- -

De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages

RiuNet: Institutional repository of the Polithecnic University of Valencia

Share/Send to

Cited by

Statistics

De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages

Show full item record

Rozenfeld, C.; Blanca Postigo, JM.; Gallego Albiach, V.; García-Carpintero, V.; Herranz-Jusdado, JG.; Pérez Igualada, LM.; Asturiano, JF.... (2019). De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages. PLoS ONE. 14(6):1-25. https://doi.org/10.1371/journal.pone.0218085

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/160081

Files in this item

Item Metadata

Title: De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages
Author: Rozenfeld, Christoffer Blanca Postigo, José Miguel Gallego Albiach, Victor García-Carpintero, Víctor Herranz-Jusdado, Juan Germán Pérez Igualada, Luz María Asturiano, Juan F. Cañizares Sales, Joaquín Peñaranda, D.S.
UPV Unit: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia
Universitat Politècnica de València. Instituto de Ciencia y Tecnología Animal - Institut de Ciència i Tecnologia Animal
Universitat Politècnica de València. Departamento de Ciencia Animal - Departament de Ciència Animal
Issued date:
Abstract:
[EN] Paralogues pairs are more frequently observed in eels (Anguilla sp.) than in other teleosts. The paralogues often show low phylogenetic distances; however, they have been assigned to the third round of whole genome ...[+]
Copyrigths: Reconocimiento (by)
Source:
PLoS ONE. (issn: 1932-6203 )
DOI: 10.1371/journal.pone.0218085
Publisher:
Public Library of Science
Publisher version: https://doi.org/10.1371/journal.pone.0218085
Project ID:
info:eu-repo/grantAgreement/EC/H2020/642893/EU/Improved production strategies for endangered freshwater species./
info:eu-repo/grantAgreement/MINECO//AGL2013-41646-R/ES/LA ANGUILA EUROPEA COMO MODELO PARA ESTUDIAR LA TEMPERATURA COMO MODULADOR DE LA MADURACION SEXUAL EN TELEOSTEOS. POTENCIAL APLICACION EN ACUICULTURA./
info:eu-repo/grantAgreement/AEI//IJCI-2017-34200/ES/AYUDAS JUAN DE LA CIERVA INCORPORACION/
Thanks:
This study received funding from the project REPRO-TEMP (AGL2013-41646-R) funded by the Spanish Ministry of Economy and Competitiveness, and from the European Union's Horizon 2020 research and innovation program under the ...[+]
Type: Artículo

References

Gu, X., Wang, Y., & Gu, J. (2002). Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nature Genetics, 31(2), 205-209. doi:10.1038/ng902

Cañestro, C., Albalat, R., Irimia, M., & Garcia-Fernàndez, J. (2013). Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates. Seminars in Cell & Developmental Biology, 24(2), 83-94. doi:10.1016/j.semcdb.2012.12.008

Llorente, B., Malpertuy, A., Neuvéglise, C., de Montigny, J., Aigle, M., Artiguenave, F., … Dujon, B. (2000). Genomic Exploration of the Hemiascomycetous Yeasts: 18. Comparative analysis of chromosome maps and synteny withSaccharomyces cerevisiae. FEBS Letters, 487(1), 101-112. doi:10.1016/s0014-5793(00)02289-4 [+]
Gu, X., Wang, Y., & Gu, J. (2002). Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nature Genetics, 31(2), 205-209. doi:10.1038/ng902

Cañestro, C., Albalat, R., Irimia, M., & Garcia-Fernàndez, J. (2013). Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates. Seminars in Cell & Developmental Biology, 24(2), 83-94. doi:10.1016/j.semcdb.2012.12.008

Llorente, B., Malpertuy, A., Neuvéglise, C., de Montigny, J., Aigle, M., Artiguenave, F., … Dujon, B. (2000). Genomic Exploration of the Hemiascomycetous Yeasts: 18. Comparative analysis of chromosome maps and synteny withSaccharomyces cerevisiae. FEBS Letters, 487(1), 101-112. doi:10.1016/s0014-5793(00)02289-4

Colbourne, J. K., Pfrender, M. E., Gilbert, D., Thomas, W. K., Tucker, A., Oakley, T. H., … Basu, M. K. (2011). The Ecoresponsive Genome of Daphnia pulex. Science, 331(6017), 555-561. doi:10.1126/science.1197761

Bailey, J. A., Gu, Z., Clark, R. A., Reinert, K., Samonte, R. V., Schwartz, S., … Eichler, E. E. (2002). Recent Segmental Duplications in the Human Genome. Science, 297(5583), 1003-1007. doi:10.1126/science.1072047

Samonte, R. V., & Eichler, E. E. (2002). Segmental duplications and the evolution of the primate genome. Nature Reviews Genetics, 3(1), 65-72. doi:10.1038/nrg705

David, L. (2003). Recent Duplication of the Common Carp (Cyprinus carpio L.) Genome as Revealed by Analyses of Microsatellite Loci. Molecular Biology and Evolution, 20(9), 1425-1434. doi:10.1093/molbev/msg173

Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., … Bernot, A. (2004). Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature, 431(7011), 946-957. doi:10.1038/nature03025

Rondeau, E. B., Minkley, D. R., Leong, J. S., Messmer, A. M., Jantzen, J. R., von Schalburg, K. R., … Koop, B. F. (2014). The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei. PLoS ONE, 9(7), e102089. doi:10.1371/journal.pone.0102089

Albalat, R., & Cañestro, C. (2016). Evolution by gene loss. Nature Reviews Genetics, 17(7), 379-391. doi:10.1038/nrg.2016.39

Hafeez, M., Shabbir, M., Altaf, F., & Abbasi, A. A. (2016). Phylogenomic analysis reveals ancient segmental duplications in the human genome. Molecular Phylogenetics and Evolution, 94, 95-100. doi:10.1016/j.ympev.2015.08.019

Chain, F. J. J., Feulner, P. G. D., Panchal, M., Eizaguirre, C., Samonte, I. E., Kalbe, M., … Reusch, T. B. H. (2014). Extensive Copy-Number Variation of Young Genes across Stickleback Populations. PLoS Genetics, 10(12), e1004830. doi:10.1371/journal.pgen.1004830

MABLE, B. K. (2004). ‘Why polyploidy is rarer in animals than in plants’: myths and mechanisms. Biological Journal of the Linnean Society, 82(4), 453-466. doi:10.1111/j.1095-8312.2004.00332.x

Otto, S. P., & Whitton, J. (2000). POLYPLOID INCIDENCE AND EVOLUTION. Annual Review of Genetics, 34(1), 401-437. doi:10.1146/annurev.genet.34.1.401

Albertin, W., & Marullo, P. (2012). Polyploidy in fungi: evolution after whole-genome duplication. Proceedings of the Royal Society B: Biological Sciences, 279(1738), 2497-2509. doi:10.1098/rspb.2012.0434

Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., … Jackson, S. A. (2010). Genome sequence of the palaeopolyploid soybean. Nature, 463(7278), 178-183. doi:10.1038/nature08670

Del Pozo, J. C., & Ramirez-Parra, E. (2015). Whole genome duplications in plants: an overview fromArabidopsis. Journal of Experimental Botany, 66(22), 6991-7003. doi:10.1093/jxb/erv432

Soltis, D. E., Visger, C. J., & Soltis, P. S. (2014). The polyploidy revolution then...and now: Stebbins revisited. American Journal of Botany, 101(7), 1057-1078. doi:10.3732/ajb.1400178

Masterson, J. (1994). Stomatal Size in Fossil Plants: Evidence for Polyploidy in Majority of Angiosperms. Science, 264(5157), 421-424. doi:10.1126/science.264.5157.421

Parisod, C., Holderegger, R., & Brochmann, C. (2010). Evolutionary consequences of autopolyploidy. New Phytologist, 186(1), 5-17. doi:10.1111/j.1469-8137.2009.03142.x

Blanc, G., & Wolfe, K. H. (2004). Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes[W]. The Plant Cell, 16(7), 1667-1678. doi:10.1105/tpc.021345

Sémon, M., & Wolfe, K. H. (2007). Consequences of genome duplication. Current Opinion in Genetics & Development, 17(6), 505-512. doi:10.1016/j.gde.2007.09.007

Inoue, J., Sato, Y., Sinclair, R., Tsukamoto, K., & Nishida, M. (2015). Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling. Proceedings of the National Academy of Sciences, 112(48), 14918-14923. doi:10.1073/pnas.1507669112

Wolfe, K. H. (2001). Yesterday’s polyploids and the mystery of diploidization. Nature Reviews Genetics, 2(5), 333-341. doi:10.1038/35072009

Kassahn, K. S., Dang, V. T., Wilkins, S. J., Perkins, A. C., & Ragan, M. A. (2009). Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates. Genome Research, 19(8), 1404-1418. doi:10.1101/gr.086827.108

Wang, X., Jin, D., Wang, Z., Guo, H., Zhang, L., Wang, L., … Paterson, A. H. (2014). Telomere‐centric genome repatterning determines recurring chromosome number reductions during the evolution of eukaryotes. New Phytologist, 205(1), 378-389. doi:10.1111/nph.12985

Glasauer, S. M. K., & Neuhauss, S. C. F. (2014). Whole-genome duplication in teleost fishes and its evolutionary consequences. Molecular Genetics and Genomics, 289(6), 1045-1060. doi:10.1007/s00438-014-0889-2

Chester, M., Gallagher, J. P., Symonds, V. V., Cruz da Silva, A. V., Mavrodiev, E. V., Leitch, A. R., … Soltis, D. E. (2012). Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proceedings of the National Academy of Sciences, 109(4), 1176-1181. doi:10.1073/pnas.1112041109

Gordon, J. L., Byrne, K. P., & Wolfe, K. H. (2011). Mechanisms of Chromosome Number Evolution in Yeast. PLoS Genetics, 7(7), e1002190. doi:10.1371/journal.pgen.1002190

Dehal, P., & Boore, J. L. (2005). Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate. PLoS Biology, 3(10), e314. doi:10.1371/journal.pbio.0030314

Christoffels, A., Koh, E. G. L., Chia, J., Brenner, S., Aparicio, S., & Venkatesh, B. (2004). Fugu Genome Analysis Provides Evidence for a Whole-Genome Duplication Early During the Evolution of Ray-Finned Fishes. Molecular Biology and Evolution, 21(6), 1146-1151. doi:10.1093/molbev/msh114

Vandepoele, K., De Vos, W., Taylor, J. S., Meyer, A., & Van de Peer, Y. (2004). Major events in the genome evolution of vertebrates: Paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proceedings of the National Academy of Sciences, 101(6), 1638-1643. doi:10.1073/pnas.0307968100

Leggatt, R. A., & Iwama, G. K. (2003). Occurrence of polyploidy in the fishes. Reviews in Fish Biology and Fisheries, 13(3), 237-246. doi:10.1023/b:rfbf.0000033049.00668.fe

COMBER, S. C. L., & SMITH, C. (2004). Polyploidy in fishes: patterns and processes. Biological Journal of the Linnean Society, 82(4), 431-442. doi:10.1111/j.1095-8312.2004.00330.x

Braasch, I., Gehrke, A. R., Smith, J. J., Kawasaki, K., Manousaki, T., Pasquier, J., … Catchen, J. (2016). The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics, 48(4), 427-437. doi:10.1038/ng.3526

Bian, C., Hu, Y., Ravi, V., Kuznetsova, I. S., Shen, X., Mu, X., … Li, X. (2016). The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. Scientific Reports, 6(1). doi:10.1038/srep24501

Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M. P., Nome, T., … Davidson, W. S. (2016). The Atlantic salmon genome provides insights into rediploidization. Nature, 533(7602), 200-205. doi:10.1038/nature17164

Blischak, P. D., Mabry, M. E., Conant, G. C., & Pires, J. C. (2018). Integrating Networks, Phylogenomics, and Population Genomics for the Study of Polyploidy. Annual Review of Ecology, Evolution, and Systematics, 49(1), 253-278. doi:10.1146/annurev-ecolsys-121415-032302

Robertson, F. M., Gundappa, M. K., Grammes, F., Hvidsten, T. R., Redmond, A. K., Lien, S., … Macqueen, D. J. (2017). Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biology, 18(1). doi:10.1186/s13059-017-1241-z

DUFOUR, S., WELTZIEN, F.-A., SEBERT, M.-E., LE BELLE, N., VIDAL, B., VERNIER, P., & PASQUALINI, C. (2005). Dopaminergic Inhibition of Reproduction in Teleost Fishes: Ecophysiological and Evolutionary Implications. Annals of the New York Academy of Sciences, 1040(1), 9-21. doi:10.1196/annals.1327.002

Henkel, C. V., Burgerhout, E., de Wijze, D. L., Dirks, R. P., Minegishi, Y., Jansen, H. J., … van den Thillart, G. E. E. J. M. (2012). Primitive Duplicate Hox Clusters in the European Eel’s Genome. PLoS ONE, 7(2), e32231. doi:10.1371/journal.pone.0032231

Lafont, A.-G., Rousseau, K., Tomkiewicz, J., & Dufour, S. (2016). Three nuclear and two membrane estrogen receptors in basal teleosts, Anguilla sp.: Identification, evolutionary history and differential expression regulation. General and Comparative Endocrinology, 235, 177-191. doi:10.1016/j.ygcen.2015.11.021

Maugars, G., & Dufour, S. (2015). Demonstration of the Coexistence of Duplicated LH Receptors in Teleosts, and Their Origin in Ancestral Actinopterygians. PLOS ONE, 10(8), e0135184. doi:10.1371/journal.pone.0135184

Morini, M., Pasquier, J., Dirks, R., van den Thillart, G., Tomkiewicz, J., Rousseau, K., … Lafont, A.-G. (2015). Duplicated Leptin Receptors in Two Species of Eel Bring New Insights into the Evolution of the Leptin System in Vertebrates. PLOS ONE, 10(5), e0126008. doi:10.1371/journal.pone.0126008

Pasqualini, C., Weltzien, F.-A., Vidal, B., Baloche, S., Rouget, C., Gilles, N., … Dufour, S. (2009). Two Distinct Dopamine D2 Receptor Genes in the European Eel: Molecular Characterization, Tissue-Specific Transcription, and Regulation by Sex Steroids. Endocrinology, 150(3), 1377-1392. doi:10.1210/en.2008-0578

Pasquier, J., Lafont, A.-G., Jeng, S.-R., Morini, M., Dirks, R., van den Thillart, G., … Dufour, S. (2012). Multiple Kisspeptin Receptors in Early Osteichthyans Provide New Insights into the Evolution of This Receptor Family. PLoS ONE, 7(11), e48931. doi:10.1371/journal.pone.0048931

Rozenfeld, C., Butts, I. A. E., Tomkiewicz, J., Zambonino-Infante, J.-L., & Mazurais, D. (2016). Abundance of specific mRNA transcripts impacts hatching success in European eel, Anguilla anguilla L. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 191, 59-65. doi:10.1016/j.cbpa.2015.09.011

Morini, M., Peñaranda, D. S., Vílchez, M. C., Nourizadeh-Lillabadi, R., Lafont, A.-G., Dufour, S., … Pérez, L. (2017). Nuclear and membrane progestin receptors in the European eel: Characterization and expression in vivo through spermatogenesis. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 207, 79-92. doi:10.1016/j.cbpa.2017.02.009

Ravi, V., & Venkatesh, B. (2018). The Divergent Genomes of Teleosts. Annual Review of Animal Biosciences, 6(1), 47-68. doi:10.1146/annurev-animal-030117-014821

Peña-Llopis, S., & Brugarolas, J. (2013). Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications. Nature Protocols, 8(11), 2240-2255. doi:10.1038/nprot.2013.141

Andrews S. FastQC: A quality control tool for high throughput sequence data. 2010. p. http://www.bioinformatics.babraham.ac.uk/projects/

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120. doi:10.1093/bioinformatics/btu170

Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., … Regev, A. (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8(8), 1494-1512. doi:10.1038/nprot.2013.084

Howe, K., Clark, M. D., Torroja, C. F., Torrance, J., Berthelot, C., Muffato, M., … Matthews, L. (2013). The zebrafish reference genome sequence and its relationship to the human genome. Nature, 496(7446), 498-503. doi:10.1038/nature12111

Kai, W., Kikuchi, K., Tohari, S., Chew, A. K., Tay, A., Fujiwara, A., … Venkatesh, B. (2011). Integration of the Genetic Map and Genome Assembly of Fugu Facilitates Insights into Distinct Features of Genome Evolution in Teleosts and Mammals. Genome Biology and Evolution, 3, 424-442. doi:10.1093/gbe/evr041

Schartl, M., Walter, R. B., Shen, Y., Garcia, T., Catchen, J., Amores, A., … Warren, W. C. (2013). The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nature Genetics, 45(5), 567-572. doi:10.1038/ng.2604

Nomura, K., Fujiwara, A., Iwasaki, Y., Nishiki, I., Matsuura, A., Ozaki, A., … Tanaka, H. (2018). Genetic parameters and quantitative trait loci analysis associated with body size and timing at metamorphosis into glass eels in captive-bred Japanese eels (Anguilla japonica). PLOS ONE, 13(8), e0201784. doi:10.1371/journal.pone.0201784

Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31(19), 3210-3212. doi:10.1093/bioinformatics/btv351

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. doi:10.1038/nprot.2016.095

Li, H., & Durbin, R. (2010). Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics, 26(5), 589-595. doi:10.1093/bioinformatics/btp698

Li, L. (2003). OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Research, 13(9), 2178-2189. doi:10.1101/gr.1224503

Capella-Gutierrez, S., Silla-Martinez, J. M., & Gabaldon, T. (2009). trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25(15), 1972-1973. doi:10.1093/bioinformatics/btp348

Lartillot, N., Lepage, T., & Blanquart, S. (2009). PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics, 25(17), 2286-2288. doi:10.1093/bioinformatics/btp368

Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M. C., … Bork, P. (2015). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research, 44(D1), D286-D293. doi:10.1093/nar/gkv1248

Finn, R. D., Clements, J., & Eddy, S. R. (2011). HMMER web server: interactive sequence similarity searching. Nucleic Acids Research, 39(suppl), W29-W37. doi:10.1093/nar/gkr367

Alexa A, Rahnenfuhrer J. topGO: Enrichment analysis for gene ontology. 2016. p. R package version 2.29.0.

Kanehisa, M., Sato, Y., & Morishima, K. (2016). BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. Journal of Molecular Biology, 428(4), 726-731. doi:10.1016/j.jmb.2015.11.006

Burgerhout, E., Minegishi, Y., Brittijn, S. A., de Wijze, D. L., Henkel, C. V., Jansen, H. J., … van den Thillart, G. E. E. J. M. (2016). Changes in ovarian gene expression profiles and plasma hormone levels in maturing European eel ( Anguilla anguilla ); Biomarkers for broodstock selection. General and Comparative Endocrinology, 225, 185-196. doi:10.1016/j.ygcen.2015.08.006

Ager-Wick, E., Dirks, R. P., Burgerhout, E., Nourizadeh-Lillabadi, R., de Wijze, D. L., Spaink, H. P., … Henkel, C. V. (2013). The Pituitary Gland of the European Eel Reveals Massive Expression of Genes Involved in the Melanocortin System. PLoS ONE, 8(10), e77396. doi:10.1371/journal.pone.0077396

Minegishi, Y., Aoyama, J., Inoue, J. G., Miya, M., Nishida, M., & Tsukamoto, K. (2005). Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences. Molecular Phylogenetics and Evolution, 34(1), 134-146. doi:10.1016/j.ympev.2004.09.003

[-]

recommendations

 

This item appears in the following Collection(s)

Show full item record