Haemoglobin is a key molecule for oxygen transport in vertebrates. It exhibits remarkable gene diversity in teleost fishes, reflecting adaptation to various aquatic environments. In this study, we present the dynamic evolution of haemoglobin subunit genes based on a comparison of high-quality genome assemblies of 24 vertebrate species, including 17 teleosts (of which six are cichlids). Our findings indicate that teleost genomes contain a range of haemoglobin genes, from as few as five in fugu to as many as 43 in salmon, with the latter being the largest repertoire found in vertebrates. We find evidence that the teleost ancestor had at least four Hbα and three or four Hbβ subunit genes, and that the current gene diversity emerged during teleost radiation, driven primarily by (tandem) gene duplications, genome compaction, and rearrangement dynamics. We provide insights into the genomic organisation of haemoglobin clusters in different teleost species. We further show that the evolution of paralogous rhbdf1 genes flanking both teleost clusters (LA and MN) supports the hypothesis for the origin of the LA cluster by rearrangement within teleosts, rather than by the teleost specific whole-genome duplication. We specifically focus on cichlid fishes, where adaptation to low oxygen environment plays role in species diversification. Our analysis of six cichlid genomes, including Pungu maclareni from the Barombi Mbo crater lake, for which we sequenced a representative genome, reveals 18-32 copies of the Hb genes, and elevated rates of non-synonymous substitutions compared to other teleosts. Overall, this work facilitates a deeper understanding of how haemoglobin genes contribute to the adaptive potential of teleosts.

Department of Aquatic Ecosystems Management Institute of Fisheries and Aquatic Sciences University of Douala Douala Cameroon

Department of Biological Sciences University of Ngaoundéré Ngaoundéré Cameroon

Department of Zoology Faculty of Science Charles University Prague Czech Republic

Institute of Ecology and Evolution Bern Switzerland

Military Health Institute Military Medical Agency Prague Czech Republic

Natural History Museum University of Oslo Oslo Norway

Zoological Institute University of Basel Basel Switzerland

Zobrazit více v PubMed

Abi‐Rached, L., A. Gilles, T. Shiina, P. Pontarotti, and H. Inoko. 2002. “Evidence of En Bloc Duplication in Vertebrate Genomes.” Nature Genetics 31, no. 1: 100–105.

Ahmed, M. H., M. S. Ghatge, and M. K. Safo. 2020. “Hemoglobin: Structure, Function and Allostery.” Sub‐Cellular Biochemistry 94: 345–382.

Archibald, J. M., and A. J. Roger. 2002. “Gene Conversion and the Evolution of Euryarchaeal Chaperonins: A Maximum Likelihood‐Based Method for Detecting Conflicting Phylogenetic Signals.” Journal of Molecular Evolution 55, no. 2: 232–245.

Baalsrud, H. T., K. L. Voje, O. K. Tørresen, et al. 2017. “Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth.” Scientific Reports 7, no. 1: 7956.

Bergstedt, J. H., T. Pfalzgraff, and P. V. Skov. 2021. “Hypoxia Tolerance and Metabolic Coping Strategies in Oreochromis niloticus.” Comparative Biochemistry and Physiology Part A: Molecular and Integrative Physiology 257: 110956.

Berner, D., and W. Salzburger. 2015. “The Genomics of Organismal Diversification Illuminated by Adaptive Radiations.” Trends in Genetics 31, no. 9: 491–499.

Betancur‐R, R., E. O. Wiley, G. Arratia, et al. 2017. “Phylogenetic Classification of Bony Fishes.” BMC Evolutionary Biology 17: 1–40.

Bolognini, D., N. Bartalucci, A. Mingrino, A. M. Vannucchi, and A. Magi. 2019. “NanoR: A User‐Friendly R Package to Analyze and Compare Nanopore Sequencing Data.” PLoS One 14, no. 5: e0216471.

Brawand, D., C. E. Wagner, Y. I. Li, et al. 2014. “The Genomic Substrate for Adaptive Radiation in African Cichlid Fish.” Nature 513, no. 7518: 375–381.

Brenner, S., G. Elgar, R. Sanford, A. Macrae, B. Venkatesh, and S. Aparicio. 1993. “Characterization of the Pufferfish (Fugu) Genome as a Compact Model Vertebrate Genome.” Nature 366, no. 6452: 265–268.

Brownlie, A., C. Hersey, A. C. Oates, et al. 2003. “Characterization of Embryonic Globin Genes of the Zebrafish.” Developmental Biology 255, no. 1: 48–61.

Chan, F. Y., J. Robinson, A. Brownlie, et al. 1997. “Characterization of Adult α‐and β‐Globin Genes in the Zebrafish.” Blood 89, no. 2: 688–700.

Chen, Z., F. Qiao, Y. He, H. Xie, and D. Qi. 2016. “Evidence for Positive Selection on α and β Globin Genes in Pikas and Zokor From the Qinghai‐Tibetan Plateau.” Gene and Translational Bioinformatics 2: 1–10.

Cortesi, F., Z. Musilová, S. M. Stieb, et al. 2015. “Ancestral Duplications and Highly Dynamic Opsin Gene Evolution in Percomorph Fishes.” Proceedings of the National Academy of Sciences of the United States of America 112, no. 5: 1493–1498.

Czelusniak, J., M. Goodman, D. Hewett‐Emmett, M. L. Weiss, P. J. Venta, and R. E. Tashian. 1982. “Phylogenetic Origins and Adaptive Evolution of Avian and Mammalian Haemoglobin Genes.” Nature 298, no. 5871: 297–300.

Darriba, D., G. L. Taboada, R. Doallo, and D. Posada. 2012. “jModelTest 2: More Models, New Heuristics and Parallel Computing.” Nature Methods 9, no. 8: 772.

Fago, A., V. Carratore, G. di Prisco, R. J. Feuerlein, L. Sottrup‐Jensen, and R. E. Weber. 1995. “The Cathodic Hemoglobin of Anguilla anguilla: Amino Acid Sequence and Oxygen Equilibria of a Reverse Bohr Effect Hemoglobin With High Oxygen Affinity and High Phosphate Sensitivity (*).” Journal of Biological Chemistry 270, no. 32: 18897–18902.

Glasauer, S. M., and S. C. Neuhauss. 2014. “Whole‐Genome Duplication in Teleost Fishes and Its Evolutionary Consequences.” Molecular Genetics and Genomics 289, no. 6: 1045–1060.

Green, J., S. A. Corbet, and E. Betney. 1973. “Ecological Studies on Crater Lakes in West Cameroon the Blood of Endemic Cichlids in Barombi Mbo in Relation to Stratification and Their Feeding Habits.” Journal of Zoology 170: 299–308.

Hahn, C., M. J. Genner, G. F. Turner, and D. A. Joyce. 2017. “The Genomic Basis of Cichlid Fish Adaptation Within the Deepwater “Twilight Zone” of Lake Malawi.” Evolution Letters 1, no. 4: 184–198.

Hardison, R. C. 2008. “Globin Genes on the Move.” Journal of Biology 7, no. 9: 35.

Hardison, R. C. 2012. “Evolution of Hemoglobin and Its Genes.” Cold Spring Harbor Perspectives in Medicine 2, no. 12: a011627.

Hoang, D. T., O. Chernomor, A. Von Haeseler, B. Q. Minh, and L. S. Vinh. 2017. “UFBoot2: Improving the Ultrafast Bootstrap Approximation.” Molecular Biology and Evolution 35, no. 2: 518–522.

Hoffmann, F. G., J. C. Opazo, and J. F. Storz. 2012. “Whole‐Genome Duplications Spurred the Functional Diversification of the Globin Gene Superfamily in Vertebrates.” Molecular Biology and Evolution 29, no. 1: 303–312.

Holland, P. W., J. Garcia‐Fernàndez, N. A. Williams, and A. Sidow. 1994. “Gene Duplications and the Origins of Vertebrate Development.” Development 1994, no. Supplement: 125–133.

Hughes, A. L., and R. Friedman. 2003. “2R or Not 2R: Testing Hypotheses of Genome Duplication in Early Vertebrates.” In Genome Evolution, edited by A. Meyer and Y. van de Peer, 85–93. Dordrecht: Springer.

Kalyaanamoorthy, S., B. Q. Minh, T. K. Wong, A. von Haeseler, and L. S. Jermiin. 2017. “ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates.” Nature Methods 14, no. 6: 587–589.

Katoh, K., and D. M. Standley. 2013. “MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability.” Molecular Biology and Evolution 30, no. 4: 772–780.

Kautt, A. F., G. Machado‐Schiaffino, and A. Meyer. 2016. “Multispecies Outcomes of Sympatric Speciation After Admixture With the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids.” PLoS Genetics 12, no. 6: e1006157.

Kearse, M., R. Moir, A. Wilson, et al. 2012. “Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data.” Bioinformatics 28, no. 12: 1647–1649.

Ko, B. J., C. Lee, J. Kim, et al. 2022. “Widespread False Gene Gains Caused by Duplication Errors in Genome Assemblies.” Genome Biology 23, no. 1: 205.

Kolmogorov, M., J. Yuan, Y. Lin, and P. A. Pevzner. 2019. “Assembly of Long, Error‐Prone Reads Using Repeat Graphs.” Nature Biotechnology 37, no. 5: 540–546.

Kondrashov, F. A. 2012. “Gene Duplication as a Mechanism of Genomic Adaptation to a Changing Environment.” Proceedings of the Royal Society B: Biological Sciences 279, no. 1749: 5048–5057.

Koop, B. F., K. R. Von Schalburg, J. Leong, et al. 2008. “A Salmonid EST Genomic Study: Genes, Duplications, Phylogeny and Microarrays.” BMC Genomics 9, no. 1: 545.

Krumsiek, J., R. Arnold, and T. Rattei. 2007. “Gepard: A Rapid and Sensitive Tool for Creating Dotplots on Genome Scale.” Bioinformatics 23, no. 8: 1026–1028.

Kuraku, S., and A. Meyer. 2009. “The Evolution and Maintenance of Hox Gen in Vertebrates and the Teleost‐Specific Genome Duplication.” International Journal of Developmental Biology 53: 765–773.

Lee, J. Y., M. Kong, J. Oh, et al. 2021. “Comparative Evaluation of Nanopore Polishing Tools for Microbial Genome Assembly and Polishing Strategies for Downstream Analysis.” Scientific Reports 11, no. 1: 20740.

Lei, Y., L. Yang, Y. Zhou, et al. 2021. “Hb Adaptation to Hypoxia in High‐Altitude Fishes: Fresh Evidence From Schizothoracinae Fishes in the Qinghai‐TiHbβn Plateau.” International Journal of Biological Macromolecules 185: 471–484.

Malinsky, M., R. Challis, A. M. Tyers, et al. 2015. “Genomic Islands of Speciation Separate Cichlid Ecomorphs in an East African Crater Lake.” Science 350, no. 6267: 1493–1498.

Malinsky, M., H. Svardal, A. M. Tyers, et al. 2018. “Whole‐Genome Sequences of Malawi Cichlids Reveal Multiple Radiations Interconnected by Gene Flow.” Nature Ecology and Evolution 2: 1940–1955.

Mao, Y., T. Peng, F. Shao, Q. Zhao, and Z. Peng. 2023. “Molecular Evolution of the Hemoglobin Gene Family Across Vertebrates.” Genetica 151, no. 3: 201–213.

Marino, K., L. Boschetto, D. de Pascale, and E. Cocca. 2007. “Organisation of the Hb 1 Genes of the Antarctic Skate Bathyraja Eatonii: New Insights Into the Evolution of Globin Genes.” Gene 406, no. 1–2: 199–208.

Mazzarella, L., G. Bonomi, M. C. Lubrano, et al. 2006. “Minimal Structural Requirements for Root Effect: Crystal Structure of the Cathodic Hemoglobin Isolated From the Antarctic Fish Trematomus newnesi.” Proteins: Structure, Function, and Bioinformatics 62, no. 2: 316–321.

McKiernan, H. E., and P. B. Danielson. 2017. “Molecular Diagnostic Applications in Forensic Science.” In Molecular diagnostics, 371–394. San Diego, CA: Academic Press.

Miller, M. A., W. Pfeiffer, and T. Schwartz. 2010. “Creating the CIPRES Science Gateway for Inference of Large Phylogenetic Trees.” In In 2010 Gateway Computing Environments Workshop (GCE), 1–8. New Orleans, LA: IEEE.

Mukherjee, S., O. Bartoš, K. Zdeňková, P. Hanák, P. Horká, and Z. Musilova. 2021. “Evolution of the Parvalbumin Genes in Teleost Fishes After the Whole‐Genome Duplication.” Fishes 6, no. 4: 70.

Musilova, Z., A. Indermaur, A. R. Bitja‐Nyom, et al. 2019. “Evolution of the Visual Sensory System in Cichlid Fishes From Crater Lake Barombi Mbo in Cameroon.” Molecular Ecology 28, no. 23: 5010–5031.

Musilova, Z., W. Salzburger, and F. Cortesi. 2021. “The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function.” Annual Review of Cell and Developmental Biology 37: 441–468.

Nery, M. F., J. I. Arroyo, and J. C. Opazo. 2013. “Genomic Organization and Differential Signature of Positive Selection in the Hbα and Hbβ Globin Gene Clusters in Two Cetacean Species.” Genome Biology and Evolution 5, no. 12: 2359–2367.

Nguyen, L. T., H. A. Schmidt, A. von Haeseler, and B. Q. Minh. 2014. “IQ‐TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum‐Likelihood Phylogenies.” Molecular Biology and Evolution 32, no. 1: 268–274.

Ohno, S. 1970. In Evolution by Gene Duplication, 132–139. New York: Springer Verlag.

Opazo, J. C., G. T. Butts, M. F. Nery, J. F. Storz, and F. G. Hoffmann. 2013. “Whole‐Genome Duplication and the Functional Diversification of Teleost Fish Hemoglobins.” Molecular Biology and Evolution 30, no. 1: 140–153.

Parey, E., A. Louis, J. Montfort, Y. Guiguen, H. R. Crollius, and C. Berthelot. 2022. “An Atlas of Fish Genome Evolution Reveals Delayed Rediploidization Following the Teleost Whole‐Genome Duplication.” Genome Research 32, no. 9: 1685–1697.

Patel, V. S., S. J. Cooper, J. E. Deakin, et al. 2008. “Platypus Globin Genes and Flanking Loci Suggest a New Insertional Model for Hbβ‐Globin Evolution in Birds and Mammals.” BMC Biology 6, no. 1: 34.

Pillai, A. S., S. A. Chandler, Y. Liu, et al. 2020. “Origin of Complexity in Haemoglobin Evolution.” Nature 581, no. 7809: 480–485.

Quinn, N. L., K. A. Boroevich, K. P. Lubieniecki, et al. 2010. “Genomic Organization and Evolution of the Atlantic Salmon Hemoglobin Repertoire.” BMC Genomics 11: 1–17.

R Core Team. 2018. A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. www.R‐project.org/.

Ratnakumar, A., S. Mousset, S. Glémin, et al. 2010. “Detecting Positive Selection Within Genomes: The Problem of Biased Gene Conversion.” Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1552: 2571–2580.

Rennison, D. J., G. L. Owens, and J. S. Taylor. 2012. “Opsin Gene Duplication and Divergence in Ray‐Finned Fish.” Molecular Phylogenetics and Evolution 62, no. 3: 986–1008.

Rohlfing, K., F. Stuhlmann, M. F. Docker, and T. Burmester. 2016. “Convergent Evolution of Hemoglobin Switching in Jawed and Jawless Vertebrates.” BMC Evolutionary Biology 16: 30.

Ronco, F., M. Matschiner, A. Böhne, et al. 2021. “Drivers and Dynamics of a Massive Adaptive Radiation in Cichlid Fishes.” Nature 589, no. 7840: 76–81.

Ronquist, F., M. Teslenko, P. Van Der Mark, et al. 2012. “MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space.” Systematic Biology 61, no. 3: 539–542.

Rutjes, H. A., M. C. Nieveen, R. E. Weber, F. Witte, and G. E. E. J. M. Van den Thillart. 2007. “Multiple Strategies of Lake Victoria Cichlids to Cope With Lifelong Hypoxia Include Hemoglobin Switching.” American Journal of Physiology‐Regulatory, Integrative and Comparative Physiology 293, no. 3: R1376–R1383.

Seehausen, O. 2000. “Explosive Speciation Rates and Unusual Species Richness in Haplochromine Cichlid Fishes: Effects of Sexual Selection.” Advances in Ecological Research 31: 237–274.

Simão, F. A., R. M. Waterhouse, P. Ioannidis, E. V. Kriventseva, and E. M. Zdobnov. 2015. “BUSCO: Assessing Genome Assembly and Annotation Completeness With Single‐Copy Orthologs.” Bioinformatics 31, no. 19: 3210–3212.

Stanke, M., and B. Morgenstern. 2005. “AUGUSTUS: A Web Server for Gene Prediction in Eukaryotes That Allows User‐Defined Constraints.” Nucleic Acids Research 33, no. suppl_2: W465–W467.

Steinke, D., W. Salzburger, I. Braasch, and A. Meyer. 2006. “Many Genes in Fish Have Species‐Specific Asymmetric Rates of Molecular Evolution.” BMC Genomics 7: 20.

Storz, J. F. 2016. “Gene Duplication and Evolutionary Innovations in Hemoglobin‐Oxygen Transport.” Physiology 31, no. 3: 223–232.

Storz, J. F. 2018. Hemoglobin: Insights Into Protein Structure, Function, and Evolution. Oxford: Oxford University Press.

Storz, J. F., J. C. Opazo, and F. G. Hoffmann. 2013. “Gene Duplication, Genome Duplication, and the Functional Diversification of Vertebrate Globins.” Molecular Phylogenetics and Evolution 66, no. 2: 469–478.

Suyama, M., D. Torrents, and P. Bork. 2006. “PAL2NAL: Robust Conversion of Protein Sequence Alignments Into the Corresponding Codon Alignments.” Nucleic Acids Research 34, no. suppl_2: W609–W612.

Svardal, H., W. Salzburger, and M. Malinsky. 2021. “Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes.” Annual Review of Animal Biosciences 9: 55–79.

van den Thillart, G., I. Wilms, M. Nieveen, R. E. Weber, and F. Witte. 2018. “Hypoxia‐Induced Changes in Hemoglobins of Lake Victoria Cichlids.” Journal of Experimental Biology 221, no. 17: jeb177832.

Walker, B. J., T. Abeel, T. Shea, et al. 2014. “Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement.” PLoS One 9, no. 11: e112963.

Wang, L. G., T. T. Y. Lam, S. Xu, et al. 2020. “Treeio: An R Package for Phylogenetic Tree Input and Output With Richly Annotated and Associated Data.” Molecular Biology and Evolution 37, no. 2: 599–603.

Wells, R. M. 1999. “Evolution of Haemoglobin Function: Molecular Adaptations to Environment.” Clinical and Experimental Pharmacology and Physiology 26, no. 8: 591–595.

Wick, R. R., L. M. Judd, and K. E. Holt. 2019. “Performance of Neural Network Basecalling Tools for Oxford Nanopore Sequencing.” Genome Biology 20: 129.

Yang, Z. 2007. “PAML 4: Phylogenetic Analysis by Maximum Likelihood.” Molecular Biology and Evolution 24, no. 8: 1586–1591.

Yokoyama, S. 2008. “Evolution of Dim‐Light and Color Vision Pigments.” Annual Review of Genomics and Human Genetics 9: 259–282.

Zobrazit více v PubMed

RefSeq
GCA_018977255.1, GCA_000004195.4, GCA_003957565.4, GCA_000001635.9, GCA_000001405.29, GCA_000258655.2, GCA_000242695.1, GCA_013347855.1, GCA_002872115.1, GCA_900964985.2, GCA_900700415.2, GCA_000002035.4, GCA_011004845.1, GCA_905237065.2, GCA_902167395.1, GCA_901000725.2, GCA_002234675.1, GCA_027789165.1, GCA_013435755.1, GCA_007364275.2, GCA_001858045.3, GCA_000238955.5, GCA_900246225.3, GCA_041757325.1, SRX7645636, PRJEB20018, NC_031969.2