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The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nat Ecol Evol 2020; 4:841-852. [PMID: 32231327 PMCID: PMC7269910 DOI: 10.1038/s41559-020-1166-x] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022]
Abstract
Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chromosome-level reference genome for the sterlet, Acipenser ruthenus. Our analysis revealed a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, such as that of the coelacanth. We uncovered a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process. While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random. A genome assembly of the sterlet, Acipenser ruthenus, reveals a whole-genome duplication early in the evolution of the entire sturgeon lineage and provides details about the rediploidization of the genome.
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Barby FF, Ráb P, Lavoué S, Ezaz T, Bertollo LAC, Kilian A, Maruyama SR, Aguiar de Oliveira E, Artoni RF, Santos MH, Ilesanmi Jegede O, Hatanaka T, Tanomtong A, Liehr T, Cioffi MDB. From Chromosomes to Genome: Insights into the Evolutionary Relationships and Biogeography of Old World Knifefishes (Notopteridae; Osteoglossiformes). Genes (Basel) 2018; 9:E306. [PMID: 29921830 PMCID: PMC6027293 DOI: 10.3390/genes9060306] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 01/13/2023] Open
Abstract
In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages; making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the diversity present in this group. However, cytogenetic and genomic data are still scarce, making it difficult to track evolutionary trajectories within this order. In addition, their wide distribution, with groups endemic to different continents, hinders an integrative study that allows a globalized view of its evolutionary process. Here, we performed a detailed chromosomal analysis in Notopteridae fishes, using conventional and advanced molecular cytogenetic methods. Moreover, the genetic distances of examined species were assessed by genotyping using diversity arrays technology sequencing (DArTseq). These data provided a clear picture of the genetic diversity between African and Asian Notopteridae species, and were highly consistent with the chromosomal, geographical, and historical data, enlightening their evolutionary diversification. Here, we discuss the impact of continental drift and split of Pangea on their recent diversity, as well as the contribution to biogeographical models that explain their distribution, highlighting the role of the Indian subcontinent in the evolutionary process within the family.
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Affiliation(s)
- Felipe Faix Barby
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic.
| | - Sébastien Lavoué
- Institute of Oceanography, National Taiwan University, Roosevelt Road, Taipei 10617, Taiwan.
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Bruce, Australian Capital Territory, Canberra, ACT 2617, Australia.
| | - Sandra Regina Maruyama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Roberto Ferreira Artoni
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84030-900 Brazil.
| | - Mateus Henrique Santos
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84030-900 Brazil.
| | - Oladele Ilesanmi Jegede
- Department of Fisheries and Aquaculture, Adamawa State University, P.M.B. 25 Mubi. Adamawa State, Nigeria.
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University, Muang, KhonKaen 40002, Thailand.
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany.
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
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Romanenko SA, Biltueva LS, Serdyukova NA, Kulemzina AI, Beklemisheva VR, Gladkikh OL, Lemskaya NA, Interesova EA, Korentovich MA, Vorobieva NV, Graphodatsky AS, Trifonov VA. Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting. Mol Cytogenet 2015; 8:90. [PMID: 26587056 PMCID: PMC4652396 DOI: 10.1186/s13039-015-0194-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/07/2015] [Indexed: 11/21/2022] Open
Abstract
Background Acipenseriformes take a basal position among Actinopteri and demonstrate a striking ploidy variation among species. The sterlet (Acipenser ruthenus, Linnaeus, 1758; ARUT) is a diploid 120-chromosomal sturgeon distributed in Eurasian rivers from Danube to Enisey. Despite a high commercial value and a rapid population decline in the wild, many genomic characteristics of sterlet (as well as many other sturgeon species) have not been studied. Results Cell lines from different tissues of 12 sterlet specimens from Siberian populations were established following an optimized protocol. Conventional cytogenetic studies supplemented with molecular cytogenetic investigations on obtained fibroblast cell lines allowed a detailed description of sterlet karyotype and a precise localization of 18S/28S and 5S ribosomal clusters. Localization of sturgeon specific HindIII repetitive elements revealed an increased concentration in the pericentromeric region of the acrocentric ARUT14, while the total sterlet repetitive DNA fraction (C0t30) produced bright signals on subtelomeric segments of small chromosomal elements. Chromosome and region specific probes ARUT1p, 5, 6, 7, 8 as well as 14 anonymous small sized chromosomes (probes A-N) generated by microdissection were applied in chromosome painting experiments. According to hybridization patterns all painting probes were classified into two major groups: the first group (ARUT5, 6, 8 as well as microchromosome specific probes C, E, F, G, H, and I) painted only a single region each on sterlet metaphases, while probes of the second group (ARUT1p, 7 as well as microchromosome derived probes A, B, D, J, K, M, and N) marked two genomic segments each on different chromosomes. Similar results were obtained on male and female metaphases. Conclusions The sterlet genome represents a complex mosaic structure and consists of diploid and tetraploid chromosome segments. This may be regarded as a transition stage from paleotetraploid (functional diploid) to diploid genome condition. Molecular cytogenetic and genomic studies of other 120- and 240-chromosomal sturgeons are needed to reconstruct genome evolution of this vertebrate group.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
| | - Larisa S Biltueva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | | | | | | | - Olga L Gladkikh
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | | | - Elena A Interesova
- Novosibirsk Branch of the Federal State Budgetary Scientific Institution "State Scientific-and-Production Centre for Fisheries (Gosrybcenter)", Novosibirsk, Russia ; Tomsk State University, Tomsk, Russia
| | - Marina A Korentovich
- Federal State Budgetary Scientific Institution "State Scientific-and-Production Centre for Fisheries (Gosrybcenter)", Tyumen, Russia
| | - Nadezhda V Vorobieva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
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Captive breeding programs based on family groups in polyploid sturgeons. PLoS One 2014; 9:e110951. [PMID: 25356794 PMCID: PMC4214717 DOI: 10.1371/journal.pone.0110951] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/17/2014] [Indexed: 11/19/2022] Open
Abstract
In species with long life cycles and discontinuous availability of individuals to reproduction, implementing a long-term captive breeding program can be difficult or impossible. In such cases, managing diversity among familiar groups instead of individuals could become a suitable approach to avoid inbreeding and increase the possibility to accomplish a breeding scheme. This is the case of several sturgeon species including the Adriatic sturgeon, whose recovery depends on the management of a few captive stocks directly descended from the same group of wild parents. In the present study, relatedness among 445 potential breeders was inferred with a novel software for pedigree reconstruction in tetraploids (“BreedingSturgeons”). This information was used to plan a breeding scheme considering familiar groups as breeding units and identifying mating priorities. A two-step strategy is proposed: a short-term breeding program, relying on the 13 remaining F0 individuals of certain wild origin; and a long-term plan based on F1 families. Simulations to evaluate the loss of alleles in the F2 generation under different pairing strategies and assess the number of individuals to breed, costs and logistical aquaculture constraints were performed. The strategy proposed is transferable to the several other tetraploid sturgeon species on the brink of extinction.
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Vishnyakova KS, Mugue NS, Zelenina DA, Mikodina EV, Kovaleva OA, Madan GV, Yegorov YE. Cell culture and karyotype of Sakhalin sturgeon Acipenser mikadoi. BIOCHEMISTRY MOSCOW SUPPLEMENT SERIES A-MEMBRANE AND CELL BIOLOGY 2009. [DOI: 10.1134/s1990747809010061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ji FY, Yu QX, Li K, Ren XH. Ag-staining pattern, FISH and ISH with rDNA probes in the rice field eel (Monopterus albus Zuiew) chromosomes. Hereditas 2004; 138:207-12. [PMID: 14641485 DOI: 10.1034/j.1601-5223.2003.01643.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The present paper reports the Results of rice field eel (Monopterus albus Zuiew) chromosomal analysis by Ag-staining techniques, FISH and ISH with 18S rDNA. Both the Ag-NORs and the hybridization signals were observed on the pericentromeric region of chromosome pairs 3 and 7. The Ag-NORs and the hybridization signals on homologous chromosomes 3 and 7 were corresponding to each other. And rDNA genes were mapped to bivalents 3q12-q24 and 7q14-q26. No heteromorphic sex chromosome pair was identified. The Results obtained were discussed with respect to the feature of Ag-NORs and the position of rDNA genes on chromosome pairs 3 and 7.
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Affiliation(s)
- F Y Ji
- College of Life Science, Wuhan University, Wuhan, PR China.
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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 2003; 46:473-7. [PMID: 12834065 DOI: 10.1139/g03-007] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The number and distribution of the 18S-28S and 5S rRNA (rDNA) gene sequences were examined on mitotic chromosomes of six sturgeon species by two-colour in situ hybridization. Four of the six species, Huso huso, Acipenser stellatus, Acipenser sturio, and Acipenser ruthenus, with about 120 chromosomes, showed from six to eight 18S-28S rDNA signals, while 5S rDNA signals were on only one chromosome pair. The two species with 250-270 chromosomes, Acipenser baerii and Acipenser transmontanus, showed from 10 to 12 18S-28S sites and two chromosome pairs bearing 5S rDNA signals. In all examined species, the rather intense 5S rDNA signals apparently overlapped those of 18S-28S rDNA. These data support the diploid-tetraploid relationships between the two chromosome groups of sturgeons. The close association between the two rDNA families in species belonging to an ancestral fish order, such as Acipenseriformes, supports the hypothesis that the association represents a primitive condition.
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Affiliation(s)
- Francesco Fontana
- Department of Biology, University of Ferrara, via L. Borsari, 46 I-44100 Ferrara, Italy.
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