Abstract
Air-breathing has evolved independently serval times with a variety of air-breathing organs (ABOs) in fish. The physiology of the air-breathing in bimodal respiration fish has been well understood, while studies on molecular mechanisms of the character are very limited. In the present study, we first determined the gill indexes of 110 fish species including 25 and 85 kinds of bimodal respiration fishes and non-air-breathing fishes, respectively. Then combined with histological observations of gills and ABOs/non-ABOs in three bimodal respiration fishes and two non-air breathing fishes, we found that the bimodal respiration fish was always of a degeneration gill and a well-vascularized ABO. Meanwhile, a comparative transcriptome analysis of posterior intestines, namely a well vascularized ABO in Misgurnus anguillicaudatus and a non-ABO in Leptobotia elongata, was performed to expound molecular variations of the air-breathing character. A total of 5,003 orthologous genes were identified. Among them, 1,189 orthologous genes were differentially expressed, which were enriched in 14 KEGG pathways. More specially, the expressions of hemoglobin genes and various HIF/VEGF signaling pathway genes were obviously upregulated in the ABO of M. anguillicaudatus. Moreover, we found that HIF-1α, VEGFAa, and MAP2K1 were co-expressed dramatically higher in ABOs of bimodal respiration fishes than those of non-ABOs of non-air-breathing fishes. These results indicated that the HIF/VEGF pathway played an important role in ABO angiogenesis/formation to promote fish to do aerial respiration. This study will contribute to our understanding of molecular mechanisms of air-breathing in fish.
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References
Abhinand CS, Raju R, Soumya SJ, Arya PS, Sudhakaran PR (2016) VEGF-A/VEGFR2 signaling network in endothelial cells relevant to angiogenesis. J Cell Commun Signal 10:347–354. https://doi.org/10.1007/s12079-016-0352-8
Brauner CJ, Rombough PJ (2012) Ontogeny and paleophysiology of the gill: new insights from larval and air-breathing fish. Respir Physiol Neurobiol 184:293–300. https://doi.org/10.1016/j.resp.2012.07.011
Chen X, Kong W, Yu Y, Dong S, Huang Z, Yu W, Xu J, Luo YZ, Wang QC, Xu Z (2018) Molecular characterization and expression analysis of interleukin 15 (IL15) and interleukin-15 receptor subunit alpha (IL15Rα) in dojo loach (Misgurnus anguillicaudatus): their salient roles during bacterial, parasitic and fungal infection. Mol Immunol 103:293–305. https://doi.org/10.1016/j.molimm.2018.10.012
Chen Y, Zhao B, Zhu Y, Zhao H, Ma C (2019) HIF-1-VEGF-Notch mediates angiogenesis in temporomandibular joint osteoarthritis. Am J Transl Res 11:2969–2982
Coates CJ, Decker H (2017) Immunological properties of oxygen-transport proteins: hemoglobin, hemocyanin and hemerythrin. Cell Mol Life Sci 74:293–317. https://doi.org/10.1007/s00018-016-2326-7
Damsgaard C, Baliga VB, Bates E, Burggren W, McKenzie DJ, Taylor E, Wright PA (2020) Evolutionary and cardio-respiratory physiology of air-breathing and amphibious fishes. Acta Physiol 228:e13406. https://doi.org/10.1111/apha.13406
De BG, Wood CM, Iftikar FI, Matey V, Scott GR, Sloman KA, Silva M, Almeida-Val VM, Val AL (2013) Interactions between hypoxia tolerance and food deprivation in Amazonian oscars, Astronotus ocellatus. J Exp Biol 216:4590–4600. https://doi.org/10.1242/jeb.082891
Deng YY, Li JQ, Wu SF, Zhu YP, Chen YW, He FC (2006) Integrated nr database in protein annotation system and its localization. Comput Eng 32:71–74
Dunn CW, Howison M, Zapata F (2013) Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14:330. https://doi.org/10.1186/1471-2105-14-330
Duong TY, Tan MH, Lee YP, Croft L, Austin CM (2020) Dataset for genome sequencing and de novo assembly of the Vietnamese bighead catfish (Clarias macrocephalus Günther, 1864). Data Brief 31:105861. https://doi.org/10.1016/j.dib.2020.105861
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340
Ernst J, Bar-Joseph Z (2006) STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics 7:191. https://doi.org/10.1186/1471-2105-7-191
Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugan D, Roos DS, Stoeckert CJ (2011) Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinformatics 35:1–19. https://doi.org/10.1002/0471250953.bi0612s35
Galperin MY, Wolf YI, Makarova KS, Vera Alvarez R, Landsman D, Koonin EV (2021) COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res 49:D274–D281. https://doi.org/10.1093/nar/gkaa1018
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raycgowdhury R, Zeng Q, Chen ZH, Mauceli E, Hacohen N, Gnirke A, Palma F, Birren B, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full length transcriptome assembly from RNA Seq data without a reference genome. Nature Biotechnol 129:644–652. https://doi.org/10.1038/nbt.1883
Graham JB, Lee HJ (2004) Breathing air in air: In what ways might extant amphibious fish biology relate to prevailing concepts about early tetrapods, the evolution of vertebrate air breathing, and the vertebrate land transition? Physiol Biochem Zool 77:720–731. https://doi.org/10.1086/425184
Haas B, Papanicolaou A, Yassour M, Grabherr M, Blood P, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protoc 8:1494–1512. https://doi.org/10.1038/nprot.2013.084
Huang SQ, Cao XJ, Tian X (2016) Transcriptomic analysis of compromise between air-breathing and nutrient uptake of posterior intestine in loach (Misgurnus anguillicaudatus), an air-breathing fish. Mar Biotechnol 18:521–533. https://doi.org/10.1007/s10126-016-9713-9
Huang Z, Yu Y, Dong S, Yin Y, Wang Q, Yu W, Luo Y, Xu J, Zhang LQ, Yu YZ, Ai TS, Xu Z (2019) Major histocompatibility complex class IIA and IIB genes of loach (Misgurnus anguillicaudatus): molecular cloning and expression analysis in response to bacterial and parasitic challenge. Aquaculture 500:359–369. https://doi.org/10.1016/j.aquaculture.2018.10.043
Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, O'Donovan C (2015) The GOA database: gene Ontology annotation updates for 2015. Nucleic Acids Res 43:D1057–D1063. https://doi.org/10.1093/nar/gku1113
Ip YK, Chew SF (2018) Air-breathing and excretory nitrogen metabolism in fishes. Acta Histochemica 120:680–690. https://doi.org/10.1016/j.acthis.2018.08.013
Ishimatus A (2012) Evolution of the cardiorespiratory system in air-breathing fishes. Auqa-Bioscience Monographs 5:1–28. https://doi.org/10.5047/absm.2012.00501.0001
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45:D353–D361. https://doi.org/10.1093/nar/gkw1092
Klopfenstein DV, Zhang L, Pedersen BS, Ramírez F, Warwick VA, Naldi A, Mungall CJ, Yunes JM, Botvinnik O, Weigel M, Dampier W, Dessimoz C, Flick P, Tang H (2018) GOATOOLS: A Python library for Gene Ontology analyses. Sci Rep 8:10872. https://doi.org/10.1038/s41598-018-28948-z
Lefevre S, Wang T, Bayley M (2014) Air-breathing fishes in aquaculture: what can we learn from physiology? J Fish Biol 84:705–731. https://doi.org/10.1111/jfb.1230
Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323. https://doi.org/10.1186/1471-2105-12-323
Li N, Bao L, Zhou T, Yuan Z, Liu S, Dunham R, Li Y, Wang K, Xu XY, Jin Y, Zeng QF, Gao S, Fu Q, Liu Y, Yang YJ, Li Q, Meyer A, Gao DY, Liu ZJ (2018) Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation. BMC Genomics 19:952. https://doi.org/10.1186/s12864-018-5355-9
Luo WW, Cao XJ, Huang SQ, Liu CS, Tomljanovic T (2016) Developmental transcriptome analysis and identification of genes involved in formation of intestinal air-breathing function of Dojo loach, Misgurnus anguillicaudatus. Sci Rep 6:31845. https://doi.org/10.1038/srep31845
Luo Y, Yu W, Yu Y, Dong S, Yin Y, Huang ZY, Wan X, Zhang LQ, Yu YZ, Ai T, Wang QC, Xu Z (2019) Molecular characterization and expression analysis of T cell receptor (TCR) γ and δ genes in dojo loach (Misgurnus anguillicaudatus) in response to bacterial, parasitic and fungal challenge. Fish Shellfish Immunol 86:641–652. https://doi.org/10.1016/j.fsi.2018.11.045
Ma X, Su B, Bangs M, Alston V, Backenstose NJC, Simora RM, Wang W, Xing D, Li SJ, Ye Z, Moss AG, Duong TY, Wang X, Dunham R (2020) Comparative genomic and transcriptomic analyses revealed twenty-six candidate genes involved in the air-breathing development and function of the bighead catfish Clarias macrocephalus. Mar Biotechnol 28. https://doi.org/10.1007/s10126-020-10005-4
Maina JN (2018) Functional morphology of the respiratory organs of the air-breathing fish with particular emphasis on the African catfishes, Clarias mossambicus and C. gariepinus. Acta Histochem 120:613–622. https://doi.org/10.1016/j.acthis.2018.08.007
Martin KL (2014) Theme and variations: amphibious air-breathing intertidal fishes. J Fish Biol 84:557–602. https://doi.org/10.1111/jfb.12270
Mélanie E, Géraldine S, Mariana C, Kevin M, Monique A, Franck L, Florent S (2008) Hypoxia-induced apelin expression regulates endothelial cell proliferation and regenerative angiogenesis. Circ Res 103:432–440. https://doi.org/10.1161/CIRCRESAHA.108.179333
Milsom WK (2012) New insights into gill chemoreception: receptor distribution and roles in water and air breathing fish. Respir Physiol Neurobiol 184:326–339. https://doi.org/10.1016/j.resp.2012.07.013
Pelster B, Wood CM, Braz-Mota S, Val AL (2020) Gills and air-breathing organ in O2 uptake, CO2 excretion, N-waste excretion, and ionoregulation in small and large pirarucu (Arapaima gigas). J Comp Physiol B 190:569–583. https://doi.org/10.1007/s00360-020-01286-1
Robinson MD, Mccarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139. https://doi.org/10.1093/bioinformatics/btp616
Salinas I (2015) The mucosal immune system of teleost fish. Biology 4:525–539. https://doi.org/10.3390/biology4030525
Sayer MDJ (2005) Adaptations of amphibious fish for surviving life out of water. Fish Fisheries 6:186–211
Schindelin J, Rueden CT, Hiner MC, Eliceiri KW (2015) The ImageJ ecosystem: an open platform for biomedical image analysis. Mol Reprod Dev 82:518–529. https://doi.org/10.1002/mrd.22489
Schmittgen TD, Livak KJ (2018) Analyzing real-time PCR data by the comparative CT method. Nat Protoc 3:1101–1108. https://doi.org/10.1038/nprot.2008.73
Stamatakis A (2004) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. https://doi.org/10.1093/bioinformatics/btu033
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Baren MJ, Salzberg S, Wold B, Pachter L (2010) Transcript assembly and quantification by RNA Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnol 28:511–515. https://doi.org/10.1038/nbt.1621
UniProt C (2021) UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res 49:D480–D489. https://doi.org/10.1093/nar/gkaa1100
Wood CM, Pelster B, Giacomin M, Sadauskas-Henrique H, Almeida-Val VM, Val AL (2016) The transition from water-breathing to air-breathing is associated with a shift in ion uptake from gills to gut: a study of two closely related erythrinid teleosts, Hoplerythrinus unitaeniatus and Hoplias malabaricus. J Comp Physiol B 186:431–445. https://doi.org/10.1007/s00360-016-0965-5
Wright PA, Turko AJ (2016) Amphibious fishes: evolution and phenotypic plasticity. J Exp Biol 219:2245–2259. https://doi.org/10.1242/jeb.126649
Wright PA, Wood CM (2012) Seven things fish know about ammonia and we don’t. Respir Physiol Neurobiol 184:231–240. https://doi.org/10.1016/j.resp.2012.07.003
Xiao W (2015) The hypoxia signaling pathway and hypoxic adaptation in fishes. Sci China Life Sci 58:148–155. https://doi.org/10.1007/s11427-015-4801-z
Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li CY, Wei LP (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39:W316–W322. https://doi.org/10.1093/nar/gkr483
Zaccone G, Lauriano ER, Capillo G, Kuciel M (2018) Air- breathing in fish: air-breathing organs and control of respiration nerves and neurotransmitters in the air-breathing organs and the skin. Acta Histochem 120:630–641. https://doi.org/10.1016/j.acthis.2018.08.009
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The raw data of comparative transcriptomic analysis are deposited in the NCBI SRA database under accession nos. from SRR12466335 to SRR12466340.
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This study was supported by the Fundamental Research Funds for the Central Universities (2662020SCPY002), the National Natural Science Foundation of China (31702015), and the National College Students Innovation and Entrepreneurship Training Program of China (202010504066).
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Songqian Huang: writing of the paper (B), performance of research (C), and data analysis (D); Lijuan Yang: C and D; Li Zhang: B and C: Bing Sun: B and C; Jian Gao: B and C; Zijian Chen: B and D; Lei Zhong: research design (A) and C; Xiaojuan Cao: A, C, and D.
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Huang, S., Yang, L., Zhang, L. et al. Endogenic upregulations of HIF/VEGF signaling pathway genes promote air breathing organ angiogenesis in bimodal respiration fish. Funct Integr Genomics 22, 65–76 (2022). https://doi.org/10.1007/s10142-021-00822-8
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DOI: https://doi.org/10.1007/s10142-021-00822-8