Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in <i>Plasmodium</i> spp.

Castillo, Andreína I.; Nelson, Andrew D. L.; Lyons, Eric

doi:10.1093/gbe/evz015

Cited by 10 publications

(7 citation statements)

References 72 publications

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“…It is worth noticing that genome architecture features separate the subgenera Laverania and Plasmodium , including A + T content, patterns of codon usage, and the distribution of low-complexity regions [ 115 – 117 ]. Furthermore, among the best-known molecular adaptations separating Laverania from Plasmodium are gene families involved in antigenic variation [ 14 , 49 ], such as the var gene family.…”

Section: Introductionmentioning

confidence: 99%

“…On the other hand, more loci may be beneficial if they have congruent phylogenetic signals, are not saturated, share patterns of rate variation across lineages, and do not require different substitution models (e.g., similar GC content). The latest is challenging to accomplish in Plasmodium genus because of the differences in GC content [ 115 ], but the mitochondria and apicoplast genomes offer an alternative [ 39 , 147 ]. Of the two, the mitochondria have been widely used in such molecular clock studies.…”

Section: Introductionmentioning

confidence: 99%

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Why Plasmodium vivax and Plasmodium falciparum are so different? A tale of two clades and their species diversities

Escalante

Cepeda

Pacheco

2022

Malar J

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The global malaria burden sometimes obscures that the genus Plasmodium comprises diverse clades with lineages that independently gave origin to the extant human parasites. Indeed, the differences between the human malaria parasites were highlighted in the classical taxonomy by dividing them into two subgenera, the subgenus Plasmodium, which included all the human parasites but Plasmodium falciparum that was placed in its separate subgenus, Laverania. Here, the evolution of Plasmodium in primates will be discussed in terms of their species diversity and some of their distinct phenotypes, putative molecular adaptations, and host–parasite biocenosis. Thus, in addition to a current phylogeny using genome-level data, some specific molecular features will be discussed as examples of how these parasites have diverged. The two subgenera of malaria parasites found in primates, Plasmodium and Laverania, reflect extant monophyletic groups that originated in Africa. However, the subgenus Plasmodium involves species in Southeast Asia that were likely the result of adaptive radiation. Such events led to the Plasmodium vivax lineage. Although the Laverania species, including P. falciparum, has been considered to share “avian characteristics,” molecular traits that were likely in the common ancestor of primate and avian parasites are sometimes kept in the Plasmodium subgenus while being lost in Laverania. Assessing how molecular traits in the primate malaria clades originated is a fundamental science problem that will likely provide new targets for interventions. However, given that the genus Plasmodium is paraphyletic (some descendant groups are in other genera), understanding the evolution of malaria parasites will benefit from studying “non-Plasmodium” Haemosporida.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Why Plasmodium vivax and Plasmodium falciparum are so different? A tale of two clades and their species diversities

Escalante

Cepeda

Pacheco

2022

Malar J

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“…The relevance of nucleotide composition (GC content) in genome evolution has been well established from a genomics ( Arndt et al 2005 ; Amit et al 2012 ; Šmarda et al 2014 ; Mugal et al 2015 ; Almpanis et al 2018 ), ecological ( Bolhuis et al 2006 ; Šmarda et al 2014 ; Luo et al 2015 ), and biological perspective ( Mann and Chen 2010 ; Udaondo et al 2016 ; Bohlin et al 2017 ; Du et al 2018 ; Castillo et al 2019a ). Specifically in proteobacteria, whole-genome GC content varies between 17% and 75% ( Brocchieri 2014 ), and multiple evolutionary mechanisms have been proposed to explain this variation.…”

Section: Introductionmentioning

confidence: 99%

Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen

Castillo

Almeida

2021

G3 Genes|Genomes|Genetics

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Nucleotide composition (GC content) varies across bacteria species, genome regions, and specific genes. In Xylella fastidiosa, a vector-borne fastidious plant pathogen infecting multiple crops, GC content ranges between ∼51-52%; however, these values were gathered using limited genomic data. We evaluated GC content variations across X. fastidiosa subspecies fastidiosa (N = 194), subsp. pauca (N = 107), and subsp. multiplex (N = 39). Genomes were classified based on plant host and geographic origin; individual genes within each genome were classified based on gene function, strand, length, ortholog group, Core vs. Accessory, and Recombinant vs. Non-recombinant. GC content was calculated for each gene within each evaluated genome. The effects of genome and gene level variables were evaluated with a mixed effect ANOVA, and the marginal-GC content was calculated for each gene. Also, the correlation between gene-specific GC content vs. natural selection (dN/dS) and recombination/mutation (r/m) was estimated. Our analyses show that intra-genomic changes in nucleotide composition in X. fastidiosa are small and influenced by multiple variables. Higher AT-richness is observed in genes involved in replication and translation, and genes in the leading strand. In addition, we observed a negative correlation between high-AT and dN/dS in subsp. pauca. The relationship between recombination and GC content varied between core and accessory genes. We hypothesize that distinct evolutionary forces and energetic constraints both drive and limit these small variations in nucleotide composition.

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“…While most Plasmodium species have A/T-rich genomes, P. vivax and P. knowlesi have much higher GC content, leading to different codon usage [ 12 ]. Mutational pressure and natural selection for certain functional protein classes were suggested to be the causes for variations in genomic GC content among Plasmodium spp [ 58 ].…”

Section: Discussionmentioning

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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Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp.

Cited by 10 publications

References 72 publications

Why Plasmodium vivax and Plasmodium falciparum are so different? A tale of two clades and their species diversities

Why Plasmodium vivax and Plasmodium falciparum are so different? A tale of two clades and their species diversities

Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen

Cryptosporidium felis differs from other Cryptosporidium spp. in codon usage

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