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

Autor: Lyubetsky VA; Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051.; Department of Mechanics and Mathematics, Lomonosov Moscow State University, Kolmogorova Str., 1, Moscow, Russia, 119234., Rubanov LI; Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051., Tereshina MB; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997.; Pirogov Russian National Research Medical University, Moscow, Russia., Ivanova AS; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997.; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, USA., Araslanova KR; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997., Uroshlev LA; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32, Vavilova Str., Moscow, Russia, 119991., Goremykina GI; Plekhanov Russian University of Economics, Stremyanny Lane 36, Moscow, Russia., Yang JR; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.; Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China., Kanovei VG; Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051., Zverkov OA; Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051., Shitikov AD; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997., Korotkova DD; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997.; Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland., Zaraisky AG; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997. azaraisky@yahoo.com.; Pirogov Russian National Research Medical University, Moscow, Russia. azaraisky@yahoo.com.
Jazyk: angličtina
Zdroj: Biology direct [Biol Direct] 2023 Aug 11; Vol. 18 (1), pp. 45. Date of Electronic Publication: 2023 Aug 11.
DOI: 10.1186/s13062-023-00405-6
Abstrakt: Background: It 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.
Results: To 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.
Conclusions: We 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.
(© 2023. BioMed Central Ltd., part of Springer Nature.)
Databáze: MEDLINE
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