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The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. / Du, Kang; Stöck, Matthias; Kneitz, Susanne et al.

In: Nature Ecology and Evolution, Vol. 4, No. 6, 01.06.2020, p. 841-852.

Research output: Contribution to journal › Article › peer-review

Harvard

Du, K, Stöck, M, Kneitz, S, Klopp, C, Woltering, JM, Adolfi, MC, Feron, R, Prokopov, D, Makunin, A, Kichigin, I, Schmidt, C, Fischer, P, Kuhl, H, Wuertz, S, Gessner, J, Kloas, W, Cabau, C, Iampietro, C, Parrinello, H, Tomlinson, C, Journot, L, Postlethwait, JH, Braasch, I, Trifonov, V, Warren, WC, Meyer, A, Guiguen, Y & Schartl, M 2020, 'The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization', Nature Ecology and Evolution, vol. 4, no. 6, pp. 841-852. https://doi.org/10.1038/s41559-020-1166-x

APA

Du, K., Stöck, M., Kneitz, S., Klopp, C., Woltering, J. M., Adolfi, M. C., Feron, R., Prokopov, D., Makunin, A., Kichigin, I., Schmidt, C., Fischer, P., Kuhl, H., Wuertz, S., Gessner, J., Kloas, W., Cabau, C., Iampietro, C., Parrinello, H., ... Schartl, M. (2020). The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nature Ecology and Evolution, 4(6), 841-852. https://doi.org/10.1038/s41559-020-1166-x

Vancouver

Du K, Stöck M, Kneitz S, Klopp C, Woltering JM, Adolfi MC et al. The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nature Ecology and Evolution. 2020 Jun 1;4(6):841-852. doi: 10.1038/s41559-020-1166-x

Author

Du, Kang ; Stöck, Matthias ; Kneitz, Susanne et al. / The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. In: Nature Ecology and Evolution. 2020 ; Vol. 4, No. 6. pp. 841-852.

BibTeX

@article{62e6b8b68f5c435ba3890e431605d553,
title = "The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization",
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.",
keywords = "RAY-FINNED FISH, DE-NOVO, TRANSPOSABLE ELEMENTS, PROVIDES INSIGHTS, WHOLE-GENOME, PHYLOGENETIC ANALYSIS, ACIPENSER-RUTHENUS, SEX DETERMINATION, PLOIDY LEVELS, HOX CLUSTERS",
author = "Kang Du and Matthias St{\"o}ck and Susanne Kneitz and Christophe Klopp and Woltering, {Joost M.} and Adolfi, {Mateus Contar} and Romain Feron and Dmitry Prokopov and Alexey Makunin and Ilya Kichigin and Cornelia Schmidt and Petra Fischer and Heiner Kuhl and Sven Wuertz and J{\"o}rn Gessner and Werner Kloas and C{\'e}dric Cabau and Carole Iampietro and Hugues Parrinello and Chad Tomlinson and Laurent Journot and Postlethwait, {John H.} and Ingo Braasch and Vladimir Trifonov and Warren, {Wesley C.} and Axel Meyer and Yann Guiguen and Manfred Schartl",
note = "This work was supported by grants supplied by the Deutsche Forschungsgemeinschaft to M.Schartl (nos. DFG SCHA 408/14-1, SCHA 408/10-1 and Scha408/16-1), J.M.W. (DFG WO-2165/2-1) and A. Meyer (DFG Me1725/24-1); by the German Federal Ministry of Food and Agriculture through the Federal Office for Agriculture and Food (grant no. 2816ERA04G) to M. Stock, S.W., J.G. and M. Schartl; by funds from the Agence Nationale de la Recherche (grant no. ANR-13-ISV7-0005, PhyloSex project) to Y.G.; and by funds from the Russian Science Foundation to V.T., A.M., I.K. and D.P. (grant no. RSF 18-44-04007). We thank the Leibniz-IGB for supporting the sterlet genome sequencing project. The GeT core facility was supported by France Genomique National infrastructure, funded as part of the Investissement d'avenir programme, managed by the Agence Nationale pour la Recherche (contract no. ANR-10-INBS-09).",
year = "2020",
month = jun,
day = "1",
doi = "10.1038/s41559-020-1166-x",
language = "English",
volume = "4",
pages = "841--852",
journal = "Nature Ecology and Evolution",
issn = "2397-334X",
publisher = "Nature Publishing Group",
number = "6",

}

RIS

TY - JOUR

T1 - The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization

AU - Du, Kang

AU - Stöck, Matthias

AU - Kneitz, Susanne

AU - Klopp, Christophe

AU - Woltering, Joost M.

AU - Adolfi, Mateus Contar

AU - Feron, Romain

AU - Prokopov, Dmitry

AU - Makunin, Alexey

AU - Kichigin, Ilya

AU - Schmidt, Cornelia

AU - Fischer, Petra

AU - Kuhl, Heiner

AU - Wuertz, Sven

AU - Gessner, Jörn

AU - Kloas, Werner

AU - Cabau, Cédric

AU - Iampietro, Carole

AU - Parrinello, Hugues

AU - Tomlinson, Chad

AU - Journot, Laurent

AU - Postlethwait, John H.

AU - Braasch, Ingo

AU - Trifonov, Vladimir

AU - Warren, Wesley C.

AU - Meyer, Axel

AU - Guiguen, Yann

AU - Schartl, Manfred

N1 - This work was supported by grants supplied by the Deutsche Forschungsgemeinschaft to M.Schartl (nos. DFG SCHA 408/14-1, SCHA 408/10-1 and Scha408/16-1), J.M.W. (DFG WO-2165/2-1) and A. Meyer (DFG Me1725/24-1); by the German Federal Ministry of Food and Agriculture through the Federal Office for Agriculture and Food (grant no. 2816ERA04G) to M. Stock, S.W., J.G. and M. Schartl; by funds from the Agence Nationale de la Recherche (grant no. ANR-13-ISV7-0005, PhyloSex project) to Y.G.; and by funds from the Russian Science Foundation to V.T., A.M., I.K. and D.P. (grant no. RSF 18-44-04007). We thank the Leibniz-IGB for supporting the sterlet genome sequencing project. The GeT core facility was supported by France Genomique National infrastructure, funded as part of the Investissement d'avenir programme, managed by the Agence Nationale pour la Recherche (contract no. ANR-10-INBS-09).

PY - 2020/6/1

Y1 - 2020/6/1

N2 - 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.

AB - 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.

KW - RAY-FINNED FISH

KW - DE-NOVO

KW - TRANSPOSABLE ELEMENTS

KW - PROVIDES INSIGHTS

KW - WHOLE-GENOME

KW - PHYLOGENETIC ANALYSIS

KW - ACIPENSER-RUTHENUS

KW - SEX DETERMINATION

KW - PLOIDY LEVELS

KW - HOX CLUSTERS

UR - http://www.scopus.com/inward/record.url?scp=85082929700&partnerID=8YFLogxK

U2 - 10.1038/s41559-020-1166-x

DO - 10.1038/s41559-020-1166-x

M3 - Article

C2 - 32231327

AN - SCOPUS:85082929700

VL - 4

SP - 841

EP - 852

JO - Nature Ecology and Evolution

JF - Nature Ecology and Evolution

SN - 2397-334X

IS - 6

ER -

ID: 23982851