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Published June 30, 2023 | Version v1
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Large-scale snake genome analyses provide insights into vertebrate development

Creators

  • 1. CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
  • 2. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
  • 3. University of Chinese Academy of Sciences, Beijing 100049, China
  • 4. College of Life Science, Neijiang Normal University, Neijiang, Sichuan 641100, China
  • 5. Departments of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu 610000, China
  • 6. Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
  • 7. Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar

Description

Peng, Changjun, Wu, Dong-Dong, Ren, Jin-Long, Peng, Zhong-Liang, Ma, Zhifei, Wu, Wei, Lv, Yunyun, Wang, Zeng, Deng, Cao, Jiang, Ke, Parkinson, Christopher L., Qi, Yin, Zhang, Zhi-Yi, Li, Jia-Tang (2023): Large-scale snake genome analyses provide insights into vertebrate development. Cell 186: 1-18, DOI: 10.1016/j.cell.2023.05.030, URL: http://dx.doi.org/10.1016/j.cell.2023.05.030

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urn:lsid:plazi.org:pub:FFCCF664C4713828FFB57965A156FFC2

Cites
Publication: 10.1007/s11427-023-2362-5 (DOI)
Publication: 10.48550/arXiv.1308.2012 (DOI)
Publication: 10.1038/srep31900 (DOI)
Publication: 10.1101/2023.03.09.531669 (DOI)
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Figure: 10.5281/zenodo.8070672 (DOI)
Figure: 10.5281/zenodo.8070674 (DOI)
Figure: 10.5281/zenodo.8070676 (DOI)
Figure: 10.5281/zenodo.8070678 (DOI)
Figure: 10.5281/zenodo.8070681 (DOI)
Figure: 10.5281/zenodo.8070683 (DOI)
Figure: 10.5281/zenodo.8070685 (DOI)
Figure: 10.5281/zenodo.8070687 (DOI)
Figure: 10.5281/zenodo.8070689 (DOI)
Figure: 10.5281/zenodo.8070691 (DOI)

References

  • 1. Zug,G.R.,Vitt,L., and Caldwell,J.P. (2001).Herpetology:an Introductory Biology of Amphibians and Reptiles (Elsevier/Academic Press).
  • 2. Uetz, P. (2022). The reptile database. Zoological Museum Hamburg. http://reptile-database.org/.
  • 3. Avila, R.W., Ferreira, V.L., and Souza, V.B. (2006). Biology of the blindsnake Typhlops brongersmianus (Typhlopidae) in a semideciduous forest from central Brazil. Herpetol. J. 16, 403-405.
  • 4. Mizuno, T., and Kojima, Y. (2015). A blindsnake that decapitates its termite prey. J. Zool. 297, 220-224.
  • 5. Goris, R.C. (2011). Infrared organs of snakes: an integral part of vision. J. Herpetol. 45, 2-14.
  • 6. Darbaniyan, F., Mozaffari, K., Liu, L., and Sharma, P. (2021). Soft matter mechanics and the mechanisms underpinning the infrared vision of snakes. Matter 4, 241-252.
  • 7. Margres, M.J., Rautsaw, R.M., Strickland, J.L., Mason, A.J., Schramer, T.D., Hofmann, E.P., Stiers, E., Ellsworth, S.A., Nystrom, G.S., Hogan, M.P., et al. (2021).The tiger rattlesnake genome reveals a complex genotype underlying a simple venom phenotype. Proc. Natl. Acad. Sci. USA 118, e2014634118.
  • 8. Myers, E.A., Strickland, J.L., Rautsaw, R.M., Mason, A.J., Schramer, T.D., Nystrom, G.S., Hogan, M.P., Yooseph, S., Rokyta, D.R., and Parkinson, C.L. (2022).De novo genome assembly highlights the role of lineage-specific gene duplications in the evolution of venom in fea's viper (Azemiops feae). Genome Biol. Evol. 14, evac082.
  • 9. Yin, W., Wang, Z.-J., Li, Q.-Y., Lian, J.-M., Zhou, Y., Lu, B.-Z., Jin, L.-J., Qiu,P.-X., Zhang,P.,Zhu,W.-B., et al.(2016).Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper. Nat. Commun. 7, 13107.
  • 10. Vonk, F.J., Casewell, N.R., Henkel, C.V., Heimberg, A.M., Jansen, H.J., McCleary, R.J., Kerkkamp, H.M., Vos, R.A., Guerreiro, I., Calvete, J.J., et al. (2013). The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proc. Natl. Acad. Sci. USA 110, 20651-20656.
  • 11. Castoe, T.A., De Koning,A.P.J., Hall, K.T., Card, D.C., Schield, D.R., Fujita, M.K., Ruggiero, R.P., Degner, J.F., Daza, J.M., Gu, W., et al. (2013). The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proc. Natl. Acad. Sci. USA 110, 20645-20650.
  • 12. Li, J.-T., Gao, Y.-D., Xie, L., Deng, C., Shi, P., Guan, M.-L., Huang, S., Ren, J.L., Wu, D.-D., Ding, L., et al. (2018). Comparative genomic investigation of high-elevation adaptation in ectothermic snakes. Proc. Natl. Acad. Sci. USA 115, 8406-8411.
  • 13. Schield, D.R., Card, D.C., Hales, N.R., Perry, B.W., Pasquesi, G.M., Blackmon, H., Adams, R.H., Corbin, A.B., Smith, C.F., Ramesh, B., et al. (2019). The origins and evolution of chromosomes, dosage compensation,and mechanisms underlying venom regulation in snakes. Genome Res. 29, 590-601.
  • 14. Yan, C., Wu, W., Dong, W., Zhu, B., Chang, J., Lv, Y., Yang, S., and Li, J.T. (2022). Temperature acclimation in hot-spring snakes and the convergence of cold response. Innovation (Camb) 3, 100295.
  • 15. Suryamohan, K., Krishnankutty, S.P., Guillory, J., Jevit, M., Schroder, M.S., Wu, M., Kuriakose, B., Mathew, O.K., Perumal, R.C., Koludarov, I., et al. (2020). The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins. Nat. Genet. 52, 106-117.
  • 16. Peng,C., Ren,J.-L., Deng,C.,Jiang,D.,Wang,J., Qu,J., Chang,J., Yan, C., Jiang, K., Murphy, R.W., et al. (2020). The genome of Shaw's sea snake (Hydrophis curtus) reveals secondary adaptation to its marine environment. Mol. Biol. Evol. 37, 1744-1760.
  • 17. Armstrong,J., Hickey,G.,Diekhans,M., Fiddes,I.T., Novak,A.M., Deran, A., Fang,Q., Xie,D., Feng,S., Stiller, J., et al. (2020).Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 587, 246-251.
  • 18. Zhang, C., Rabiee, M., Sayyari, E., and Mirarab, S. (2018). ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19 (Supplement 6 ), 153.
  • 19. Figueroa, A., McKelvy, A.D., Grismer, L.L., Bell, C.D., and Lailvaux, S.P. (2016). A species-level phylogeny of extant snakes with description of a new colubrid subfamily and genus. PLoS One 11, e0161070.
  • 20. Zaher,H., Murphy,R.W., Arredondo,J.C., Graboski,R., Machado-Filho, P.R., Mahlow, K., Montingelli, G.G., Quadros, A.B., Orlov, N.L., Wilkinson, M., et al. (2019). Large-scale molecular phylogeny, morphology, divergence-time estimation,and the fossil record of advanced caenophidian snakes (Squamata: Serpentes). PLoS One 14, e0216148.
  • 21. Hsiang, A.Y., Field, D.J., Webster, T.H., Behlke, A.D., Davis, M.B., Racicot, R.A., and Gauthier, J.A. (2015). The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record. BMC Evol. Biol. 15, 87.
  • 22. Klein, C.G., Pisani, D., Field, D.J., Lakin, R., Wills, M.A., and Longrich, N.R. (2021). Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction. Nat. Commun. 12, 5335.
  • 23. Zheng, Y., and Wiens, J.J. (2016). Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species.Mol.Phylogenet. Evol. 94, 537-547.
  • 24. Scotese,C.R.(2001).Atlas of Earth History (University of Texas at Arlington, Department of Geology).
  • 25. Roscito, J.G., Sameith, K., Pippel, M., Francoijs, K.-J., Winkler, S., Dahl, A., Papoutsoglou, G., Myers, G., and Hiller, M. (2018).The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly. GigaScience 7, giy141.
  • 26. Lind, A.L., Lai, Y.Y.Y., Mostovoy, Y., Holloway, A.K., Iannucci, A., Mak, A.C.Y., Fondi, M., Orlandini, V., Eckalbar, W.L., Milan, M., et al. (2019). Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. Nat. Ecol. Evol. 3, 1241-1252.
  • 27. Shaffer, H.B., Minx, P., Warren, D.E., Shedlock, A.M., Thomson, R.C., Valenzuela, N., Abramyan, J., Amemiya, C.T., Badenhorst, D., Biggar, K.K., et al. (2013). The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol. 14, R28.
  • 28. Wan,Q.-H., Pan,S.-K.,Hu,L., Zhu,Y.,Xu,P.-W.,Xia,J.-Q.,Chen,H.,He, G.-Y., He, J., Ni, X.-W., et al. (2013).Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator. Cell Res. 23, 1091-1105.
  • 29. Hillier, L.W., Miller, W., Birney, E., Warren, W., Hardison, R.C., Ponting, C.P., Bork, P., Burt, D.W., Groenen, M.A.M., Delany, M.E., et al. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695-716.
  • 30. Pasquesi, G.I.M., Adams, R.H., Card, D.C., Schield, D.R., Corbin, A.B., Perry, B.W., Reyes-Velasco, J., Ruggiero, R.P., Vandewege, M.W., Shortt, J.A., et al. (2018). Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals.Nat. Commun. 9, 2774.
  • 31. Rhie,A., McCarthy,S.A., Fedrigo, O., Damas,J., Formenti,G., Koren, S., Uliano-Silva,M., Chow,W., Fungtammasan,A., Kim,J., et al. (2021).Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737-746.
  • 32. Weber, C.C., Boussau, B., Romiguier, J., Jarvis, E.D., and Ellegren, H. (2014). Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biol. 15, 549.
  • 33. Duret, L., and Galtier, N. (2009). Biased gene conversion and the evolution of mammalian genomic landscapes. Annu. Rev. Genomics Hum. Genet. 10, 285-311.
  • 34. Sanderson,M.J. (2003).R8s:inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19, 301-302.
  • 35. Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., et al. (2019). Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 364, eaav6202.
  • 36. Roscito, J.G., Sameith, K., Parra,G., Langer,B.E., Petzold, A., Moebius, C., Bickle, M., Rodrigues, M.T., and Hiller, M. (2018). Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nat. Commun. 9, 4737.
  • 37. Pyron, R.A., Burbrink, F.T., and Wiens, J.J. (2013). A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol. Biol. 13, 93.
  • 38. Morinaga, G., and Bergmann, P.J. (2020). Evolution of fossorial locomotion in the transition from tetrapod to snake-like in lizards.Proc. Biol. Sci. 287, 20200192.
  • 39. Pees, M., Kiefer, I., Thielebein, J., Oechtering, G., and Krautwald-Junghanns, M.E. (2009). Computed tomography of the lung of healthy snakes of the species Python regius, boa constrictor, Python reticulatus, Morelia viridis, Epicrates cenchria, and Morelia spilota. Vet.Radiol.Ultrasound 50, 487-491.
  • 40. van Soldt, B.J., Metscher, B.D., Poelmann, R.E., Vervust, B., Vonk, F.J., Muller, G.B., and Richardson, M.K. (2015). Heterochrony and early left-right asymmetry in the development of the cardiorespiratory system of snakes. PLoS One 10, e116416.
  • 41. Lillywhite, H.B. (2014). How Snakes Work: Structure, Function and Behavior of the World's Snakes (Oxford University Press).
  • 42. Cohn, M.J., and Tickle, C. (1999). Developmental basis of limblessness and axial patterning in snakes. Nature 399, 474-479.
  • 43. Apesteguia, S., and Zaher, H. (2006).A Cretaceous terrestrial snake with robust hindlimbs and a sacrum. Nature 440, 1037-1040.
  • 44. Kvon,E.Z.,Kamneva,O.K., Melo,U.S., Barozzi,I., Osterwalder,M.,Mannion, B.J., Tissieres, V., Pickle, C.S., Plajzer-Frick, I., Lee, E.A., et al. (2016).Progressive loss of function in a limb enhancer during snake Evolution. Cell 167, 633-642.e11.
  • 45. Sandell, L.L., Sanderson, B.W., Moiseyev, G., Johnson, T., Mushegian, A., Young, K., Rey, J.P., Ma, J.X., Staehling-Hampton, K., and Trainor, P.A. (2007). RDH10 is essential for synthesis of embryonic retinoic acid and is required for limb, craniofacial, and organ development. Genes Dev. 21, 1113-1124.
  • 46. Makino, S., Masuya, H., Ishijima, J., Yada, Y., and Shiroishi, T. (2001). A Spontaneous mouse mutation,mesenchymal dysplasia (mes), is caused by a deletion of the most C-terminal cytoplasmic domain of patched (ptc). Dev. Biol. 239, 95-106.
  • 47. Goodrich, L.V., Milenkovic ยด, L., Higgins, K.M., and Scott, M.P. (1997). Altered neural cell fates and medulloblastoma in mouse patched mutants. Science 277, 1109-1113.
  • 48. Damerla, R.R., Cui, C., Gabriel, G.C., Liu, X., Craige, B., Gibbs, B.C., Francis, R., Li, Y., Chatterjee, B., San Agustin, J.T., et al. (2015). Novel Jbts17 mutant mouse model of Joubert syndrome with cilia transition zone defects and cerebellar and other ciliopathy related anomalies. Hum. Mol. Genet. 24, 3994-4005.
  • 49. Chidambaram, A., Goldstein,A.M., Gailani, M.R., Gerrard, B., Bale, S.J., DiGiovanna,J.J., Bale,A.E.,and Dean,M.(1996).Mutations in the human homologue of the Drosophila patched gene in Caucasian and African-American nevoid basal cell carcinoma syndrome patients. Cancer Res. 56, 4599-4601.
  • 50. Palmer, K., Fairfield, H., Borgeia, S., Curtain, M., Hassan, M.G., Dionne, L., Yong Karst, S.Y., Coombs, H., Bronson, R.T., Reinholdt, L.G., et al. (2016). Discovery and characterization of spontaneous mouse models of craniofacial dysmorphology. Dev. Biol. 415, 216-227.
  • 51. van den Boogaard, M.-J.H., Dorland, M., Beemer,F.A., and van Amstel, H.K.P. (2000). MSX1 mutation is associated with orofacial clefting and tooth agenesis in humans. Nat. Genet. 24, 342-343.
  • 52. Vastardis,H., Karimbux,N., Guthua, S.W., Seidman,J.G., and Seidman, C.E. (1996). A human MSX1 homeodomain missense mutation causes selective tooth agenesis. Nat. Genet. 13, 417-421.
  • 53. Secor, S.M., and Diamond, J. (1995). Adaptive responses to feeding in Burmese pythons: pay before pumping. J. Exp. Biol. 198, 1313-1325.
  • 54. Secor, S.M., and Diamond, J. (1998). A vertebrate model of extreme physiological regulation. Nature 395, 659-662.
  • 55. Wang,T.,and Rindom,E. (2021).The physiological response to digestion in snakes:A feast for the integrative physiologist.Comp.Biochem.Physiol. A Mol. Integr. Physiol. 254, 110891.
  • 56. Perry, B.W., Andrew, A.L., Mostafa Kamal, A.H., Card, D.C., Schield, D.R., Pasquesi, G.I.M., Pellegrino, M.W., Mackessy, S.P., Chowdhury, S.M., Secor, S.M., et al. (2019). Multi-species comparisons of snakes identify coordinated signalling networks underlying post-feeding intestinal regeneration. Proc. Biol. Sci. 286, 20190910.
  • 57. Kitazawa, T., and Kaiya, H. (2019). Regulation of gastrointestinal motility by motilin and ghrelin in vertebrates. Front. Endocrinol. 10, 278.
  • 58. Ryu, S., Huh, I.-S., Cho, E.-Y., Cho, Y., Park, T., Yoon, S.C., Joo, Y.H., and Hong, K.S. (2016). Association study of 60 candidate genes with antipsychotic-induced weight gain in schizophrenia patients. Pharmacopsychiatry 49, 51-56.
  • 59. Schroeter,J.C., Fenn, C.M., and Small, B.C. (2015). Elucidating the roles of gut neuropeptides on channel catfish feed intake,glycemia,and hypothalamic NPY and POMC expression. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 188, 168-174.
  • 60. Costantini, V.J.A., Vicentini, E., Sabbatini, F.M., Valerio, E., Lepore, S., Tessari, M., Sartori, M., Michielin, F., Melotto, S., Bifone, A., et al. (2011). GSK1614343, a novel ghrelin receptor antagonist, produces an unexpected increase of food intake and body weight in rodents and dogs. Neuroendocrinology 94, 158-168.
  • 61. Vergnes,L., Lee, J.M., Chin,R.G., Auwerx,J., and Reue, K. (2013).Diet1 functions in the FGF15/19 enterohepatic signaling axis to modulate bile acid and lipid levels. Cell Metab. 17, 916-928.
  • 62. Zhang, H., Ables, E.T., Pope, C.F., Washington, M.K., Hipkens, S., Means, A.L., Path, G., Seufert, J., Costa, R.H., Leiter, A.B., et al. (2009). Multiple, temporal-specific roles for HNF6 in pancreatic endocrine and ductal differentiation. Mech. Dev. 126, 958-973.
  • 63. MacDonald, R.J., Stary, S.J., and Swift, G.H. (1982). Two similar but nonallelic rat pancreatic trypsinogens. Nucleotide sequences of the cloned cDNAs. J. Biol. Chem. 257, 9724-9732.
  • 64. Boot, R.G., Verhoek, M., Donker-Koopman, W., Strijland, A., Van Marle, J., Overkleeft, H.S., Wennekes,T., and Aerts, J.M.F.G. (2007).Identification of the non-lysosomal glucosylceramidase as b -glucosidase 2. J. Biol. Chem. 282, 1305-1312.
  • 65. Toomey, C.B., Kelly, U., Saban, D.R., and Bowes Rickman, C.B. (2015). Regulation of age-related macular degeneration-like pathology by complement factor H. Proc. Natl. Acad. Sci. USA 112, E3040-E3049.
  • 66. Leal,F., and Cohn,M.J.(2018).Developmental,genetic,and genomic insights into the evolutionary loss of limbs in snakes. Genesis 56, e23077.
  • 67. Choorapoikayil, S., Willems, B., Strohle, P., and Gajewski, M. (2012). Analysis of her1 and her7 mutants reveals a spatio temporal separation of the somite clock module. PLoS One 7, e39073.
  • 68. Van Eeden, F.J., Granato, M., Schach, U., Brand, M., Furutani-Seiki,M., Haffter, P., Hammerschmidt, M., Heisenberg, C.-P., Jiang, Y.-J., Kane, D.A., et al. (1996). Mutations affecting somite formation and patterning in the zebrafish, Danio rerio. Development 123, 153-164.
  • 69. Kume,T., Jiang, H., Topczewska,J.M., and Hogan,B.L. (2001). The murine winged helix transcription factors, Foxc1 and Foxc2, are both required for cardiovascular development and somitogenesis. Genes Dev. 15, 2470-2482.
  • 70. Skuntz, S., Mankoo, B., Nguyen, M.-T.T., Hustert, E., Nakayama, A., Tournier-Lasserve, E., Wright, C.V.E., Pachnis, V., Bharti, K., and Arnheiter, H. (2009). Lack of the mesodermal homeodomain protein MEOX1 disrupts sclerotome polarity and leads to a remodeling of the cranio-cervical joints of the axial skeleton. Dev. Biol. 332, 383-395.
  • 71. Mankoo,B.S., Skuntz, S., Harrigan, I., Grigorieva, E., Candia, A., Wright, C.V.E., Arnheiter, H., and Pachnis, V. (2003). The concerted action of Meox homeobox genes is required upstream of genetic pathways essential for the formation, patterning and differentiation of somites. Development 130, 4655-4664.
  • 72. Kawamura, A., Koshida, S., Hijikata, H., Ohbayashi, A., Kondoh, H., and Takada, S. (2005). Groucho-associated transcriptional repressor ripply1 is required for proper transition from the presomitic mesoderm to somites. Dev. Cell 9, 735-744.
  • 73. Chan,T., Kondow, A., Hosoya,A., Hitachi,K.,Yukita,A., Okabayashi,K., Nakamura, H., Ozawa,H., Kiyonari, H., Michiue, T., et al. (2007). Ripply2 is essential for precise somite formation during mouse early development. FEBS Lett. 581, 2691-2696.
  • 74. Supp, D.M., Brueckner, M., Kuehn, M.R., Witte, D.P., Lowe, L.A., McGrath, J., Corrales, J., and Potter, S.S. (1999). Targeted deletion of the ATP binding domain of left-right dynein confirms its role in specifying development of left-right asymmetries. Development 126, 5495-5504.
  • 75. Tian, T., Zhao, L., Zhang, M., Zhao, X., and Meng, A. (2009). Both foxj1a and foxj1b are implicated in left-right asymmetric development in zebrafish embryos. Biochem. Biophys. Res. Commun. 380, 537-542.
  • 76. Wallmeier, J., Frank, D., Shoemark, A., Nothe-Menchen, T., Cindric, S., Olbrich, H., Loges, N.T., Aprea, I., Dougherty, G.W., Pennekamp, P., et al. (2019). De novo mutations in FOXJ1 result in a motile ciliopathy with hydrocephalus and randomization of left/right body asymmetry. Am. J. Hum. Genet. 105, 1030-1039.
  • 77. Pelletier, G.J., Brody, S.L., Liapis, H., White, R.A., and Hackett, B.P. (1998). A human forkhead/winged-helix transcription factor expressed in developing pulmonary and renal epithelium. Am. J. Physiol. 274, L351-L359.
  • 78. Lyerla,T.A., Rusiniak,M.E., Borchers,M., Jahreis,G.,Tan,J., Ohtake,P., Novak, E.K., and Swank, R.T. (2003). Aberrant lung structure, composition, and function in a murine model of Hermansky-Pudlak syndrome. Am. J. Physiol. Lung Cell. Mol. Physiol. 285, L643-L653.
  • 79. Hsu, Y.-C., Osinski, J., Campbell, C.E., Litwack, E.D., Wang, D., Liu, S., Bachurski, C.J., and Gronostajski, R.M. (2011). Mesenchymal nuclear factor I B regulates cell proliferation and epithelial differentiation during lung maturation. Dev. Biol. 354, 242-252.
  • 80. Mahlapuu, M., Enerback, S., and Carlsson, P. (2001). Haploinsufficiency of the forkhead gene Foxf1, a target for sonic hedgehog signaling,causes lung and foregut malformations. Development 128, 2397-2406.
  • 81. Zhang, Y., Rath, N., Hannenhalli, S., Wang, Z., Cappola, T., Kimura, S., Atochina-Vasserman, E., Lu, M.M., Beers, M.F., and Morrisey, E.E. (2007). GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo. Development 134, 189-198.
  • 82. Lee, J.H., Kim, T.S., Yang, T.H., Koo, B.K., Oh, S.P., Lee, K.P., Oh, H.J., Lee, S.H., Kong, Y.Y., Kim, J.M., et al. (2008). A crucial role of WW45 in developing epithelial tissues in the mouse. EMBO J. 27, 1231-1242.
  • 83. Yi, H., and Norell, M.A. (2015). The burrowing origin of modern snakes. Sci. Adv. 1, e1500743.
  • 84. Simoes, B.F., Sampaio, F.L., Jared, C., Antoniazzi, M.M., Loew, E.R., Bowmaker, J.K., Rodriguez, A., Hart, N.S., Hunt, D.M., Partridge, J.C., et al. (2015). Visual system evolution and the nature of the ancestral snake. J. Evol. Biol. 28, 1309-1320.
  • 85. Senn, D.G., and Northcutt, R.G. (1973). The forebrain and midbrain of some squamates and their bearing on the origin of snakes. J. Morphol. 140, 135-151.
  • 86. Caprette,C.L., Lee, M.S.Y., Shine, R., Mokany,A., and Downhower, J.F. (2004). The origin of snakes (Serpentes) as seen through eye anatomy. Biol. J. Linn. Soc. 81, 469-482.
  • 87. Harada, T., Harada, C., Watanabe, M., Inoue, Y., Sakagawa, T., Nakayama, N., Sasaki, S., Okuyama, S., Watase, K., Wada, K., et al. (1998). Functions of the two glutamate transporters GLAST and GLT-1 in the retina. Proc. Natl. Acad. Sci. USA 95, 4663-4666.
  • 88. Gaudet, P., Livstone, M.S., Lewis, S.E., and Thomas, P.D. (2011). Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief. Bioinform. 12, 449-462.
  • 89. Veleri, S., Manjunath, S.H., Fariss, R.N., May-Simera, H., Brooks, M., Foskett, T.A., Gao, C., Longo, T.A., Liu, P., Nagashima, K., et al. (2014). Ciliopathy-associated gene Cc2d2a promotes assembly of subdistal appendages on the mother centriole during cilia biogenesis. Nat. Commun. 5, 4207.
  • 90. Lee, S., Lee, D.-K., Dou, Y., Lee, J., Lee, B., Kwak, E., Kong, Y.-Y., Lee, S.-K., Roeder, R.G., and Lee, J.W. (2006). Coactivator as a target gene specificity determinant for histone H3 lysine 4 methyltransferases. Proc. Natl. Acad. Sci. USA 103, 15392-15397.
  • 91. Fettiplace, R. (1987).Electrical tuning of hair cells in the inner ear.Trends Neurosci. 10, 421-425.
  • 92. Manley,G.A.(2002).Evolution of structure and function of the hearing organ of lizards. J. Neurobiol. 53, 202-211.
  • 93. Christensen, C.B., Christensen-Dalsgaard, J., Brandt, C., and Madsen, P.T. (2012). Hearing with an atympanic ear: good vibration and poor sound-pressure detection in the royal python, Python regius. J. Exp. Biol. 215, 331-342.
  • 94. Miller, M.R. (1978). Scanning electron microscope studies of the papilla basilaris of some turtles and snakes. Am. J. Anat. 151, 409-435.
  • 95. Miller, M.R., and Beck, J. (1990). Further serial transmission electron microscopy studies of auditory hair cell innervation in lizards and in a snake. Am. J. Anat. 188, 175-184.
  • 96. Delprat,B., Boulanger, A., Wang, J., Beaudoin,V., Guitton,M.J., Venteo, S., Dechesne, C.J., Pujol, R., Lavigne-Rebillard, M., Puel, J.-L., et al. (2002). Downregulation of otospiralin, a novel inner ear protein, causes hair cell degeneration and deafness. J. Neurosci. 22, 1718-1725.
  • 97. Zou, J., Zheng, T., Ren, C., Askew, C., Liu, X.-P., Pan, B., Holt, J.R., Wang, Y., and Yang, J. (2014). Deletion of PDZD7 disrupts the Usher syndrome type 2 protein complex in cochlear hair cells and causes hearing loss in mice. Hum. Mol. Genet. 23, 2374-2390.
  • 98. Sajan, S.A., Rubenstein, J.L.R., Warchol, M.E., and Lovett, M. (2011). Identification of direct downstream targets of Dlx5 during early inner ear development. Hum. Mol. Genet. 20, 1262-1273.
  • 99. Tasaki,T.,Sohr,R., Xia,Z., Hellweg,R., Hortnagl,H., Varshavsky,A., and Kwon, Y.T. (2007).Biochemical and genetic studies of UBR3,a ubiquitin ligase with a function in olfactory and other sensory systems. J. Biol. Chem. 282, 18510-18520.
  • 100. Kroll, J.C. (1973). Taste buds in the oral epithelium of the blind snake, Leptotyphlops dulcis (Reptilia: Leptotyphlopidae). Southwest. Nat. 17, 365-370.
  • 101. Emerling,C.A.(2017).Genomic regression of claw keratin,taste receptor and light-associated genes provides insights into biology and evolutionary origins of snakes. Mol. Phylogenet. Evol. 115, 40-49.
  • 102. Kley, N.J. (2006). Morphology of the lower jaw and suspensorium in the Texas blindsnake, Leptotyphlops dulcis (Scolecophidia: Leptotyphlopidae). J. Morphol. 267, 494-515.
  • 103. Gehlbach, F.R., Watkins, J.F., and Kroll, J.C. (1971). Pheromone trail-following studies of typhlopid, leptotyphlopid, and colubrid snakes. Behaviour 40, 282-294.
  • 104. Nguyen-Ba-Charvet,K.T., Plump,A.S., Tessier-Lavigne, M., and Chedotal,A.(2002).Slit1 and slit2 proteins control the development of the lateral olfactory tract. J. Neurosci. 22, 5473-5480.
  • 105. Boot, R.G.,Blommaart,E.F., Swart,E., Ghauharali-van der Vlugt, K., Bijl, N., Moe, C., Place, A., and Aerts, J.M. (2001). Identification of a novel acidic mammalian chitinase distinct from chitotriosidase. J. Biol. Chem. 276, 6770-6778.
  • 106. Hartl, D., He, C.H., Koller, B., Da Silva, C.A., Homer, R., Lee, C.G., and Elias, J.A. (2008). Acidic mammalian chitinase is secreted via an ADAM17/epidermal growth factor receptor-dependent pathway and stimulates chemokine production by pulmonary epithelial cells. J. Biol. Chem. 283, 33472-33482.
  • 107. Janiak, M.C., Chaney, M.E., and Tosi, A.J. (2018). Evolution of acidic mammalian chitinase genes (CHIA) is related to body mass and insectivory in primates. Mol. Biol. Evol. 35, 607-622.
  • 108. Tabata, E., Itoigawa, A., Koinuma, T., Tayama, H., Kashimura, A., Sakaguchi, M., Matoska, V., Bauer, P.O., and Oyama, F. (2022). Noninsectbased diet leads to structural and functional changes of acidic chitinase in carnivora. Mol. Biol. Evol. 39, msab331.
  • 109. Gracheva, E.O., Ingolia, N.T., Kelly, Y.M., Cordero-Morales, J.F., Hollopeter, G., Chesler, A.T., Sanchez, E.E., Perez, J.C., Weissman, J.S., and Julius, D. (2010). Molecular basis of infrared detection by snakes. Nature 464, 1006-1011.
  • 110. Foltz, I.N., Gerl, R.E., Wieler, J.S., Luckach, M., Salmon, R.A., and Schrader, J.W. (1998). Human mitogen-activated protein kinase kinase 7 (MKK7) is a highly conserved c-Jun N-terminal kinase/stress-activated protein kinase (JNK/SAPK) activated by environmental stresses and physiological stimuli. J. Biol. Chem. 273, 9344-9351.
  • 111. Sun, Y., Dykes, I.M., Liang, X., Eng, S.R., Evans, S.M., and Turner, E.E. (2008). A central role for Islet1 in sensory neuron development linking sensory and spinal gene regulatory programs. Nat. Neurosci. 11, 1283-1293.
  • 112. Okamoto, Y., Pehlivan, D., Wiszniewski, W., Beck, C.R., Snipes, G.J., Lupski, J.R., and Khajavi, M. (2013). Curcumin facilitates a transitory cellular stress response in trembler-J mice. Hum. Mol. Genet. 22, 4698-4705.
  • 113. Kumbasar, A., Plachez, C., Gronostajski, R.M., Richards, L.J., and Litwack, E.D.(2009).Absence of the transcription factor Nfib delays the formation of the basilar pontine and other mossy fiber nuclei.J. Comp.Neurol. 513, 98-112.
  • 114. Kajitani, R., Toshimoto, K., Noguchi, H., Toyoda, A., Ogura, Y., Okuno, M., Yabana, M., Harada, M., Nagayasu, E., Maruyama, H., et al. (2014). Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res. 24, 1384-1395.
  • 115. Mcglothlin, J.W., Chuckalovcak, J.P., Janes, D.E., Edwards, S.V., Feldman, C.R., Brodie, E.D., Pfrender, M.E., and Brodie,E.D. (2014). Parallel evolution of tetrodotoxin resistance in three voltage-gated sodium channel genes in the garter snake Thamnophis sirtalis. Mol. Biol. Evol. 31, 2836-2846.
  • 116. Tang, C.-Y., Zhang, X., Xu, X., Sun, S., Peng, C., Song, M.-H., Yan, C., Sun, H., Liu, M., Xie, L., et al. (2023). Genetic mapping and molecular mechanism behind color variation in the Asian vine snake. Genome Biol. 24, 46.
  • 117. Aird, S.D., Arora, J., Barua, A., Qiu, L., Terada, K., and Mikheyev, A.S. (2017). Population genomic analysis of a pitviper reveals microevolutionary forces underlying venom chemistry. Genome Biol. Evol. 9, 2640-2649.
  • 118. Zhang, Z.-Y., Lv, Y., Wu, W., Yan, C., Tang,C.-Y., Peng, C., and Li, J.-T. (2022). The structural and functional divergence of a neglected threefinger toxin subfamily in lethal elapids. Cell Rep. 40, 111079.
  • 119. Wang, Z., Peng, C., Wu,W., Yan,C., Lv,Y., and Li, J.-T. (2023).Developmental regulation of conserved non-coding element evolution provides insights into limb loss in squamates. Sci. China Life Sci. https://doi.org/ 10.1007/s11427-023-2362-5.
  • 120. Andrade,P., Pinho,C., Perez i de Lanuza,G., Afonso,S., Brejcha,J., Rubin, C.-J., Wallerman, O., Pereira, P., Sabatino, S.J., Bellati, A., et al. (2019). Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard. Proc. Natl. Acad. Sci. USA 116, 5633-5642.
  • 121. Alfoldi, J., Di Palma, F.D., Grabherr, M., Williams, C., Kong, L., Mauceli, E., Russell, P., Lowe, C.B., Glor, R.E., Jaffe, J.D., et al. (2011). The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477, 587-591.
  • 122. Yan, C., Zhang, Z.-Y., Lv, Y., Wang, Z., Jiang, K., and Li, J.-T. (2022). Genome of Laudakia sacra provides new insights into high-altitude adaptation of ectotherms. Int. J. Mol. Sci. 23, 10081.
  • 123. Mellough, C.B., Bauer, R., Collin, J., Dorgau, B., Zerti,D., Dolan, D.W.P., Jones,C.M., Izuogu, O.G., Yu, M., Hallam,D., et al. (2019).An integrated transcriptional analysis of the developing human retina. Development 146, dev169474.
  • 124. Chen, S., Zhou, Y., Chen, Y., and Gu, J. (2018).fastp: an ultra-fast all-inone FASTQ preprocessor. Bioinformatics 34, i884-i890.
  • 125. Marcais, G., and Kingsford, C. (2011). A fast, lock-free approach for efficient parallel counting of occurrences of k- mers. Bioinformatics 27, 764-770.
  • 126. Liu, B., Shi, Y., Yuan, J., Hu,X., Zhang, H., Li, N., Li, Z., Chen, Y., Mu, D., and Fan, W. (2013). Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects https://doi.org/10.48550/ arXiv.1308.2012.
  • 127. Vurture, G.W., Sedlazeck, F.J., Nattestad, M., Underwood, C.J., Fang, H., Gurtowski, J., and Schatz, M.C. (2017). GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202-2204.
  • 128. Ye, C., Hill, C.M., Wu, S., Ruan, J., and Ma, Z.S. (2016). DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies. Sci.Rep. 6, 31900. https://doi.org/ 10.1038/srep31900.
  • 129. Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Meth. 9, 357-359.
  • 130. Li, H., and Durbin, R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595.
  • 131. Hu, J., Wang,Z., Sun,Z., Hu, B., Ayoola,A.O., Liang,F., Li, J., Sandoval, J.R., Cooper, D.N., Ye, K., et al. (2023). An efficient error correction and accurate assembly tool for noisy long reads https://doi.org/10.1101/ 2023.03.09.531669.
  • 132. Hu, J., Fan, J., Sun, Z., and Liu, S. (2020).NextPolish:a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36, 2253-2255.
  • 133. Ruan, J., and Li, H. (2020). Fast and accurate long-read assembly with wtdbg2. Nat. Meth. 17, 155-158.
  • 134. Servant,N., Varoquaux,N.,Lajoie,B.R.,Viara,E.,Chen,C.-J.,Vert,J.-P., Heard, E., Dekker, J., and Barillot, E. (2015). HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259.
  • 135. Durand, N.C., Shamim, M.S., Machol, I., Rao, S.S.P., Huntley, M.H., Lander, E.S., and Aiden, E.L. (2016). Juicer provides a one-click system for analyzing loop-resolution Hi-C Experiments. Cell. Syst. 3, 95-98.
  • 136. Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., et al. (2017).De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92-95.
  • 137. Burton, J.N., Adey, A., Patwardhan, R.P., Qiu, R., Kitzman, J.O., and Shendure, J. (2013). Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119-1125.
  • 138. Simao, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V., and Zdobnov, E.M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210-3212.
  • 139. Flynn, J.M., Hubley, R., Goubert, C., Rosen, J., Clark, A.G., Feschotte, C., and Smit, A.F. (2020). RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl. Acad. Sci. USA 117, 9451-9457.
  • 140. Tarailo-Graovac, M., and Chen, N. (2009). Chapter 4. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics Chapter 4, 4.10.1-4.10.14.
  • 141. Stanke, M., Diekhans, M., Baertsch, R., and Haussler, D. (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24, 637-644.
  • 142. Keilwagen, J., Wenk, M., Erickson, J.L., Schattat, M.H., Grau, J., and Hartung, F. (2016). Using intron position conservation for homology-based gene prediction. Nucleic Acids Res. 44, e89.
  • 143. Kovaka, S., Zimin, A.V., Pertea, G.M., Razaghi, R., Salzberg, S.L., and Pertea, M. (2019). Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol. 20, 278.
  • 144. Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., and Gingeras, T.R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21.
  • 145. Haas, B.J., Salzberg, S.L., Zhu, W., Pertea, M., Allen, J.E., Orvis, J., White, O., Buell, C.R., and Wortman, J.R. (2008). Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7.
  • 146. Tang,S., Lomsadze,A.,and Borodovsky,M. (2015). Identification of protein coding regions in RNA transcripts. Nucleic Acids Res. 43, e78.
  • 147. Urasaki, N., Takagi, H., Natsume, S., Uemura, A., Taniai, N., Miyagi, N., Fukushima, M., Suzuki, S., Tarora, K., Tamaki, M., et al. (2017). Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions. DNA Res. 24, 51-58.
  • 148. Zhang,Z., Schwartz,S., Wagner,L., and Miller,W. (2000).A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7, 203-214.
  • 149. Kim,J., Farre, M., Auvil,L., Capitanu,B., Larkin,D.M., Ma,J., and Lewin, H.A. (2017). Reconstruction and evolutionary history of eutherian chromosomes. Proc. Natl. Acad. Sci. USA 114, E5379-E5388.
  • 150. Krzywinski, M., Schein,J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J., and Marra, M.A. (2009). Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645.
  • 151. Emms, D.M., and Kelly, S. (2015). OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 157.
  • 152. Quinlan, A.R., and Hall, I.M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842.
  • 153. Chen,T., Liu,Y.-X., and Huang,L. (2022).ImageGP:an easy-to-use data visualization web server for scientific researchers. iMeta 1, e5.
  • 154. Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag).
  • 155. Capella-Gutierrez, S., Silla-Martinez, J.M., and Gabaldon, T. (2009). trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972-1973.
  • 156. Nguyen, L.-T., Schmidt, H.A., von Haeseler, A., and Minh, B.Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268-274.
  • 157. Loytynoja,A., and Goldman,N. (2008).Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320, 1632-1635.
  • 158. Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591.
  • 159. Sayyari, E., Whitfield, J.B., and Mirarab, S. (2018). DiscoVista: interpretable visualizations of gene tree discordance.Mol. Phylogenet. Evol. 122, 110-115.
  • 160. Beckstette, M., Homann, R., Giegerich, R., and Kurtz, S. (2006). Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics 7, 389.
  • 161. Kim, D., Langmead, B., and Salzberg, S.L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nat. Meth. 12, 357-360.
  • 162. Langfelder, P., and Horvath, S. (2008). WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559.
  • 163. Supek, F., Boห˜snjak, M., ห˜Skunca, N., and ห˜Smuc, T. (2011). REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One 6, e21800.
  • 164. Hiller, M., Schaar, B.T., Indjeian, V.B., Kingsley, D.M., Hagey, L.R., and Bejerano, G. (2012). A ''forward genomics'' approach links genotype to phenotype using independent phenotypic losses among related species. Cell. Rep. 2, 817-823.
  • 165. Li, B., and Dewey, C.N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323.
  • 166. Choi,Y., Sims, G.E., Murphy, S., Miller,J.R., and Chan, A.P. (2012).Predicting the functional effect of amino acid substitutions and indels. PLoS One 7, e46688.
  • 167. Li, B., Fillmore, N., Bai, Y., Collins, M., Thomson, J.A., Stewart, R., and Dewey, C.N. (2014). Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biol. 15, 553.
  • 168. Love, M.I., Huber, W., and Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550.
  • 169. Robinson, M.D., McCarthy, D.J., and Smyth, G.K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140.
  • 170. Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644-652.
  • 171. Li, W., and Godzik, A. (2006). Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.Bioinformatics 22, 1658-1659.
  • 172. Kosakovsky Pond, S.L., Poon, A.F.Y., Velazquez, R.V., Weaver, S., Hepler, N.L., Murrell, B., Shank, S.D., Magalis, B.R., Bouvier, D., Nekrutenko, A., et al. (2020). HyPhy 2.5-A customizable platform for evolutionary hypothesis testing using phylogenies. Mol. Biol. Evol. 37, 295-299.
  • 173. Burbrink, F.T., Grazziotin, F.G., Pyron, P.A., Cundall, D., Donnellan, S., Frances, I., Keogh, J.S., Kraus, F., Murphy, R.W., Noonan, N., et al. (2019). Interrogating genomic-scale data for Squamata (Lizards,Snakes, and Amphisbaenians) shows no support for key traditional morphological relationships. Syst. Biol. 69, 502-520.
  • 174. Chen, H., Rangasamy, M., Tan, S.Y., Wang, H., and Siegfried, B.D. (2010). Evaluation of five methods for total DNA extraction from western corn rootworm beetles. PLoS One 5, e11963.
  • 175. Liu, Z., Zhang, L., Yan, Z., Ren, Z., Han, F., Tan, X., Xiang, Z., Dong, F., Yang, Z., Liu, G., et al. (2020). Genomic mechanisms of physiological and morphological adaptations of limestone langurs to karst habitats. Mol. Biol. Evol. 37, 952-968.
  • 176. Zoonomia Consortium (2020). A comparative genomics multitool for scientific discovery and conservation. Nature 587, 240-245.
  • 177. McLean, C.Y., Bristor, D., Hiller, M., Clarke, S.L., Schaar, B.T., Lowe, C.B., Wenger,A.M.,and Bejerano,G.(2010).GREAT improves functional interpretation of cis- regulatory regions. Nat. Biotechnol. 28, 495-501.
  • 178. Hoang, D.T.,Chernomor,O., von Haeseler,A.,Minh, B.Q., and Vinh,L.S. (2018). UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518-522.
  • 179. Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A., and Jermiin, L.S. (2017). ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Meth. 14, 587-589.
  • 180. Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., ห˜Ziยด dek, A., Potapenko, A., et al. (2021). Highly accurate protein structure prediction with AlphaFold. Nature 596, 583-589.
  • 181. Zheng,R., Wan,C., Mei,S., Qin,Q., Wu,Q., Sun,H., Chen,C.-H., Brown, M., Zhang, X., Meyer, C.A., et al. (2019). Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Res. 47, D729-D735.
  • 182. Castillo-Davis, C.I., Kondrashov, F.A., Hartl, D.L., and Kulathinal, R.J. (2004). The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. Genome Res. 14, 802-811.
  • 183. Kosakovsky Pond,S.L.,Frost,S.D.W., and Muse,S.V.(2005).HyPhy:hypothesis testing using phylogenies 21, 676-679.
  • 184. Eisenberg, E., and Levanon, E.Y. (2013). Human housekeeping genes, revisited. Trends Genet. 29, 569-574.
  • 185. Ebert,J. (2008).Infrared sense in snakes:behavioural and anatomical examinations (Crotalus atrox, Python regius, Corallus hortulanus). Doctoral (Rheinische Friedrich Wilhelms Univ. Bonn.).