Phylodynamics of G4P[8] and G2P[4] strains of rotavirus A isolated in Russia in 2017 based on full-genome analyses

Морозова, О. В.; Алексеева, А. Е.; Сашина, Т. А.; Бруснигина, Н. Ф.; Епифанова, Н. В.; Kashnikov, A. U.; Зверев, В. В.; Новикова, Н. А.

doi:10.1007/s11262-020-01771-3

Cited by 13 publications

(10 citation statements)

References 46 publications

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“…Furthermore, columns viii and ix of Table 8 translate a log2 value of a gene in an animal into either low or excessive expression of this gene during divergence of both domestic and wild forms of this animal from their most recent common ancestor. Recently [ 57 , 58 ], an RNA-Seq data analysis was based on this oldest phylogeny concept [ 59 ] widely used elsewhere [ 60 , 61 , 62 , 63 ]. Let us look at these orthologous genes one by one and discuss effects of their expression changes on reproductive potential in humans as well as during divergence of domestic and wild animals from their most recent com-mon ancestor [ 24 , 25 , 28 , 29 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 ] ( Table 8 ).…”

Section: Discussionmentioning

confidence: 99%

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

Chadaeva

Пономаренко

Kozhemyakina

et al. 2021

Animals

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Belyaev’s concept of destabilizing selection during domestication was a major achievement in the XX century. Its practical value has been realized in commercial colors of the domesticated fox that never occur in the wild and has been confirmed in a wide variety of pet breeds. Many human disease models involving animals allow to test drugs before human testing. Perhaps this is why investigators doing transcriptomic profiling of domestic versus wild animals have searched for breed-specific patterns. Here we sequenced hypothalamic transcriptomes of tame and aggressive rats, identified their differentially expressed genes (DEGs), and, for the first time, applied principal component analysis to compare them with all the known DEGs of domestic versus wild animals that we could find. Two principal components, PC1 and PC2, respectively explained 67% and 33% of differential-gene-expression variance (hereinafter: log2 value) between domestic and wild animals. PC1 corresponded to multiple orthologous DEGs supported by homologs; these DEGs kept the log2 value sign from species to species and from tissue to tissue (i.e., a common domestication pattern). PC2 represented stand-alone homologous DEG pairs reversing the log2 value sign from one species to another and from tissue to tissue (i.e., representing intraspecific and interspecific variation).

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Section: Discussionmentioning

confidence: 99%

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

Chadaeva

Пономаренко

Kozhemyakina

et al. 2021

Animals

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“…Then, by means of PubMed [43], we compiled independent publicly available experimental in vivo RNA-Seq data sets on domestic versus wild animals [26,28,29], as depicted in Figure 1 (Step-2) and presented in Table 1. For the RNA-Seq data analysis, here, we, for the first time, resumed the use of one of the eldest [44] commonly accepted (e.g., see [45]) and widely used (e.g., see [46]) concepts of "divergence from the nearest common ancestor (NCA)" within the framework of the microevolution theory in relation to domesticated and wild animals, whose differentially expressed genes (DEGs) were compared with orthologous human genes under this study, as depicted in Figure 1. After that, we found 28 pairs of orthologous genes in humans and animals among all genes analyzed in this work, as depicted by a Venn diagram in Figure 1 (Step-3).…”

Section: The Bioinformatics Model Developedmentioning

confidence: 99%

“…The only novelty of this work is that for the RNA-Seq data analysis, we, for the first time, resumed the use of one of the most ancient [44] conventional (e.g., see [45]) and actual (e.g., see [46]) microevolutional concepts of "divergence from the nearest common ancestor (NCA)" in the case of domestic and wild animals, whose differentially expressed genes (DEGs) were compared with orthologous human genes under this study (Figure 1: Step-3). This allows us to compare the effects of co-directional changes in the expression of orthologous genes on human reproductive potential and on the divergence of domestic and wild animals from their NCA, as shown in Tables 2 and 4, as well as in Figure 1 (Step-4).…”

Section: Degs Of Domestic Animals Compared To Their Wild Congenersmentioning

confidence: 99%

A Bioinformatics Model of Human Diseases on the Basis of Differentially Expressed Genes (of Domestic Versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes

Vasiliev

Chadaeva

Рассказов

et al. 2021

IJMS

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Earlier, after our bioinformatic analysis of single-nucleotide polymorphisms of TATA-binding protein-binding sites within gene promoters on the human Y chromosome, we suggested that human reproductive potential diminishes during self-domestication. Here, we implemented bioinformatics models of human diseases using animal in vivo genome-wide RNA-Seq data to compare the effect of co-directed changes in the expression of orthologous genes on human reproductive potential and during the divergence of domestic and wild animals from their nearest common ancestor (NCA). For example, serotonin receptor 3A (HTR3A) deficiency contributes to sudden death in pregnancy, consistently with Htr3a underexpression in guinea pigs (Cavia porcellus) during their divergence from their NCA with cavy (C. aperea). Overall, 25 and three differentially expressed genes (hereinafter, DEGs) in domestic animals versus 11 and 17 DEGs in wild animals show the direction consistent with human orthologous gene-markers of reduced and increased reproductive potential. This indicates a reliable association between DEGs in domestic animals and human orthologous genes reducing reproductive potential (Pearson’s χ2 test p < 0.001, Fisher’s exact test p < 0.05, binomial distribution p < 0.0001), whereas DEGs in wild animals uniformly match human orthologous genes decreasing and increasing human reproductive potential (p > 0.1; binomial distribution), thus enforcing the norm (wild type).

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“…A total of 3080 DEGs of domestic versus wild animals were analyzed here, which are freely available in the PubMed database (Lu, 2011), as described in Table 2 and characterized by examples in Table 3. At the same time, according to (Klimova et al, 2021;Vasiliev et al, 2021), here, RNA-Seq data were examined in accordance with one of the oldest (Samet, 1985), widely used (Sun et al, 2008;Morozova et al, 2020;Hakizimana et al, 2021), and fundamental (Zhang et al, 2021) concepts of phylogenetic analysis -"most recent common ancestor" (Samet, 1985). In this regard, domestic animals and their wild relatives were studied by means of oppositely directed equivalent changes in gene expression in comparison with their unknown most recent common ancestor.…”

mentioning

confidence: 99%

A bioinformatic search for correspondence between differentially expressed genes of domestic versus wild animals and orthologous human genes altering reproductive potential

et al. 2022

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One of the greatest achievements of genetics in the 20th century is D.K. Belyaev’s discovery of destabilizing selection during the domestication of animals and that this selection affects only gene expression regulation (not gene structure) and influences systems of neuroendocrine control of ontogenesis in a stressful environment. Among the experimental data generalized by Belyaev’s discovery, there are also findings about accelerated extinction of testes’ hormonal function and disrupted seasonality of reproduction of domesticated foxes in comparison with their wild congeners. To date, Belyaev’s discovery has already been repeatedly confirmed, for example, by independent observations during deer domestication, during the use of rats as laboratory animals, after the reintroduction of endangered species such as Przewalski’s horse, and during the creation of a Siberian reserve population of the Siberian grouse when it had reached an endangered status in natural habitats. A genome-wide comparison among humans, several domestic animals, and some of their wild congeners has given rise to the concept of self-domestication syndrome, which includes autism spectrum disorders. In our previous study, we created a bioinformatic model of human self-domestication syndrome using differentially expressed genes (DEGs; of domestic animals versus their wild congeners) orthologous to the human genes (mainly, nervous-system genes) whose changes in expression affect reproductive potential, i.e., growth of the number of humans in the absence of restrictions caused by limiting factors. Here, we applied this model to 68 human genes whose changes in expression alter the reproductive health of women and men and to 3080 DEGs of domestic versus wild animals. As a result, in domestic animals, we identified 16 and 4 DEGs, the expression changes of which are codirected with changes in the expression of the human orthologous genes decreasing and increasing human reproductive potential, respectively. The wild animals had 9 and 11 such DEGs, respectively. This difference between domestic and wild animals was significant according to Pearson’s χ2 test (p < 0.05) and Fisher’s exact test (p < 0.05). We discuss the results from the standpoint of restoration of endangered animal species whose natural habitats are subject to an anthropogenic impact.

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Phylodynamics of G4P[8] and G2P[4] strains of rotavirus A isolated in Russia in 2017 based on full-genome analyses

Cited by 13 publications

References 46 publications

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

A Bioinformatics Model of Human Diseases on the Basis of Differentially Expressed Genes (of Domestic Versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes

A bioinformatic search for correspondence between differentially expressed genes of domestic versus wild animals and orthologous human genes altering reproductive potential

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