Access the full text.
Sign up today, get DeepDyve free for 14 days.
S. Boissinot (2022)
On the Base Composition of Transposable ElementsInternational Journal of Molecular Sciences, 23
Anne-Marie Dion-Côté, S. Renaut, É. Normandeau, L. Bernatchez (2014)
RNA-seq reveals transcriptomic shock involving transposable elements reactivation in hybrids of young lake whitefish species.Molecular biology and evolution, 31 5
Veronika Borůvková, W. Howell, Dominik Matoulek, R. Symonová (2021)
Quantitative Approach to Fish Cytogenetics in the Context of Vertebrate Genome EvolutionGenes, 12
R. Arai (2011)
Fish karyotypes. A Checklist
Valerie Schneider, Tina Graves-Lindsay, K. Howe, Nathan Bouk, Hsiu-Chuan Chen, P. Kitts, T. Murphy, K. Pruitt, F. Thibaud-Nissen, Derek Albracht, R. Fulton, Milinn Kremitzki, V. Magrini, C. Markovic, S. McGrath, K. Steinberg, Katherine Auger, W. Chow, J. Collins, G. Harden, T. Hubbard, S. Pelan, J. Simpson, Glen Threadgold, J. Torrance, J. Wood, Laura Clarke, S. Koren, Matthew Boitano, P. Peluso, Heng Li, C. Chin, A. Phillippy, R. Durbin, R. Wilson, P. Flicek, E. Eichler, D. Church (2016)
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assemblyGenome Research, 27
S. Nurk, S. Koren, A. Rhie, M. Rautiainen, A. Bzikadze, Alla Mikheenko, Mitchell Vollger, N. Altemose, L. Uralsky, Ariel Gershman, S. Aganezov, Savannah Hoyt, M. Diekhans, Glennis Logsdon, Michael Alonge, S. Antonarakis, M. Borchers, G. Bouffard, Shelise Brooks, G. Caldas, Haoyu Cheng, Chen-Shan Chin, W. Chow, L. Lima, Philip Dishuck, R. Durbin, T. Dvorkina, Ian Fiddes, G. Formenti, R. Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick Grady, Tina Graves-Lindsay, Ira Hall, Nancy Hansen, Gabrielle Hartley, Marina Haukness, K. Howe, M. Hunkapiller, Chirag Jain, Miten Jain, E. Jarvis, Peter Kerpedjiev, Melanie Kirsche, M. Kolmogorov, J. Korlach, Milinn Kremitzki, Heng Li, V. Maduro, T. Marschall, Ann McCartney, Jennifer McDaniel, Danny Miller, Jim Mullikin, E. Myers, Nathan Olson, B. Paten, P. Peluso, P. Pevzner, David Porubsky, T. Potapova, E. Rogaev, J. Rosenfeld, S. Salzberg, Valerie Schneider, F. Sedlazeck, Kishwar Shafin, Colin Shew, Alaina Shumate, Y. Sims, A. Smit, D. Soto, Ivan Sovic, Jessica Storer, Aaron Streets, B. Sullivan, F. Thibaud-Nissen, J. Torrance, Justin Wagner, B. Walenz, A. Wenger, J. Wood, Chunlin Xiao, Stephanie Yan, Alice Young, Samantha Zarate, U. Surti, R. McCoy, M. Dennis, I. Alexandrov, J. Gerton, R. O’Neill, W. Timp, J. Zook, M. Schatz, E. Eichler, Karen Miga, A. Phillippy (2021)
The complete sequence of a human genomeScience (New York, N.Y.), 376
(2011)
Fish Karyotypes
D. Neafsey, S. Palumbi (2003)
Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes.Genome research, 13 5
M. Gaffaroğlu, Zuzana Majtánová, R. Symonová, Š. Pelikánová, S. Unal, Z. Lajbner, P. Ráb (2020)
Present and Future Salmonid CytogeneticsGenes, 11
Zuzana Majtánová, R. Symonová, L. Arias-Rodriguez, L. Sallan, P. Ráb (2017)
"Holostei versus Halecostomi" Problem: Insight from Cytogenetics of Ancient Nonteleost Actinopterygian Fish, Bowfin Amia calva.Journal of experimental zoology. Part B, Molecular and developmental evolution, 328 7
L. Bargelloni, M. Babbucci, S. Ferraresso, C. Papetti, N. Vitulo, R. Carraro, M. Pauletto, G. Santovito, M. Lucassen, F. C. Mark, L. Zane, T. Patarnello (2019)
Draft genome assembly and transcriptome data of the icefish Chionodraco myersi reveal the key role of mitochondria for a life without hemoglobin at subzero temperatures, 2
Dominik Matoulek, Veronika Borůvková, K. Ocalewicz, R. Symonová (2020)
GC and Repeats Profiling along Chromosomes—The Future of Fish Compositional CytogenomicsGenes, 12
G. Lu, Mingkun Luo (2020)
Genomes of major fishes in world fisheries and aquaculture: Status, application and perspectiveAquaculture and Fisheries, 5
R. Symonová, Zuzana Majtánová, L. Arias-Rodriguez, Libor Mořkovský, T. Kořínková, L. Cavin, M. Pokorná, Marie Doležálková, M. Flajšhans, É. Normandeau, P. Ráb, A. Meyer, L. Bernatchez (2017)
Genome Compositional Organization in Gars Shows More Similarities to Mammals than to Other Ray-Finned Fish.Journal of experimental zoology. Part B, Molecular and developmental evolution, 328 7
J. Nelson, Terry. Grande, Mark Wilson (2016)
Fishes of the World: Nelson/Fishes of the World
R. Lehmann, A. Kovařík, K. Ocalewicz, L. Kirtiklis, A. Zuccolo, J. Tegnér, J. Wanzenböck, L. Bernatchez, D. Lamatsch, R. Symonová (2021)
DNA Transposon Expansion is Associated with Genome Size Increase in MudminnowsGenome Biology and Evolution, 13
C. Sotero-Caio, Roy Platt, Alexander Suh, D. Ray (2017)
Evolution and Diversity of Transposable Elements in Vertebrate GenomesGenome Biology and Evolution, 9
Francesca Luca, R. Hudson, D. Witonsky, A. Rienzo (2011)
A reduced representation approach to population genetic analyses and applications to human evolution.Genome research, 21 7
Swarajpal Randhawa, R. Pawar (2021)
Fish genomes: Sequencing trends, taxonomy and influence of taxonomy on genome attributesJournal of Applied Ichthyology
R. Symonová, M. Flajšhans, A. Sember, M. Havelka, D. Gela, T. Kořínková, M. Rodina, M. Rábová, P. Ráb (2013)
Molecular Cytogenetics in Artificial Hybrid and Highly Polyploid Sturgeons: An Evolutionary Story Narrated by Repetitive SequencesCytogenetic and Genome Research, 141
INTRODUCTIONBiologists have been facing a tremendous data explosion during the last years. This is particularly apparent in the still increasing amount of sequenced genomes. However, it is not always straightforward to understand and properly utilize these data that may be publicly available in an incomplete form. This is the case of the current flood of fish genomes among others. In reaction to this situation a recent study by Randhawa and Pawar (2021) tried to exploit these data, however, in an improper way. This study is not the only one suffering from serious problems with handling genomic data and contextualizing them in organismal evolution. On the other hand (Randhawa & Pawar, 2021) accumulated several serious issues in a single paper and further analysed their incorrect findings. This short communication aims to elucidate unclarities in that study and to provide some simple hints how to avoid similar issues. This is particularly relevant for fish genomics, where an immense biodiversity results in a so far unexplored diversity of genome traits.MANUAL CURATION AND COMMON SENSE ARE HIGHLY REQUIREDThe study by Randhawa and Pawar (2021) is based on the NCBI repository of genomic data (Genome, 2022). Even such excellent and indispensable tools like NCBI/Genome are not absolutely flawless
Journal of Applied Ichthyology – Wiley
Published: Nov 16, 2022
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.