CMB_2024v14n5

Computational Molecular Biology 2024, Vol.14, No.5, 202-210 http://bioscipublisher.com/index.php/cmb 209 Amano T., 2020, Gene regulatory landscape of the sonic hedgehog locus in embryonic development, Development, 62: 334-342. https://doi.org/10.1111/dgd.12668 Andersson D.I., Jerlström-Hultqvist J., and Näsvall J., 2015, Evolution of new functions de novo and from preexisting genes, Cold Spring Harbor Perspectives in Biology, 7(6): a017996. https://doi.org/10.1101/cshperspect.a017996 Ding Y., Zhou Q., and Wang W., 2012, Origins of new genes and evolution of their novel functions, Annual Review of Ecology Evolution and Systematics, 43(1): 345-363. https://doi.org/10.1146/ANNUREV-ECOLSYS-110411-160513 Dufour H., Koshikawa S., and Finet C., 2020, Temporal flexibility of gene regulatory network underlies a novel wing pattern in flies, Proceedings of the National Academy of Sciences of the United States of America, 117: 11589-11596. https://doi.org/10.1073/pnas.2002092117 Fang J., 2024, Breeding 3.0: The precise revolution of genotype selection, Molecular Plant Breeding, 15(1): 8-14. https://doi.org/10.5376/mpb.2024.15.0002 Fernandez-Valverde S., Aguilera F., and Ramos-Díaz R., 2018, Inference of developmental gene regulatory networks beyond classical model systems: new approaches in the post-genomic era, Integrative and Comparative Biology, 58(4): 640-653. https://doi.org/10.1093/icb/icy061 Gouy A., Daub J.T., and Excoffier L., 2017, Detecting gene subnetworks under selection in biological pathways, Nucleic Acids Research, 45(16): e149-e149. https://doi.org/10.1101/128306 Irion U., and Nüsslein-Volhard C., 2022, Developmental genetics with model organisms, Proceedings of the National Academy of Sciences of the United States of America, 119(30): e2122148119. https://doi.org/10.1073/pnas.2122148119 Jean-Baptiste K., McFaline-Figueroa J., Alexandre C., Dorrity M., Saunders L., Bubb K., Trapnell C., Fields S., Queitsch C., and Cuperus J., 2019, Dynamics of gene expression in single root cells of Arabidopsis thaliana, The Plant Cell, 31: 993-1011. https://doi.org/10.1105/tpc.18.00785 Kulkarni A., Lopez D.H., and Extavour C.G., 2020, Shared cell biological functions may underlie pleiotropy of molecular interactions in the germ lines and nervous systems of animals, Frontiers in Ecology and Evolution, 8: 215. https://doi.org/10.3389/fevo.2020.00215 Mattenberger F., Sabater-Muñoz B., Toft C., and Fares M., 2016, The phenotypic plasticity of duplicated genes in saccharomyces cerevisiae and the origin of adaptations, G3: Genes|Genomes|Genetics, 7: 63-75. https://doi.org/10.1534/g3.116.035329 Montañés J.C., Huertas M., Messeguer X., Albà M.M., and O'Connell M., 2023, Evolutionary trajectories of new duplicated and putative de novo genes, Molecular Biology and Evolution, 40(5): msad098. https://doi.org/10.1093/molbev/msad098 Moutinho A.F., Eyre-Walker A., and Dutheil J.Y., 2022, Strong evidence for the adaptive walk model of gene evolution in Drosophila and Arabidopsis, PLoS Biology, 20(9): e3001775. https://doi.org/10.1371/journal.pbio.3001775 Moyers B., and Zhang J., 2016, Evaluating phylostratigraphic evidence for widespread de novo gene birth in genome evolution, Molecular Biology and Evolution, 33(50): 1245-56. https://doi.org/10.1093/molbev/msw008 Muñoz-Nava L.M., Alvarez H.A., Flores-Flores M., Chara O., and Nahmad M., 2020, A dynamic cell recruitment process drives growth of the Drosophila wing by overscaling the Vestigial expression pattern, Developmental Biology, 462(2): 141-151. https://doi.org/10.1016/j.ydbio.2020.03.009 Pérez‐Losada M., Arenas M., Galán J., Bracho M., Hillung J., García-González N., and González-Candelas F., 2020, High-throughput sequencing (HTS) for the analysis of viral populations, Infection Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 80: 104208. https://doi.org/10.1016/j.meegid.2020.104208 Prabh N., and Roedelsperger C., 2022, Multiple pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes, Genome Research, 32: 1315-1327. https://doi.org/10.1101/gr.276431.121 Ranz J.M., and Parsch J., 2012, Newly evolved genes: moving from comparative genomics to functional studies in model systems, BioEssays, 34(6): 477-483. https://doi.org/10.1002/bies.201100177 Roy U., Singh D., Vincent N., Haritas C.K., and Jolly M.K., 2022, Spatiotemporal patterning enabled by gene regulatory networks, ACS Omega, 8(4): 3713-3725. https://doi.org/10.1101/2022.04.13.488152 Shapiro E., Biezuner T., and Linnarsson S., 2013, Single-cell sequencing-based technologies will revolutionize whole-organism science, Nature Reviews Genetics, 14(9): 618-630. https://doi.org/10.1038/nrg3542

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