Additional file 1 of Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies

• Main Authors: Mikalsen, Svein-Ole, Tausen, Marni, Kongsstovu, Sunnvør
• Format: Text
• Language: unknown
• Published: figshare 2020
• Subjects: Genetics; FOS Biological sciences; atlantic cod; Gadus morhua
• Online Access: https://dx.doi.org/10.6084/m9.figshare.11972433; https://springernature.figshare.com/articles/Additional_file_1_of_Phylogeny_of_teleost_connexins_reveals_highly_inconsistent_intra-_and_interspecies_use_of_nomenclature_and_misassemblies_in_recent_teleost_chromosome_assemblies/11972433

Additional file 1. Suppl. Figure 1. Human (Homo sapiens) connexins. Suppl. Figure 2. Mouse (Mus musculus) connexins. Suppl. Figure 3. Opossum (Monodelphis domestica) connexins. Suppl. Figure 4. GJC1like and GJA9 connexin sequences from other marsupials and platypus. Suppl. Figure 5. Zebrafish (Danio rerio) connexins. Suppl. Figure 6. Japanese pufferfish (Fugu; Takifugu rubripes) connexins. Suppl. Figure 7. Green spotted pufferfish (Tetraodon nigroviridis) connexins. Suppl. Figure 8. Three-spined stickleback (Gasterosteus aculeatus) connexins. Suppl. Figure 9. Atlantic herring (Clupea harengus) connexins. Suppl. Figure 10. Atlantic cod (Gadus morhua) connexins. Suppl. Figure 11. Japanese eel (Anguilla japonica) connexins. Suppl. Figure 12. Connexin39.2 (“gjd2like”) from mammals. Suppl. Figure 13. Comparisons of human “GJA4P” against connexin39.2 and GJA4. A. Alignment of conserved domains in human “GJA4P” (NG_026166) against connexin39.2 (“gjd2like”) in various species at protein level. B. Alignment of conserved domains in human “GJA4P” (NG_026166) against GJA4 (connexin37) from human and eel at protein level. Suppl. Figure 14. Expanded branches from the phylogenetic tree shown in Fig. 1. A. Expanded view of the mammalian and teleost GJA1 branch. B. Expanded view of mammalian and teleost GJA3 branch, and the associated teleost cx39.9. C. Expanded view of the mammalian and teleost GJA4 branch. D. Expanded view of the mammalian and teleost GJA5 branch. E. Expanded view of the mammalian and teleost GJA9 and GJA10 branches. F. Expanded view of the teleost cx34.5 and cx32.2 branches. G. Expanded view of the mammalian and teleost GJB1 branch. H. Expanded view of mammalian and teleost GJB2 and GJB6 branch, and teleost cx30.3 branches. I. Expanded view of the mammalian GJB3 and teleost cx35.4 branches. J. Expanded view of mammalian GJB4 and GJB5, and teleost cx34.4. K. Expanded view of the mammalian and teleost GJB7 branch. L. Expanded view of the teleost cx28.6 group, and its relationship with GJB3/GJB4/GJB5. M. Expanded view of eutherian GJC3 and marsupial GJC1like and GJC2like branches. N. Expanded view of mammalian and teleost GJC1 and teleost cx43.4 branches. O. Expanded view of mammalian and teleost GJC2, and its relationship with GJC1 and cx43.4. P. Expanded view of mammalian and teleost Cx39.2 branch. Q. Expanded view over the central GJD2 complex. R. Expanded view of mammalian and teleost GJD3 branch. S. Expanded view of mammalian and teleost GJD4 branch. T. Expanded view of teleost cx36.7 branch. Suppl. Figure 15. Compressed phylogenetic tree illustrating long-branch attraction between gjc3, gjd4 and gje1 groups. Suppl. Figure 16. Searching for positions of connexins lacking in chromosome assemblies. A. Problem in cod assembly of chromosome 20 at assumed position of gja5. B. Alignments with sequences from herring and stickleback point to the same area on cod chromosome 21, indicated expected position of gja10-cx52.6. C. Alignments of herring and stickleback scaffolds containing cx52.6. Suppl. Figure 17. A homogeneous and consistent nomenclature for gap junction protein genes. Suppl. Figure 18. Schematic outline of the major procedures.