References

Bibliography

Briggs, J.A., Weinreb, C., Wagner, D.E., Megason, S., Peshkin, L., Kirschner, M.W. and Klein, A.M. (2018). The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science, 360(6392). https://doi.org/10.1126/science.aar5780

Cazet, J., Siebert, S., Little, H.M., Bertemes, P., Primack, A.S., Ladurner, P., Achrainer, M., Fredriksen, M.T., Moreland, R.T., Singh, S. and Zhang, S. (2022). New Hydra genomes reveal conserved principles of hydrozoan transcriptional regulation. bioRxiv. https://doi.org/10.1101/2022.06.21.496857

Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D.M., Hill, A.J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F.J. and Trapnell, C. (2019). The single-cell transcriptional landscape of mammalian organogenesis. Nature, 566(7745). https://doi.org/10.1038/s41586-019-0969-x

Cheng, S., Pei, Y., He, L., Peng, G., Reinius, B., Tam, P.P., Jing, N. and Deng, Q. (2019). Single-cell RNA-seq reveals cellular heterogeneity of pluripotency transition and X chromosome dynamics during early mouse development. Cell reports, 26(10). https://doi.org/10.1016/j.celrep.2019.02.031

Domazet-Loso, T., Brajkovic J. and Tautz D. (2007). A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends in Genetics, 23(11). https://doi.org/10.1016/j.tig.2007.08.014

Domazet-Loso, T. and Tautz. D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature, 468(7325). https://doi.org/10.1038/nature09632

Drost, H.G., Gabel, A., Grosse, I. and Quint M. (2015). Evidence for active maintenance of phylotranscriptomic hourglass patterns in animal and plant embryogenesis. Molecular biology and evolution, 32(5). https://doi.org/10.1093%2Fmolbev%2Fmsv012

Drost, H.G., Gabel, A., Liu, J., Quint, M. and Grosse, I. (2018). myTAI: evolutionary transcriptomics with R. Bioinformatics, 34(9). https://doi.org/10.1093/bioinformatics/btx835

Emms, D.M. and Kelly, S. (2019). OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome biology, 20(1). https://doi.org/10.1186/s13059-019-1832-y

Farrell, J.A., Wang, Y., Riesenfeld, S.J., Shekhar, K., Regev, A. and Schier, A.F. (2018). Single-cell reconstruction of developmental tra jectories during zebrafish embryogenesis. Science, 360(6392). https://doi.org/10.1126/science.aar3131

Gossmann, T.I., Saleh, D., Schmid, M.W., Spence, M.A. and Schmid, K.J. (2016). Transcriptomes of plant gametophytes have a higher proportion of rapidly evolving and young genes than sporophytes. Molecular biology and evolution, 33(7). https://doi.org/10.1093/molbev/msw044

Harris, C.R., Millman, K.J., Van Der Walt, S.J., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N.J. and Kern, R. (2020). Array programming with NumPy. Nature, 585(7825). https://doi.org/10.1038/s41586-020-2649-2

Hernández-Plaza, A., Szklarczyk, D., Botas, J., Cantalapiedra, C.P., Giner-Lamia, J., Mende, D.R., Kirsch, R., Rattei, T., Letunic, I., Jensen, L.J. and Bork, P. (2022). eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Research, 51(D1). https://doi.org/10.1093%2Fnar%2Fgkac1022

Huerta-Cepas, J., Serra, F. and Bork, P. (2016). ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Molecular biology and evolution, 33(6). https://doi.org/10.1093/molbev/msw046

Julca, I., Ferrari, C., Flores-Tornero, M., Proost, S., Lindner, A.-C., Hackenberg, D., Steinbachov́a, L., Michaelidis, C., Gomes Pereira, S., Misra, C.S., Kawashima, T., Borg, M., Berger, F., Goldberg, J., Johnson, M., Honys, D., Twell, D., Sprunck, S., Dresselhaus, T., Becker, J.D., Mutwil, M. (2021). Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants. Nature Plants, 7(8). https://doi.org/10.1038/s41477-021-00958-2

Kiełbasa S.M., Wan R., Sato K., Horton P., Frith M.C. (2011). Adaptive seeds tame genomic sequence comparison. Genome Research, 21(3)*. https://doi.org/10.1101/gr.113985.110

Liu, J. and Robinson-Rechavi, M. (2018). Developmental Constraints on Genome Evolution in Four Bilaterian Model Species Genome Biology and Evolution, 10(9). https://doi.org/10.1093/gbe/evy177

Liu, J., Frochaux, M. , Gardeux, V., Deplancke, B. and Robinson-Rechavi, M. (2020). Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo. BMC biology, 18(1). https://doi.org/10.1186/s12915-020-00842-z

Ma, F., Lau, C.Y. and Zheng, C. (2021). Large genetic diversity and strong positive selection in F-box and GPCR genes among the wild isolates of Caenorhabditis elegans. Genome Biology and Evolution, 13(5). https://doi.org/10.1093/gbe/evab048

Ma, F. and Zheng, C. (2023). Transcriptome age of individual cell types in caenorhabditis elegans. Proceedings of the National Academy of Sciences, 120(9). https://doi.org/10.1073/pnas.2216351120

McInnes, L., Healy, J. and Melville, J. (2018). Umap: Uniform manifold approximation and projection for dimension reduction. arXiv preprint, arXiv:1802.03426. https://doi.org/10.48550/arXiv.1802.03426

McKinney, W. (2011). pandas: a foundational python library for data analysis and statistics. Python for high performance and scientific computing, 14(9). https://www.dlr.de/sc/portaldata/15/resources/dokumente/pyhpc2011/submissions/pyhpc2011_submission_9.pdf

Mohammed, H., Hernando-Herraez, I., Savino, A., Scialdone, A., Macaulay, I., Mulas, C., Chandra, T., Voet, T., Dean, W., Nichols, J. and Marioni, J.C. (2017). Single-cell landscape of transcriptional heterogeneity and cell fate decisions during mouse early gastrulation. Cell reports, 20(5). https://doi.org/10.1016/j.celrep.2017.07.009

Packer, J.S., Zhu, Q., Huynh, C., Sivaramakrishnan, P., Preston, E., Dueck, H., Stefanik, D., Tan, K., Trapnell, C., Kim, J. and Waterston, R.H., (2019). A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science, 365(6459). https://doi.org/10.1126/science.aax1971

Pijuan-Sala, B., Griffiths, J.A., Guibentif, C., Hiscock, T.W., Jawaid, W., Calero-Nieto, F.J., Mulas, C., Ibarra-Soria, X., Tyser, R.C., Ho, D.L.L. and Reik, W. (2019). A single-cell molecular map of mouse gastrulation and early organogenesis. Nature, 566(7745). https://doi.org/10.1038/s41586-019-0933-9

Plass, M., Solana, J., Wolf, F.A., Ayoub, S., Misios, A., Glažar, P., Obermayer, B., Theis, F.J., Kocks, C. and Rajewsky, N. (2018). Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics. Science, 360(6391). https://doi.org/10.1126/science.aaq1723

Qiu, C., Cao, J., Martin, B.K., Li, T., Welsh, I.C., Srivatsan, S., Huang, X., Calderon, D., Noble, W.S., Disteche, C.M. and Murray, S.A. (2022). Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nature genetics, 54(3). https://doi.org/10.1038/s41588-022-01018-x

Quint, M., Drost, H.-G., Gabel, A., Ullrich, K.K., Bönn, M. and Grosse, I. (2012). A transcriptomic hourglass in plant embryogenesis. Nature, 490(7418). https://doi.org/10.1038/nature11394

Sun, S., Rödelsperger, C. and Sommer, R.J., (2021). Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes. Genome research, 31(9). https://doi.org/10.1101/gr.275303.121

Tarashansky, A.J., Musser, J.M., Khariton, M., Li, P., Arendt, D., Quake, S.R. and Wang, B. (2021). Mapping single-cell atlases throughout metazoa unravels cell type evolution. Elife, 10. https://doi.org/10.7554/elife.66747

Ullrich, K.K. (2020). CRBHits: From conditional reciprocal best hits to codon alignments and Ka/Ks in R. The Journal of Open Source Software, 5(55). https://doi.org/10.21105/joss.02424

Van Bel, M., Silvestri, F., Weitz, E.M., Kreft, L., Botzki, A., Coppens, F. and Vandepoele, K. (2022). PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants. Nucleic Acids Research, 50(D1). https://doi.org/10.1093/nar/gkab1024

Wagner, D.E., Weinreb, C., Collins, Z.M., Briggs, J.A., Megason, S.G. and Klein, A.M. (2018). Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science, 360(6392). https://doi.org/10.1126%2Fscience.aar4362

Wolf, F.A., Angerer, P. and Theis, F.J. (2018). SCANPY: large-scale single-cell gene expression data analysis. Genome biology, 19(1). https://doi.org/10.1186/s13059-017-1382-0