Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Biology Direct

Research

Jian-Rong Yang¹  Leonid A. Uroshlev²  Oleg A. Zverkov³  Vladimir G. Kanovei³  Lev I. Rubanov³  Vassily A. Lyubetsky⁴  Galina I. Goremykina⁵  Karina R. Araslanova⁶  Alexander D. Shitikov⁶  Anastasiya S. Ivanova⁷  Daria D. Korotkova⁸  Maria B. Tereshina⁹  Andrey G. Zaraisky⁹ 

[1] Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, China;Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, China;Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32, Vavilova Str., 119991, Moscow, Russia;Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., 127051, Moscow, Russia;Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., 127051, Moscow, Russia;Department of Mechanics and Mathematics, Lomonosov Moscow State University, Kolmogorova Str., 1, 119234, Moscow, Russia;Plekhanov Russian University of Economics, Stremyanny Lane 36, Moscow, Russia;Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., 117997, Moscow, Russia;Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., 117997, Moscow, Russia;Department of Molecular Medicine, The Scripps Research Institute, La Jolla, USA;Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., 117997, Moscow, Russia;Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland;Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., 117997, Moscow, Russia;Pirogov Russian National Research Medical University, Moscow, Russia;

关键词: Loss or emergence of genes;    Loss or emergence of the phenotypic traits;    Changes of gene expression;    Xenopus;    Gene regulators of regeneration;    Gene knockdown;    Fast algorithm;    Effective computer program;   

DOI  :  10.1186/s13062-023-00405-6

 received in 2023-02-02, accepted in 2023-08-07,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid contents of proteins. Recently, evidence has accumulated that significant evolutionary transformations could also be associated with the loss/emergence of whole genes. The targeted identification of such genes is a challenging problem for both bioinformatics and evo-devo research.ResultsTo solve this problem we propose the WINEGRET method, named after the first letters of the title. Its main idea is to search for genes that satisfy two requirements: first, the desired genes were lost/emerged at the same evolutionary stage at which the phenotypic trait of interest was lost/emerged, and second, the expression of these genes changes significantly during the development of the trait of interest in the model organism. To verify the first requirement, we do not use existing databases of orthologs, but rely purely on gene homology and local synteny by using some novel quickly computable conditions. Genes satisfying the second requirement are found by deep RNA sequencing. As a proof of principle, we used our method to find genes absent in extant amniotes (reptiles, birds, mammals) but present in anamniotes (fish and amphibians), in which these genes are involved in the regeneration of large body appendages. As a result, 57 genes were identified. For three of them, c-c motif chemokine 4, eotaxin-like, and a previously unknown gene called here sod4, essential roles for tail regeneration were demonstrated. Noteworthy, we established that the latter gene belongs to a novel family of Cu/Zn-superoxide dismutases lost by amniotes, SOD4.ConclusionsWe present a method for targeted identification of genes whose loss/emergence in evolution could be associated with the loss/emergence of a phenotypic trait of interest. In a proof-of-principle study, we identified genes absent in amniotes that participate in body appendage regeneration in anamniotes. Our method provides a wide range of opportunities for studying the relationship between the loss/emergence of phenotypic traits and the loss/emergence of specific genes in evolution.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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