolates is 99.9 % (9365 SNVs), it is only 96.0 % (362 894 SNVs) between them and the fox-derived isolate. In agreement with this, the fox-derived isolate possesses more subtelomeric genes encoding invasion-related protein families. Therefore, the change in subtelomeric GC content appears to be responsible for the more GC-balanced C. canis genomes, and the fox-derived isolate could represent a new Cryptosporidium species.

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“… 7 Various tools and packages, such as coRdon, 9 CodonW ( http://codonw.sourceforge.net ), and BCAWT. 8 are available for assessing and measuring CUB. However, there is currently a lack of specialized software specifically designed to examine the co-adaptation of codon usage between parasites and their hosts.…”

Section: Introductionmentioning

confidence: 99%

parazitCUB: An R package to streamline the process of investigating the adaptations of parasites' codon usage bias

Anwar,

Bayoumi,

Elzalabany

et al. 2023

F1000Res

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Examining the intricate association between parasites and their hosts, particularly at the codon level, assumes paramount importance in comprehending evolutionary processes and forecasting the characteristics of novel parasites. While diverse metrics and statistical analyses are available to explore codon usage bias (CUB), there presently exists no dedicated tool for examining the co-adaptation of codon usage between parasites and hosts. Therefore, we introduce the parazitCUB R package to address this challenge in a scalable and efficient manner, as it is capable of handling extensive datasets and simultaneously analyzing of multiple parasites with optimized performance. parazitCUB enables the elucidation of parasite-host interactions and the evolutionary patterns of parasites through the implementation of various indices, cluster analysis, multivariate analysis, and data visualization techniques. The tool can be accessed at the following location: https://github.com/AliYoussef96/parazitCUB

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BCAWT: Automated tool for codon usage bias analysis for molecular evolution

Cited by 8 publications

References 7 publications

Cryptosporidium felis differs from other Cryptosporidium spp. in codon usage

Cryptosporidium felis differs from other Cryptosporidium spp. in codon usage

High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species

parazitCUB: An R package to streamline the process of investigating the adaptations of parasites' codon usage bias

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