Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (Acipenser ruthenus) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order.

Keywords:
Genome sequencing, Acipenseridae, DNA repeats, FISH mapping, Sturgeon
1.
Barbosa P, de Oliveira LA, Pucci MB, Santos MH, Moreira-Filho O, et al: Identification and chromosome mapping of repetitive elements in the Astyanax scabripinnis (Teleostei: Characidae) species complex. Genetica 143:55-62 (2015).
2.
Birstein VJ, Vasiliev VP: Tetraploid-octoploid relationships and karyological evolution in the order Acipenseriformes (Pisces) karyotypes, nucleoli, and nucleolus-organizer regions in four acipenserid species. Genetica 72:3-12 (1987).
3.
Breen M: Canine cytogenetics - from band to basepair. Cytogenet Genome Res 120:50-60 (2008).
4.
Cabral-de-Mello DC, Martins C: Breaking down the genome organization and karyotype differentiation through the epifluorescence microscope lens: insects and fish as models. Microsc Sci Technol Appl Educ 1:658-669 (2010).
5.
Charlesworth D, Charlesworth B, Marais G: Steps in the evolution of heteromorphic sex chromosomes. Heredity 95:118-128 (2005).
6.
Cioffi MB, Bertollo LAC: Chromosomal distribution and evolution of repetitive DNAs in fish. Genome Dyn 7:197-221 (2012).
7.
Costa GW, Cioffi MB, Bertollo LAC, Molina WF: Transposable elements in fish chromosomes: a study in the marine cobia species. Cytogenet Genome Res 141:126-132 (2013).
8.
Crow KD, Smith CD, Cheng JF, Wagner GP, Amemiya CT: An independent genome duplication inferred from Hox paralogs in the American paddlefish—a representative basal ray-finned fish and important comparative reference. Genome Biol Evol 4:937-953 (2012).
9.
de la Herrán R, Fontana F, Lanfredi M, Congiu L, Leis M, et al: Slow rates of evolution and sequence homogenization in an ancient satellite DNA family of sturgeons. Mol Biol Evol 18:432-436 (2001).
10.
Devlin RH, Nagahama Y: Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences. Aquaculture 208:191-364 (2002).
11.
Eickbush TH, Eickbush DG: Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics 175:477-485 (2007).
12.
Ellegren H: Sex-chromosome evolution: recent progress and the influence of male and female heterogamety. Nat Rev Genet 12:157-166 (2011).
13.
Ezaz T, Quinn AE, Miura I, Sarre SD, Georges A, Marshall Graves JA: The dragon lizard Pogona vitticeps has ZZ/ZW micro-sex chromosomes. Chromosome Res 13:763-776 (2005).
14.
Faber-Hammond JJ, Phillips RB, Brown KH: Comparative analysis of the shared sex-determination region (SDR) among salmonid fishes. Genome Biol Evol 7:1972-1987 (2015).
15.
Fernández R, Barragán MJ, Bullejos M, Marchal JA, Diaz De La Guardia R, Sanchez A: New C-band protocol by heat denaturation in the presence of formamide. Hereditas 137:145-148 (2002).
16.
Ferreira DC, Porto-Foresti F, Oliveira C, Foresti F: Transposable elements as a potential source for understanding the fish genome. Mob Genet Elements 1:112-117 (2011).
17.
Flynn SR, Matsuoka M, Reith M, Martin-Robichaud DJ, Benfey TJ: Gynogenesis and sex determination in shortnose sturgeon, Acipenser brevirostrum Lesuere. Aquaculture 253:721-727 (2006).
18.
Fontana F, Lanfredi M, Chicca M, Aiello V, Rossi R: Localization of the repetitive telomeric sequence (TTAGGG)n in four sturgeon species. Chromosome Res 6:303-306 (1998).
19.
Fontana F, Tagliavini J, Congiu L: Sturgeon genetics and cytogenetics: recent advancements and perspectives. Genetica 111:359-373 (2001).
20.
Fontana F, Lanfredi M, Congiu L, Leis M, Chicca M, Rossi R: Chromosomal mapping of 18S-28S and 5S rRNA genes by two-colour fluorescent in situ hybridization in six sturgeon species. Genome 46:473-477 (2003).
21.
Ghigliotti L, Cheng CH, Bonillo C, Coutanceau JP, Pisano E: In situ gene mapping of two genes supports independent evolution of sex chromosomes in cold-adapted Antarctic fish. Biomed Res Int 2013:243938 (2013).
22.
Gold JR, Li C, Shipley NS, Powers PK: Improved methods for working with fish chromosomes with a review of metaphase chromosome banding. J Fish Biol 37:563-575 (1990).
23.
Hanson R, Zhao XP, Islam-Faridi MN, Paterson A, Zwick M, et al: Evolution of interspersed repetitive elements in Gossypium (Malvaceae). Am J Bot 85:1364-1368 (1998).
24.
Havelka M, Kaspar V, Hulák M, Flajshans M: Sturgeon genetics and cytogenetics: a review related to ploidy levels and interspecific hybridization. Folia Zool 60:93-103 (2011).
25.
Kosyakova N, Hamid AB, Chaveerach A, Pinthong K, Siripiyasing P, et al: Generation of multicolor banding probes for chromosomes of different species. Mol Cytogenet 6:6 (2013).
26.
Krieger J, Fuerst PA: Evidence for a slowed rate of molecular evolution in the order Acipenseriformes. Mol Biol Evol 19:891-897 (2002).
27.
Kuznetsova IS, Thevasagayam NM, Sridatta PSR, Komissarov AS, Saju JM, et al: Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome. Front Genet 5:223 (2014).
28.
Lanfredi M, Congiu L, Garrido-Ramos MA, de la Herrán R, Leis M, et al: Chromosomal location and evolution of a satellite DNA family in seven sturgeon species. Chromosome Res 9:47-52 (2001).
29.
Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, et al: The Atlantic salmon genome provides insights into rediploidization. Nature 533:200-205 (2016).
30.
Ludwig A, Belfiore NM, Pitra C, Svirsky V, Jenneckens I: Genome duplication events and functional reduction of ploidy levels in sturgeon (Acipenser, Huso and Scaphirhynchus). Genetics 158:1203-1215 (2001).
31.
Machado TC, Pansonato-Alves JC, Pucci MB, Nogaroto V, Almeida MC, et al: Chromosomal painting and ZW sex chromosomes differentiation in Characidium (Characiformes, Crenuchidae). BMC Genet 12:65 (2011).
32.
Mazzuchelli J, Kocher TD, Yang F, Martins C: Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish. BMC Genomics 13:463 (2012).
33.
Medrano L, Bernardi G, Couturier J, Dutrillaux B, Bernardi G: Chromosome banding and genome compartmentalization in fishes. Chromosoma 96:178-183 (1988).
34.
Ohno S: Sex Chromosomes and Sex-Linked Genes (Springer, Berlin 1967).
35.
Peng Z, Ludwig A, Wang D, Diogo R, Wei Q, He S: Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes). Mol Phylogenet Evol 42:854-862 (2007).
36.
Piscor D, Parise-Maltempi PP: Microsatellite organization in the B chromosome and A chromosome complement in Astyanax (Characiformes, Characidae) species. Cytogenet Genome Res 148:44-51 (2016).
37.
Robles F, de la Herrán R, Ludwig A, Ruiz Rejón C, Ruiz Rejón M, Garrido-Ramos MA: Evolution of ancient satellite DNAs in sturgeon genomes. Gene 338:133-142 (2004).
38.
Romanenko SA, Biltueva LS, Serdyukova NA, Kulemzina AI, Beklemisheva VR, et al: Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting. Mol Cytogenet 8:90 (2015).
39.
Ross JA, Urton JR, Boland J, Shapiro MD, Peichel CL: Turnover of sex chromosomes in the stickleback fishes (Gasterosteidae). PLoS Genet 5:e1000391 (2009).
40.
Saber MH, Hallajian A: Study of sex determination system in ship sturgeon, Acipenser nudiventris using meiotic gynogenesis. Aquacult Int 22:273-279 (2014).
41.
Sambrook J, Fritsch EF, Maniatis EF: Molecular Cloning: A Laboratory Manual, ed 2 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor 1989).
42.
Scacchetti PC, Utsunomia R, Pansonato-Alves JC, da Costa Silva GJ, Vicari MR, et al: Repetitive DNA sequences and evolution of ZZ/ZW sex chromosomes in Characidium (Teleostei: Characiformes). PLoS One 10:e0137231 (2015).
43.
Schartl M, Schmid M, Nanda I: Dynamics of vertebrate sex chromosome evolution: from equal size to giants and dwarfs. Chromosoma 125:553-571 (2016).
44.
Seabright M: A rapid banding technique for human chromosomes. Lancet 2:971-972 (1971).
45.
Symonová R, Flajšhans M, Sember A, Havelka M, Gela D, et al: Molecular cytogenetics in artificial hybrid and highly polyploid sturgeons: an evolutionary story narrated by repetitive sequences. Cytogenet Genome Res 141:153-162 (2013).
46.
Symonová R, Majtánová Z, Arias-Rodriguez L, Mořkovský L, Kořínková T, et al: Genome compositional organization in gars shows more similarities to mammals than to other ray-finned fish. J Exp Zool B Mol Dev Evol, E-pub ahead of print (2016).
47.
Trifonov VA, Paoletti A, Caputo Barucchi V, Kalinina T, O'Brien PCM, et al: Comparative chromosome painting and NOR distribution suggest a complex hybrid origin of triploid Lepidodactylus lugubris (Gekkonidae). PLoS One 10:e0132380 (2015).
48.
Trifonov VA, Romanenko SS, Beklemisheva VR, Biltueva LS, Makunin AI, et al: Evolutionary plasticity of acipenseriform genomes. Chromosoma 125:661-668 (2016).
49.
Vicari MR, Artoni RF, Moreira-Filho O, Bertollo LAC: Colocalization of repetitive DNAs and silencing of major rRNA genes. A case report of the fish Astyanax janeiroensis. Cytogenet Genome Res 122:67-72 (2008).
50.
Vicari MR, Nogaroto V, Noleto RB, Cestari MM, Cioffi MB, et al: Satellite DNA and chromosomes in Neotropical fishes: methods, applications and perspectives. J Fish Biol 76:1094-1116 (2010).
51.
Wang Y, Drader T, Tiwari VK, Dong L, Kumar A, et al: Development of a D genome specific marker resource for diploid and hexaploid wheat. BMC Genomics 16:646 (2015).
52.
Wiberg UH: Sex determination in the European eel (Anguilla Anguilla, L.). A hypothesis based on cytogenetic results, correlated with the findings of skewed sex ratios in eel culture ponds. Cytogenet Cell Genet 36:589-598 (1983).
53.
Yano CF, Bertollo LAC, Molina W, Liehr T, Cioffi MB: Genomic organization of repetitive DNAs and its implications for male karyotype and the neo-Y chromosome differentiation in Erythrinus erythrinus (Characiformes, Erythrinidae). Comp Cytogenet 8:139-151 (2014a).
54.
Yano CF, Poltronieri J, Bertollo LAC, Artoni RF, Liehr T, Cioffi MB: Chromosomal mapping of repetitive DNAs in Triportheus trifurcatus (Characidae, Characiformes): insights into the differentiation of the Z and W chromosomes. PLoS One 9:e90946 (2014b).
© 2017 S. Karger AG, Basel
2017
Copyright / Drug Dosage / Disclaimer
Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.
You do not currently have access to this content.