@article{HoehneProkopovKuhletal.2021,
  author    = {H{\"o}hne, Christin and Prokopov, Dmitry and Kuhl, Heiner and Du, Kang and Klopp, Christophe and Wuertz, Sven and Trifonov, Vladimir and St{\"o}ck, Matthias},
  title     = {The immune system of sturgeons and paddlefish (Acipenseriformes): a review with new data from a chromosome-scale sturgeon genome},
  series = {Reviews in Aquaculture},
  volume    = {13},
  journal   = {Reviews in Aquaculture},
  number    = {3},
  doi       = {10.1111/raq.12542},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-239865},
  pages     = {1709 -- 1729},
  year      = {2021},
  abstract  = {Sturgeon immunity is relevant for basic evolutionary and applied research, including caviar- and meat-producing aquaculture, protection of wild sturgeons and their re-introduction through conservation aquaculture. Starting from a comprehensive overview of immune organs, we discuss pathways of innate and adaptive immune systems in a vertebrate phylogenetic and genomic context. The thymus as a key organ of adaptive immunity in sturgeons requires future molecular studies. Likewise, data on immune functions of sturgeon-specific pericardial and meningeal tissues are largely missing. Integrating immunological and endocrine functions, the sturgeon head kidney resembles that of teleosts. Recently identified pattern recognition receptors in sturgeon require research on downstream regulation. We review first acipenseriform data on Toll-like receptors (TLRs), type I transmembrane glycoproteins expressed in membranes and endosomes, initiating inflammation and host defence by molecular pattern-induced activation. Retinoic acid-inducible gene-I-like (RIG-like) receptors of sturgeons present RNA and key sensors of virus infections in most cell types. Sturgeons and teleosts share major components of the adaptive immune system, including B cells, immunoglobulins, major histocompatibility complex and the adaptive cellular response by T cells. The ontogeny of the sturgeon innate and onset of adaptive immune genes in different organs remain understudied. In a genomics perspective, our new data on 100 key immune genes exemplify a multitude of evolutionary trajectories after the sturgeon-specific genome duplication, where some single-copy genes contrast with many duplications, allowing tissue specialization, sub-functionalization or both. Our preliminary conclusion should be tested by future evolutionary bioinformatics, involving all >1000 immunity genes. This knowledge update about the acipenseriform immune system identifies several important research gaps and presents a basis for future applications.},
  language  = {en}
}
@article{KuhlGuiguenHoehneetal.2021,
  author    = {Kuhl, Heiner and Guiguen, Yann and H{\"o}hne, Christin and Kreuz, Eva and Du, Kang and Klopp, Christophe and Lopez-Roques,, C{\´e}line and Yebra-Pimentel, Elena Santidrian and Ciorpac, Mitica and Gessner, J{\"o}rn and Holostenco, Daniela and Kleiner, Wibke and Kohlmann, Klaus and Lamatsch, Dunja K. and Prokopov, Dmitry and Bestin, Anastasia and Bonpunt, Emmanuel and Debeuf, Bastien and Haffray, Pierrick and Morvezen, Romain and Patrice, Pierre and Suciu, Radu and Dirks, Ron and Wuertz, Sven and Kloas, Werner and Schartl, Manfred and St{\"o}ck, Matthias},
  title     = {A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes},
  series = {Philosophical Transactions of the Royal Society B},
  volume    = {376},
  journal   = {Philosophical Transactions of the Royal Society B},
  doi       = {10.1098/rstb.2020.0089},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-363050},
  year      = {2021},
  abstract  = {Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet (Acipenser ruthenus). Using chromosome-scale assemblies and pool-sequencing, we first identified an approximately 16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages (A. sturio, A. oxyrinchus versus A. ruthenus, Huso huso), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species (A. gueldenstaedtii, A. baerii). Conservation of a female-specific sequence for a long period, representing 180 Myr of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.},
  language  = {en}
}
@article{FofanovProkopovKuhletal.2020,
  author    = {Fofanov, Mikhail V. and Prokopov, Dmitry Yu. and Kuhl, Heiner and Schartl, Manfred and Trifonov, Vladimir A.},
  title     = {Evolution of microRNA biogenesis genes in the sterlet (Acipenser ruthenus) and other polyploid vertebrates},
  series = {International Journal of Molecular Sciences},
  volume    = {21},
  journal   = {International Journal of Molecular Sciences},
  number    = {24},
  issn      = {1422-0067},
  doi       = {10.3390/ijms21249562},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-285230},
  year      = {2020},
  abstract  = {MicroRNAs play a crucial role in eukaryotic gene regulation. For a long time, only little was known about microRNA-based gene regulatory mechanisms in polyploid animal genomes due to difficulties of polyploid genome assembly. However, in recent years, several polyploid genomes of fish, amphibian, and even invertebrate species have been sequenced and assembled. Here we investigated several key microRNA-associated genes in the recently sequenced sterlet (Acipenser ruthenus) genome, whose lineage has undergone a whole genome duplication around 180 MYA. We show that two paralogs of drosha, dgcr8, xpo1, and xpo5 as well as most ago genes have been retained after the acipenserid-specific whole genome duplication, while ago1 and ago3 genes have lost one paralog. While most diploid vertebrates possess only a single copy of dicer1, we strikingly found four paralogs of this gene in the sterlet genome, derived from a tandem segmental duplication that occurred prior to the last whole genome duplication. ago1,3,4 and exportins1,5 look to be prone to additional segment duplications producing up to four-five paralog copies in ray-finned fishes. We demonstrate for the first time exon microsatellite amplification in the acipenserid drosha2 gene, resulting in a highly variable protein product, which may indicate sub- or neofunctionalization. Paralogous copies of most microRNA metabolism genes exhibit different expression profiles in various tissues and remain functional despite the rediploidization process. Subfunctionalization of microRNA processing gene paralogs may be beneficial for different pathways of microRNA metabolism. Genetic variability of microRNA processing genes may represent a substrate for natural selection, and, by increasing genetic plasticity, could facilitate adaptations to changing environments.},
  language  = {en}
}