Comparative Analysis of Sea Turtle Genomes

Using dot plots, 20 Mb windows were visually screened to identify regions of reduced collinearity (RRCs; SI Appendix, Fig. S5). Several genomic features (e.g., GC content, repeat elements) were compared between RRCs and equisized regions directly up- and down-stream to determine whether these were influencing collinearity (Dataset S5). Interproscan (119 (link)) was used to identify the functions of genes found within RRCs, and overall GO-term proportions for each chromosome were estimated using PANTHER (120 (link)); SI Appendix, Fig. S25). The two sea turtle genomes were aligned using Progressive Cactus (121 (link), 122 (link)) to examine whether RRCs presented patterns of sequence divergence and/or gene duplication between the species.

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Bentley B.P., Carrasco-Valenzuela T., Ramos E.K., Pawar H., Souza Arantes L., Alexander A., Banerjee S.M., Masterson P., Kuhlwilm M., Pippel M., Mountcastle J., Haase B., Uliano-Silva M., Formenti G., Howe K., Chow W., Tracey A., Sims Y., Pelan S., Wood J., Yetsko K., Perrault J.R., Stewart K., Benson S.R., Levy Y., Todd E.V., Shaffer H.B., Scott P., Henen B.T., Murphy R.W., Mohr D.W., Scott A.F., Duffy D.J., Gemmell N.J., Suh A., Winkler S., Thibaud-Nissen F., Nery M.F., Marques-Bonet T., Antunes A., Tikochinski Y., Dutton P.H., Fedrigo O., Myers E.W., Jarvis E.D., Mazzoni C.J, & Komoroske L.M. (2023). Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. Proceedings of the National Academy of Sciences of the United States of America, 120(7), e2201076120.

Publication 2023

Cactus Chromosome Gene duplication Genes functions Genomes Sea turtle

Corresponding Organization :

Other organizations : University of Massachusetts Amherst, Leibniz Institute for Zoo and Wildlife Research, Berlin Center for Genomics in Biodiversity Research, Universidade Estadual de Campinas (UNICAMP), Institut de Biologia Evolutiva, Pompeu Fabra University, University of Otago, National Center for Biotechnology Information, University of Vienna, Max Planck Institute of Molecular Cell Biology and Genetics, Center for Systems Biology Dresden, Rockefeller University, Wellcome Sanger Institute, University of Florida, Sea Turtle Conservancy, Ocean Foundation, NOAA National Marine Fisheries Service Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Moss Landing Marine Laboratories, University of Haifa, Deakin University, California Department of Conservation, University of California, Los Angeles, West Texas A&M University, United States Marine Corps, Royal Ontario Museum, Johns Hopkins University, Science for Life Laboratory, University of East Anglia, Uppsala University, Centre for Genomic Regulation, Institució Catalana de Recerca i Estudis Avançats, Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Universidade do Porto, Ruppin Academic Center, TU Dresden

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Variable analysis

independent variables

Regions of reduced collinearity (RRCs)
Genomic features (e.g., GC content, repeat elements)

dependent variables

Collinearity patterns between the two sea turtle genomes
Sequence divergence and/or gene duplication between the species

control variables

Equisized regions directly up- and down-stream of the RRCs

controls

No positive or negative controls were explicitly mentioned.

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