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In Silico Analysis: Genome-Wide Identification, Characterization and Evolutionary Adaptations of Bone Morphogenetic Protein (BMP) Gene Family in Homo sapiens

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Abstract

We systematically analyzed BMP gene family in H. sapiens to elucidate genetic structure, phylogenetic relationships, adaptive evolution and tissue-specific expression pattern. Total of 13 BMPs genes were identified in the H. sapiens genome. Bone morphogenetic proteins (BMPs) are composed of a variable number of exons ranging from 2 to 21. They exhibit a molecular weight ranging from 31,081.81 to 82,899.61 Da. These proteins possess hydrophilic characteristics, display thermostability, and exhibit a pH range from acidic to basic. We identified four segmental and two tandem duplication events in BMP gene family of H. sapiens. All of the vertebrate species that were studied show the presence of BMPs 1, 2, 3, 4, 5, 6, 7, 8A, and 15, however only Homo sapiens demonstrated the presence of BMP9 and BMP11. The pathway and process enrichment analysis of BMPs genes showed that these were considerably enriched in positive regulation of pathway-restricted SMAD protein phosphorylation (92%) and cartilage development (77%) biological processes. These genes exhibited positive selection signals that were shown to be conserved across vertebrate lineages. The results showed that BMP2/3/5/6/8a/15 proteins underwent adaptive selection at many amino acid locations and increased positive selection was detected in TGF-β propeptide and TGF-β super family domains which were involved in dorso-ventral patterning, limb bud development. More over the expression pattern of BMP genes revealed that BMP1 and BMP5; BMP4 and BMP6 exhibited substantially identical expression patterns in all tissues while BMP10, BMP15, and BMP3 showed tissue-specific expression.

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References

  1. Abrams, K. L., Xu, J., Nativelle-Serpentini, C., Dabirshahsahebi, S., & Rogers, M. B. (2004). An evolutionary and molecular analysis of Bmp2 expression. Journal of Biological Chemistry, 279(16), 15916–15928. https://doi.org/10.1074/jbc.M313531200

    Article  CAS  PubMed  Google Scholar 

  2. Adiba, M., Das, T., Paul, A., Das, A., Chakraborty, S., Hosen, M. I., & Nabi, A. H. M. N. (2021). In silico characterization of coding and non-coding SNPs of the androgen receptor gene. Informatics in Medicine Unlocked, 24, 100556. https://doi.org/10.1016/j.imu.2021.100556

    Article  Google Scholar 

  3. Ahmad, H. I., Zhou, J., Ahmad, M. J., Afzal, G., Jiang, H., Zhang, X., Elokil, A. A., Khan, M. A., Li, L., Li, H., **, L., & Chen, J. (2020). Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates. Aging, 12(4), 3516–3557. https://doi.org/10.18632/aging.102827

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Al-Amrani, S., Al-Jabri, Z., Al-Zaabi, A., Alshekaili, J., & Al-Khabori, M. (2021). Proteomics: Concepts and applications in human medicine. World Journal of Biological Chemistry, 12(5), 57–69. https://doi.org/10.4331/wjbc.v12.i5.57

    Article  PubMed  PubMed Central  Google Scholar 

  5. Asharani, P. V., Keupp, K., Semler, O., Wang, W., Li, Y., Thiele, H., Yigit, G., Pohl, E., Becker, J., Frommolt, P., Sonntag, C., Altmüller, J., Zimmermann, K., Greenspan, D. S., Akarsu, N. A., Netzer, C., Schönau, E., Wirth, R., Hammerschmidt, M., …, Carney, T. J. (2012). Attenuated BMP1 function compromises osteogenesis, leading to bone fragility in humans and zebrafish. The American Journal of Human Genetics, 90(4), 661–674. https://doi.org/10.1016/j.ajhg.2012.02.026

  6. Ashkenazy, H., Abadi, S., Martz, E., Chay, O., Mayrose, I., Pupko, T., & Ben-Tal, N. (2016). ConSurf 2016: An improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Research, 44(W1), W344-350. https://doi.org/10.1093/nar/gkw408

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Bailey, T. L., Johnson, J., Grant, C. E., & Noble, W. S. (2015). The MEME suite. Nucleic Acids Research, 43(W1), W39-49. https://doi.org/10.1093/nar/gkv416

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Baker, F. N., & Porollo, A. (2016). CoeViz: A web-based tool for coevolution analysis of protein residues. BMC Bioinformatics, 17(1), 119. https://doi.org/10.1186/s12859-016-0975-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Baker, F. N., & Porollo, A. (2018). CoeViz: A web-based integrative platform for interactive visualization of large similarity and distance matrices. Data, 3(1), 4.

    Article  PubMed  PubMed Central  Google Scholar 

  10. Bal, Z., & Kushioka, J. (2020). BMP and TGFβ use and release in bone regeneration. Turkish Journal of Medical Sciences, 50(2), 1707–1722. https://doi.org/10.3906/sag-2003-127

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Canty-Laird, E., Carré, G.-A., Mandon-Pépin, B., Kadler, K. E., & Fabre, S. (2010). First evidence of bone morphogenetic protein 1 expression and activity in sheep ovarian follicles1. Biology of Reproduction, 83(1), 138–146. https://doi.org/10.1095/biolreprod.109.082115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Cao, X., & Chen, D. (2005). The BMP signaling and in vivo bone formation. Gene, 357(1), 1–8. https://doi.org/10.1016/j.gene.2005.06.017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Cecchi, S., Bennet, S. J., & Arora, M. (2016). Bone morphogenetic protein-7: Review of signalling and efficacy in fracture healing. Journal of Orthopaedic Translation, 4, 28–34. https://doi.org/10.1016/j.jot.2015.08.001

    Article  PubMed  Google Scholar 

  14. Chatzou, M., Magis, C., Chang, J.-M., Kemena, C., Bussotti, G., Erb, I., & Notredame, C. (2015). Multiple sequence alignment modeling: Methods and applications. Briefings in Bioinformatics, 17(6), 1009–1023. https://doi.org/10.1093/bib/bbv099

    Article  CAS  PubMed  Google Scholar 

  15. Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., & **a, R. (2020). TBtools: An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 13(8), 1194–1202. https://doi.org/10.1016/j.molp.2020.06.009

    Article  CAS  PubMed  Google Scholar 

  16. Chen, G., Xu, H., Yao, Y., Xu, T., Yuan, M., Zhang, X., Lv, Z., & Wu, M. (2020). BMP signaling in the development and regeneration of cranium bones and maintenance of calvarial stem cells. Frontiers in Cell and Developmental Biology, 8, 135. https://doi.org/10.3389/fcell.2020.00135

    Article  PubMed  PubMed Central  Google Scholar 

  17. Corcoran, D., Maltbie, N., Sudalairaj, S., Baker, F. N., Hirschfeld, J., & Porollo, A. (2021). CoeViz 2: Protein graphs derived from amino acid covariance. Frontiers in Bioinformatics. https://doi.org/10.3389/fbinf.2021.653681

    Article  PubMed  PubMed Central  Google Scholar 

  18. Cui, G., Feng, S., Yan, Y., Wang, L., He, X., Li, X., Duan, Y., Chen, J., Tang, K., Zheng, P., Tam, P. P. L., Si, W., **g, N., & Peng, G. (2022). Spatial and molecular anatomy of germ layers in the gastrulating Cynomolgus monkey embryo. bioRxiv, 2022.2001.2026.474719. https://doi.org/10.1101/2022.01.26.474719

  19. Dathe, K., Kjaer, K. W., Brehm, A., Meinecke, P., Nürnberg, P., Neto, J. C., Brunoni, D., Tommerup, N., Ott, C. E., Klopocki, E., Seemann, P., & Mundlos, S. (2009). Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2. The American Journal of Human Genetics, 84(4), 483–492. https://doi.org/10.1016/j.ajhg.2009.03.001

    Article  CAS  PubMed  Google Scholar 

  20. Del Amparo, R., Branco, C., Arenas, J., Vicens, A., & Arenas, M. (2021). Analysis of selection in protein-coding sequences accounting for common biases. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbaa431

    Article  PubMed  Google Scholar 

  21. Delolme, F., Anastasi, C., Alcaraz, L. B., Mendoza, V., Vadon-Le Goff, S., Talantikite, M., Capomaccio, R., Mevaere, J., Fortin, L., Mazzocut, D., Damour, O., Zanella-Cléon, I., Hulmes, D. J. S., Overall, C. M., Valcourt, U., Lopez-Casillas, F., & Moali, C. (2015). Proteolytic control of TGF-β co-receptor activity by BMP-1/tolloid-like proteases revealed by quantitative iTRAQ proteomics. Cellular and Molecular Life Sciences, 72(5), 1009–1027. https://doi.org/10.1007/s00018-014-1733-x

    Article  CAS  PubMed  Google Scholar 

  22. Delport, W., Poon, A. F. Y., Frost, S. D. W., & Kosakovsky Pond, S. L. (2010). Datamonkey 2010: A suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics, 26(19), 2455–2457. https://doi.org/10.1093/bioinformatics/btq429

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Deng, Z. H., Li, Y. S., Gao, X., Lei, G. H., & Huard, J. (2018). Bone morphogenetic proteins for articular cartilage regeneration. Osteoarthritis and Cartilage, 26(9), 1153–1161. https://doi.org/10.1016/j.joca.2018.03.007

    Article  CAS  PubMed  Google Scholar 

  24. Ducy, P., & Karsenty, G. (2000). The family of bone morphogenetic proteins. Kidney International, 57(6), 2207–2214. https://doi.org/10.1046/j.1523-1755.2000.00081.x

    Article  CAS  PubMed  Google Scholar 

  25. Ehata, S., & Miyazono, K. (2022). Bone morphogenetic protein signaling in cancer; some topics in the recent 10 years. Frontiers in Cell and Developmental Biology, 10, 883523. https://doi.org/10.3389/fcell.2022.883523

    Article  PubMed  PubMed Central  Google Scholar 

  26. Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., & Bairoch, A. (2003). ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31(13), 3784–3788. https://doi.org/10.1093/nar/gkg563

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S. E., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In J. M. Walker (Ed.), The proteomics protocols handbook (pp. 571–607). Humana Press.

    Chapter  Google Scholar 

  28. Ge, G., & Greenspan, D. S. (2006). BMP1 controls TGFbeta1 activation via cleavage of latent TGFbeta-binding protein. Journal of Cell Biology, 175(1), 111–120. https://doi.org/10.1083/jcb.200606058

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Gipson, G. R., Goebel, E. J., Hart, K. N., Kappes, E. C., Kattamuri, C., McCoy, J. C., & Thompson, T. B. (2020). Structural perspective of BMP ligands and signaling. Bone, 140, 115549. https://doi.org/10.1016/j.bone.2020.115549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Graham, S. J. L., Wicher, K. B., Jedrusik, A., Guo, G., Herath, W., Robson, P., & Zernicka-Goetz, M. (2014). BMP signalling regulates the pre-implantation development of extra-embryonic cell lineages in the mouse embryo. Nature Communications, 5(1), 5667. https://doi.org/10.1038/ncomms6667

    Article  CAS  PubMed  Google Scholar 

  31. Guha, U., Gomes, W. A., Kobayashi, T., Pestell, R. G., & Kessler, J. A. (2002). In vivo evidence that BMP signaling is necessary for apoptosis in the mouse limb. Developmental Biology, 249(1), 108–120. https://doi.org/10.1006/dbio.2002.0752

    Article  CAS  PubMed  Google Scholar 

  32. Guo, A. Y., Zhu, Q. H., Chen, X., & Luo, J. C. (2007). GSDS: A gene structure display server. Yi Chuan, 29(8), 1023–1026.

    Article  CAS  PubMed  Google Scholar 

  33. Hall, B. G. (2013). Building phylogenetic trees from molecular data with MEGA. Molecular Biology and Evolution, 30(5), 1229–1235. https://doi.org/10.1093/molbev/mst012

    Article  CAS  PubMed  Google Scholar 

  34. Hoffmann, A., & Gross, G. (2001). BMP signaling pathways in cartilage and bone formation. Critical Reviews in Eukaryotic Gene Expression, 11(1–3), 23–45.

    CAS  PubMed  Google Scholar 

  35. Hopkins, D. R., Keles, S., & Greenspan, D. S. (2007). The bone morphogenetic protein 1/Tolloid-like metalloproteinases. Matrix Biology, 26(7), 508–523. https://doi.org/10.1016/j.matbio.2007.05.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Hu, B., **, J., Guo, A. Y., Zhang, H., Luo, J., & Gao, G. (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31(8), 1296–1297. https://doi.org/10.1093/bioinformatics/btu817

    Article  PubMed  Google Scholar 

  37. Huang, Y., & Umulis, D. M. (2019). Scale invariance of BMP signaling gradients in zebrafish. Scientific Reports, 9(1), 5440. https://doi.org/10.1038/s41598-019-41840-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Jha, K., & Saha, S. (2020). Amalgamation of 3D structure and sequence information for protein–protein interaction prediction. Scientific Reports, 10(1), 19171. https://doi.org/10.1038/s41598-020-75467-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. John, M., Kim, K.-J., Bae, S. D. W., Qiao, L., & George, J. (2019). Role of BMP-9 in human liver disease. Gut, 68(11), 2097. https://doi.org/10.1136/gutjnl-2018-317543

    Article  CAS  PubMed  Google Scholar 

  40. Katagiri, T., & Watabe, T. (2016). Bone morphogenetic proteins. Cold Spring Harbor Perspectives in Biology, 8(6), a021899. https://doi.org/10.1101/cshperspect.a021899

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Kokabu, S., & Rosen, V. (2018). BMP3 expression by osteoblast lineage cells is regulated by canonical Wnt signaling. FEBS Open Bio, 8(2), 168–176. https://doi.org/10.1002/2211-5463.12347

    Article  CAS  PubMed  Google Scholar 

  42. Lademann, F., Hofbauer, L. C., & Rauner, M. (2020). The bone morphogenetic protein pathway: The osteoclastic perspective. Frontiers in Cell and Developmental Biology, 8, 586031. https://doi.org/10.3389/fcell.2020.586031

    Article  PubMed  PubMed Central  Google Scholar 

  43. Lei, L., Zhu, J., Chen, C., Wang, Y., Wu, C., Qi, M., Wang, Y., Liu, X., Hong, X., Yu, L., Chen, H., Wei, C., Liu, Y., Li, W., & Zhu, X. (2023). Genome-wide identification, evolution and expression analysis of bone morphogenetic protein (BMP) gene family in Chinese soft-shell turtle (Pelodiscus sinensis). Frontires in Genetics. https://doi.org/10.3389/fgene.2023.1109478

    Article  Google Scholar 

  44. Letunic, I., & Bork, P. (2021). Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Research, 49(W1), W293-w296. https://doi.org/10.1093/nar/gkab301

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Li, Y., Lv, X., Wang, S., Cao, X., Yuan, Z., Getachew, T., Mwacharo, J. M., Haile, A., & Sun, W. (2022). BMP7 functions to regulate proliferation of dermal papilla cells in Hu sheep. Genes, 13(2), 201.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Liu, M., Goldman, G., MacDougall, M., & Chen, S. (2022). BMP signaling pathway in dentin development and diseases. Cells. https://doi.org/10.3390/cells11142216

    Article  PubMed  PubMed Central  Google Scholar 

  47. Liu, F., Hata, A., Baker, J. C., Doody, J., Cárcamo, J., Harland, R. M., & Massagué, J. (1996). A human Mad protein acting as a BMP-regulated transcriptional activator. Nature, 381(6583), 620–623. https://doi.org/10.1038/381620a0

  48. Liu, X., Liu, F., Xu, H., Yang, Y., Wang, Y., Hong, X., Li, W., Yu, L., Chen, C., Xu, H., & Zhu, X. (2022). Characterization of the in vitro cultured ovarian cells in the Asian Yellow Pond Turtle (Mauremys mutica). Biology (Basel), 11(10), 1404. https://doi.org/10.3390/biology11101404

    Article  CAS  PubMed  Google Scholar 

  49. Lochab, A. K., & Extavour, C. G. (2017). Bone morphogenetic protein (BMP) signaling in animal reproductive system development and function. Developmental Biology, 427(2), 258–269. https://doi.org/10.1016/j.ydbio.2017.03.002

    Article  CAS  PubMed  Google Scholar 

  50. Ma, Y., Liu, Y., & Cheng, J. (2018). Protein secondary structure prediction based on data partition and semi-random subspace method. Scientific Reports, 8(1), 9856. https://doi.org/10.1038/s41598-018-28084-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Ma, Y., **ao, Y., **ao, Z., Wu, Y., Zhao, H., Gao, G., Wu, L., Wang, T., Zhao, N., & Li, J. (2022). Genome-wide identification, characterization and expression analysis of the BMP family associated with beak-like teeth in Oplegnathus. Front Genet, 13, 938473. https://doi.org/10.3389/fgene.2022.938473

  52. Madende, M., & Osthoff, G. (2019). Comparative genomics of casein genes. Journal of Dairy Research, 86(3), 323–330. https://doi.org/10.1017/s0022029919000414

    Article  CAS  PubMed  Google Scholar 

  53. Manzari-Tavakoli, A., Babajani, A., Farjoo, M. H., Ha**asrollah, M., Bahrami, S., & Niknejad, H. (2022). The cross-talks among bone morphogenetic protein (BMP) signaling and other prominent pathways involved in neural differentiation. Frontiers in Molecular Neuroscience, 15, 827275. https://doi.org/10.3389/fnmol.2022.827275

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Mao, L., Yano, M., Kawao, N., Tamura, Y., Okada, K., & Kaji, H. (2013). Role of matrix metalloproteinase-10 in the BMP-2 inducing osteoblastic differentiation. Endocrine Journal, 60(12), 1309–1319. https://doi.org/10.1507/endocrj.ej13-0270

    Article  CAS  PubMed  Google Scholar 

  55. Marchler-Bauer, A., Derbyshire, M. K., Gonzales, N. R., Lu, S., Chitsaz, F., Geer, L. Y., Geer, R. C., He, J., Gwadz, M., Hurwitz, D. I., Lanczycki, C. J., Lu, F., Marchler, G. H., Song, J. S., Thanki, N., Wang, Z., Yamashita, R. A., Zhang, D., Zheng, C., & Bryant, S. H. (2015). CDD: NCBI’s conserved domain database. Nucleic Acids Research, 43(Database issue), D222–D226. https://doi.org/10.1093/nar/gku1221

    Article  CAS  PubMed  Google Scholar 

  56. Morgan, C. C., & Hart, M. W. (2019). Molecular evolution of mammalian genes with epistatic interactions in fertilization. BMC Evolutionary Biology, 19(1), 154. https://doi.org/10.1186/s12862-019-1480-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Asharani, P. V., Keupp, K., Semler, O., Wang, W., Li, Y., Thiele, H., Yigit, G., Pohl, E., Becker, J., Frommolt, P., Sonntag, C., Altmüller, J., Zimmermann, K., Greenspan, D. S., Akarsu, N. A., Netzer, C., Schönau, E., Wirth, R., Hammerschmidt, M., …, Carney, T. J. (2012). Attenuated BMP1 function compromises osteogenesis, leading to bone fragility in humans and zebrafish. The American Journal of Human Genetics, 90, 661–674. doi: https://doi.org/10.1016/j.ajhg.2012.02.026

  58. Pertea, M., Kim, D., Pertea, G. M., Leek, J. T., & Salzberg, S. L. (2016). Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols, 11(9), 1650–1667. https://doi.org/10.1038/nprot.2016.095

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Pham, H. G., Mukherjee, S., Choi, M. J., & Yun, J. W. (2021). BMP11 regulates thermogenesis in white and brown adipocytes. Cell Biochemistry and Function, 39(4), 496–510. https://doi.org/10.1002/cbf.3615

    Article  CAS  PubMed  Google Scholar 

  60. Qu, X., Liu, Y., & Cao, D. (2019). BMP10 preserves cardiac function through its dual activation of SMAD-mediated and STAT3-mediated pathways. Journal of Biological Chemistry, 294(52), 19877–19888. https://doi.org/10.1074/jbc.RA119.010943

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Sangsin, A., Kuptanon, C., Srichomthong, C., Pongpanich, M., Suphapeetiporn, K., & Shotelersuk, V. (2017). Two novel compound heterozygous BMP1 mutations in a patient with osteogenesis imperfecta: A case report. BMC Medical Genetics, 18(1), 25. https://doi.org/10.1186/s12881-017-0384-9

    Article  PubMed  PubMed Central  Google Scholar 

  62. Shah, T. A., Zhu, Y., Shaikh, N. N., Harris, M. A., Harris, S. E., & Rogers, M. B. (2017). Characterization of new bone morphogenetic protein (Bmp)-2 regulatory alleles. Genesis, 55(7), e23035. https://doi.org/10.1002/dvg.23035

    Article  CAS  Google Scholar 

  63. Smith, M. D., Wertheim, J. O., Weaver, S., Murrell, B., Scheffler, K., & Kosakovsky Pond, S. L. (2015). Less is more: An adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Molecular Biology and Evolution, 32(5), 1342–1353. https://doi.org/10.1093/molbev/msv022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Su, Z., He, L., Shang, H., Dai, T., Xu, F., & Zhao, J. (2020). Overexpression of bone morphogenetic protein-1 promotes osteogenesis of bone marrow mesenchymal stem cells in vitro. Medical Science Monitor, 26, e920122. https://doi.org/10.12659/msm.920122

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A. L., Fang, T., Doncheva, N. T., Pyysalo, S., Bork, P., Jensen, L. J., & von Mering, C. (2022). The STRING database in 2023: Protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research, 51(D1), D638–D646. https://doi.org/10.1093/nar/gkac1000

    Article  CAS  PubMed Central  Google Scholar 

  66. Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Thakur, V., & Kumar, P. (2018). Analysis of hepatitis E virus (HEV) X-domain structural model. Bioinformation, 14, 398–403. https://doi.org/10.6026/97320630014398

    Article  Google Scholar 

  68. von Bubnoff, A., Peiffer, D. A., Blitz, I. L., Hayata, T., Ogata, S., Zeng, Q., Trunnell, M., & Cho, K. W. Y. (2005). Phylogenetic footprinting and genome scanning identify vertebrate BMP response elements and new target genes. Developmental Biology, 281(2), 210–226. https://doi.org/10.1016/j.ydbio.2005.02.014

    Article  CAS  Google Scholar 

  69. Wang, R. N., Green, J., Wang, Z., Deng, Y., Qiao, M., Peabody, M., Zhang, Q., Ye, J., Yan, Z., Denduluri, S., Idowu, O., Li, M., Shen, C., Hu, A., Haydon, R. C., Kang, R., Mok, J., Lee, M. J., Luu, H. L., & Shi, L. L. (2014). Bone morphogenetic protein (BMP) signaling in development and human diseases. Genes & Diseases, 1(1), 87–105. https://doi.org/10.1016/j.gendis.2014.07.005

    Article  Google Scholar 

  70. Weaver, S., Shank, S., Spielman, S., Li, M., Muse, S., & Pond, S. (2018). Datamonkey 2.0: A modern web application for characterizing selective and other evolutionary processes. Molecular Biology and Evolution, 35, 773–777. https://doi.org/10.1093/molbev/msx335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Wei, Z., Salmon, R. M., Upton, P. D., Morrell, N. W., & Li, W. (2014). Regulation of bone morphogenetic protein 9 (BMP9) by redox-dependent proteolysis. Journal of Biological Chemistry, 289(45), 31150–31159. https://doi.org/10.1074/jbc.M114.579771

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Wu, X., Gong, Q., Chen, Y., Liu, Y., Song, M., Li, F., Li, P., & Lai, J. (2022). Full-length transcriptome and analysis of bmp-related genes in Platypharodon extremus. Heliyon, 8(10), e10783. https://doi.org/10.1016/j.heliyon.2022.e10783

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Xu, J., & Rogers, M. B. (2007). Modulation of bone morphogenetic protein (BMP) 2 gene expression by Sp1 transcription factors. Gene, 392(1–2), 221–229. https://doi.org/10.1016/j.gene.2006.12.032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Xu, S., Zhang, S., Zhang, W., Liu, H., Wang, M., Zhong, L., Bian, W., & Chen, X. (2022). Genome-wide identification, phylogeny, and expression profile of the Dmrt (doublesex and Mab-3 related transcription factor) gene family in channel catfish (Ictalurus punctatus). Frontiers in Genetics, 13, 891204. https://doi.org/10.3389/fgene.2022.891204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Xu, X., Lv, F., Song, Y., Li, L., Asan, Wei, X., Zhao, X., Jiang, Y., Wang, O., **ng, X., **a, W., & Li, M. (2019). Novel mutations in BMP1 induce a rare type of osteogenesis imperfecta. Clinica Chimica Acta, 489, 21–28. https://doi.org/10.1016/j.cca.2018.11.004

    Article  CAS  Google Scholar 

  76. Yan, Y., & Wang, Q. (2021). BMP signaling: Lighting up the way for embryonic dorsoventral patterning. Frontiers in Cell and Developmental Biology, 9, 799772. https://doi.org/10.3389/fcell.2021.799772

    Article  PubMed  PubMed Central  Google Scholar 

  77. Yang, D., Yang, X., Dai, F., Wang, Y., Yang, Y., Hu, M., & Cheng, Y. (2021). The role of bone morphogenetic protein 4 in ovarian function and diseases. Reproductive Sciences, 28(12), 3316–3330. https://doi.org/10.1007/s43032-021-00600-8

    Article  PubMed  Google Scholar 

  78. You, J., Wang, W., Chang, H.-M., Yi, Y., Zhao, H., Zhu, H., Sun, Y., Tang, M., Wang, C., Sang, Y., Feng, G., Cheng, S., Leung, P. C. K., & Zhu, Y.-M. (2021). The BMP2 signaling axis promotes invasive differentiation of human trophoblasts. Frontiers in Cell and Developmental Biology. https://doi.org/10.3389/fcell.2021.607332

    Article  PubMed  PubMed Central  Google Scholar 

  79. Yu, H., Wang, Y., Wang, M., Liu, Y., Cheng, J., & Zhang, Q. (2020). Growth differentiation factor 9 (gdf9) and bone morphogenetic protein 15 (bmp15) are potential intraovarian regulators of steroidogenesis in Japanese flounder (Paralichthys olivaceus). General and Comparative Endocrinology, 297, 113547. https://doi.org/10.1016/j.ygcen.2020.113547

    Article  CAS  PubMed  Google Scholar 

  80. Zhang, C., Wang, W., & Wang, D. (2022). Genome-wide identification and characterization of the WRKY gene family in Scutellaria baicalensis Georgi under diverse abiotic stress. International Journal of Molecular Sciences, 23(8), 4225. https://doi.org/10.3390/ijms23084225

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Zhang, C., Xu, X., Xu, X., Li, Y., Zhao, P., Chen, X., Shen, X., Zhang, Z., Chen, Y., Liu, S., Xu, X., Yuling, L., Lai, Z., & Lai, Z. (2022). Genome-wide identification, evolution analysis of cytochrome P450 monooxygenase multigene family and their expression patterns during the early somatic embryogenesis in Dimocarpus longan Lour. Gene, 826, 146453. https://doi.org/10.1016/j.gene.2022.146453

    Article  CAS  PubMed  Google Scholar 

  82. Zhang, H., Zhang, W., Bai, G., Gao, L., & Li, K. (2021). Bone morphogenetic protein-7 (BMP-7) promotes neuronal differentiation of bone marrow mesenchymal stem cells (BMSCs) in vitro. BioMed Research International, 2021, 7239783. https://doi.org/10.1155/2021/7239783

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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  1. Zainab Riaz, Muhammad Hussain and Saba Saeed contributed equally.

Authors and Affiliations

  1. Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan

    Zainab Riaz, Shakeela Parveen, Mehwish Sultana, Saba Saeed, Urwah Ishaque & Zunaira Faiz

  2. Department of Veterinary and Animal Sciences, University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan

    Muhammad Hussain

  3. Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Punjab, Pakistan

    Shakeela Parveen

  4. Institue of Zoology, University of the Punjab, Lahore, Punjab, Pakistan

    Saba Saeed

  5. Department of Zoology, Government College University Faisalabad, Faisalabad, Punjab, Pakistan

    Muhammad Tayyab

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Contributions

ZR: Conceptualization, Data Analysis, original draft writing; MH: Investigation, original draft writing; SP: Investigation, Supervision, Review and editing; MS: Investigation, original draft writing; SS: Original draft writing, Review and editing; UI: Original draft writing, ZF: Original draft writing, MT: Original draft writing; Investigation.

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Riaz, Z., Hussain, M., Parveen, S. et al. In Silico Analysis: Genome-Wide Identification, Characterization and Evolutionary Adaptations of Bone Morphogenetic Protein (BMP) Gene Family in Homo sapiens. Mol Biotechnol (2023). https://doi.org/10.1007/s12033-023-00944-3

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