Adaptive Molecular Evolution of <i>AKT3</i> Gene for Positive Diversifying Selection in Mammals

Farmanullah,; Hosseini, Seyed Mahdi; Liang, Aixin; Hua, Guohua; Rehman, Zia Ur; Talpur, Hira Sajjad; Salim, Mohammad; Ahmad, Saeed Nazari Soltan; Abulaiti, Adili; KHAN, M H; Safdar, Muhammad; Kakar, Ihsan Ullah; Ahmad, Zahoor; Ahmad, Muhammad Zulfiqar; Ye, Tingzhu; Schreurs, Nicola M.; Bano, Iqra; Yang, Liguo

doi:10.1155/2020/2584627

Cited by 4 publications

(2 citation statements)

References 60 publications

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“…Coincidentally, DAXX was identified as a CDG for the lumbar muscle area and lumbar muscle depth in Duroc pigs [ 15 ]. Some studies found that AKT3 is one of the CDGs for the number of nipples and promotes milk fat production of mammals such as cattle [ 35 , 36 ]. AKT3 is also involved in various biological functions, including inflammatory response, lipolysis metabolism, and muscle fiber characteristics [ 37 , 38 , 39 ].…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig

Zhang

Long

et al. 2023

Animals

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As important livestock species, pigs provide essential meat resources for humans, so understanding the genetic evolution behind their domestic history could help with the genetic improvement of domestic pigs. This study aimed to investigate the evolution of convergence and divergence under selection in European and Asian domestic pigs by using public genome-wide data. A total of 164 and 108 candidate genes (CDGs) were obtained from the Asian group (wild boar vs. domestic pig) and the European group (wild boar vs. domestic pig), respectively, by taking the top 5% of intersected windows of a pairwise fixation index (FST) and a cross population extended haplotype homozygosity test (XPEHH). GO and KEGG annotated results indicated that most CDGs were related to reproduction and immunity in the Asian group. Conversely, rich CDGs were enriched in muscle development and digestion in the European group. Eight CDGs were subjected to parallel selection of Eurasian domestic pigs from local wild boars during domestication. These CDGs were mainly involved in olfactory transduction, metabolic pathways, and progesterone-mediated oocyte maturation. Moreover, 36 and 18 haplotypes of INPP5B and TRAK2 were identified in this study, respectively. In brief, this study did not only improve the understanding of the genetic evolution of domestication in pigs, but also provides valuable CDGs for future breeding and genetic improvement of pigs.

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Section: Resultsmentioning

confidence: 99%

Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig

Zhang

Long

et al. 2023

Animals

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“…In addition, Siah1 has recently been identified as an upstream regulator of Akt3 (Akt signaling is an important regulator of neural development) (133)(134)(135), and it is responsible for the ubiquitination and degradation of Akt3, suggesting that Siah1 may play a key role in neural development (135).…”

Section: Siah1 In Nervous System Diseasesmentioning

confidence: 99%

Siah1 in cancer and nervous system diseases (Review)

Zhang

Wang

et al. 2021

Oncol Rep

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The dysregulation of the ubiquitin-proteasome system will result in the abnormal accumulation and dysfunction of proteins, thus leading to severe diseases. Seven in absentia homolog 1 (Siah1), an E3 ubiquitin ligase, has attracted wide attention due to its varied functions in physiological and pathological conditions, and the numerous newly discovered Siah1 substrates. In cancer and nervous system diseases, the functions of Siah1 as a promoter or a suppressor of diseases are related to the change in cellular microenvironment and subcellular localization. At the same time, complex upstream regulations make Siah1 different from other E3 ubiquitin ligases. Understanding the molecular mechanism of Siah1 will help the study of various signaling pathways and benefit the therapeutic strategy of human diseases (e.g., cancer and nervous system diseases). In the present review, the functions and regulations of Siah1 are described. Moreover, novel substrates of Siah1 discovered in recent studies will be highlighted in cancer and nervous system diseases, providing ideas for future research and clinical targeted therapies using Siah1. Contents1. Introduction 2. Structure of Siah1 and characteristics of Siah1-interacting proteins (SIPs) 3. Siah1 in cancer 4. Siah1 in nervous system diseases 5. Clinical significance of Siah1 in human diseases 6. Discussion

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Adaptive evolution and functional significance of the PPARGC1A gene across diverse animal species

Hosseini,

Ullah,

Ahmad

et al. 2024

Ecology and Evolution

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Codon‐based analyses of the PPARGC1A gene across 38 vertebrate species were deployed to elucidate patterns of evolutionary change. Employing maximum likelihood assessments through MEGA, we scrutinized 447 codon positions addressing the entire coding region, excluding positions mired by gaps or missing data. Distinct codons manifested variance in selection pressures, particularly codons 4, 11, 66, and 123, which exhibited positive dN‐dS values suggestive of positive selection. Codon 137 displayed the most pronounced dN‐dS value, signifying intensified selective advantage. Meanwhile, codons 30 and 90 portrayed near‐neutral scores, indicative of purifying selection. Complementary computational methods (IFEL, REL, FUBAR, and SLAC) confirmed positive selection at specific codon sites, with varying degrees of corroboration. The integration of mixed‐effect modeling (MEME) identified episodic diversifying selection, pinpointing codons that underwent selection episodes in certain lineages. Refined codon model selection lent insight into substitution rates, revealing nuanced degrees of evolutionary conservation among different codons. Supporting these genetic insights, the phylogenetic analysis highlighted relationships among the PPARGC1A sequences and domain analysis confirmed conserved features across species, while protein–protein interaction networks suggested a complex web of functional interdependencies. These findings advance our understanding of the PPARGC1A gene's evolutionary trajectory and underscore the gene's potential adaptive significance within diverse vertebrate lineages.

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Adaptive Molecular Evolution of AKT3 Gene for Positive Diversifying Selection in Mammals

Cited by 4 publications

References 60 publications

Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig

Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig

Siah1 in cancer and nervous system diseases (Review)

Adaptive evolution and functional significance of the PPARGC1A gene across diverse animal species

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