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Zhang H, Zhou Y, Yang Z. Genetic adaptations of marine invertebrates to hydrothermal vent habitats. Trends Genet 2024; 40:1047-1059. [PMID: 39277449 DOI: 10.1016/j.tig.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 08/15/2024] [Accepted: 08/16/2024] [Indexed: 09/17/2024]
Abstract
Hydrothermal vents are unique habitats like an oases of life compared with typical deep-sea, soft-sediment environments. Most animals that live in these habitats are invertebrates, and they have adapted to extreme vent environments that include high temperatures, hypoxia, high sulfide, high metal concentration, and darkness. The advent of next-generation sequencing technology, especially the coming of the new era of omics, allowed more studies to focus on the molecular adaptation of these invertebrates to vent habitats. Many genes linked to hydrothermal adaptation have been studied. We summarize the findings related to these genetic adaptations and discuss which new techniques can facilitate studies in the future.
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Affiliation(s)
- Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
| | - Yang Zhou
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Zhuo Yang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Drozdova PB, Madyarova EV, Gurkov AN, Saranchina AE, Romanova EV, Petunina JV, Peretolchina TE, Sherbakov DY, Timofeyev MA. Lake Baikal amphipods and their genomes, great and small. Vavilovskii Zhurnal Genet Selektsii 2024; 28:317-325. [PMID: 38952708 PMCID: PMC11214899 DOI: 10.18699/vjgb-24-36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 07/03/2024] Open
Abstract
Endemic amphipods (Crustacea: Amphipoda) of Lake Baikal represent an outstanding example of large species flocks occupying a wide range of ecological niches and originating from a handful of ancestor species. Their development took place at a restricted territory and is thus open for comprehensive research. Such examples provide unique opportunities for studying behavioral, anatomic, or physiological adaptations in multiple combinations of environmental conditions and thus attract considerable attention. The existing taxonomies of this group list over 350 species and subspecies, which, according to the molecular phylogenetic studies of marker genes, full transcriptomes and mitochondrial genomes, originated from at least two introductions into the lake. The studies of allozymes and marker genes have revealed a significant cryptic diversity in Baikal amphipods, as well as a large variance in genetic diversity within some morphological species. Crossing experiments conducted so far for two morphological species suggest that the differences in the mitochondrial marker (cytochrome c oxidase subunit I gene) can potentially be applied for making predictions about reproductive isolation. For about one-tenth of the Baikal amphipod species, nuclear genome sizes and chromosome numbers are known. While genome sizes vary within one order of magnitude, the karyotypes are relatively stable (2n = 52 for most species studied). Moreover, analysis of the diversity of repeated sequences in nuclear genomes showed significant between-species differences. Studies of mitochondrial genomes revealed some unusual features, such as variation in length and gene order, as well as duplications of tRNA genes, some of which also underwent remolding (change in anticodon specificity due to point mutations). The next important steps should be (i) the assembly of whole genomes for different species of Baikal amphipods, which is at the moment hampered by complicated genome structures with high repeat content, and (ii) updating species taxonomy taking into account all the data.
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Affiliation(s)
- P B Drozdova
- Irkutsk State University, Irkutsk, Russia Baikal Research Centre, Irkutsk, Russia
| | | | - A N Gurkov
- Irkutsk State University, Irkutsk, Russia Baikal Research Centre, Irkutsk, Russia
| | | | - E V Romanova
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - J V Petunina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - T E Peretolchina
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - D Y Sherbakov
- Irkutsk State University, Irkutsk, Russia Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia Novosibirsk State University, Novosibirsk, Russia
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Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov SV. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Sci Rep 2023; 13:9382. [PMID: 37296138 PMCID: PMC10256749 DOI: 10.1038/s41598-023-35979-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans.
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Affiliation(s)
- Alexandra A Vetrova
- Laboratory of Morphogenesis Evolution, Koltzov Institute of Developmental Biology RAS, Vavilova 26, Moscow, 119334, Russia
| | - Daria M Kupaeva
- Department of Embryology, Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory 1/12, Moscow, 119234, Russia
| | - Alena Kizenko
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Tatiana S Lebedeva
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Peter Walentek
- Renal Division, Internal Medicine IV, Medical Center, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Nikoloz Tsikolia
- Institute of Anatomy and Embryology, University Medical Center Göttingen, Kreuzbergring 36, 37085, Göttingen, Germany
| | - Stanislav V Kremnyov
- Laboratory of Morphogenesis Evolution, Koltzov Institute of Developmental Biology RAS, Vavilova 26, Moscow, 119334, Russia.
- Department of Embryology, Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory 1/12, Moscow, 119234, Russia.
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Drozdova P, Saranchina A, Madyarova E, Gurkov A, Timofeyev M. Experimental Crossing Confirms Reproductive Isolation between Cryptic Species within Eulimnogammarus verrucosus (Crustacea: Amphipoda) from Lake Baikal. Int J Mol Sci 2022; 23:ijms231810858. [PMID: 36142769 PMCID: PMC9506054 DOI: 10.3390/ijms231810858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/26/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Ancient lakes are known speciation hotspots. One of the most speciose groups in the ancient Lake Baikal are gammaroid amphipods (Crustacea: Amphipoda: Gammaroidea). There are over 350 morphological species and subspecies of amphipods in Baikal, but the extent of cryptic variation is still unclear. One of the most common species in the littoral zone of the lake, Eulimnogammarus verrucosus (Gerstfeldt, 1858), was recently found to comprise at least three (pseudo)cryptic species based on molecular data. Here, we further explored these species by analyzing their mitogenome-based phylogeny, genome sizes with flow cytometry, and their reproductive compatibility. We found divergent times of millions of years and different genome sizes in the three species (6.1, 6.9 and 8 pg), further confirming their genetic separation. Experimental crossing of the western and southern species, which are morphologically indistinguishable and have adjacent ranges, showed their separation with a post-zygotic reproductive barrier, as hybrid embryos stopped developing roughly at the onset of gastrulation. Thus, the previously applied barcoding approach effectively indicated the separate biological species within E. verrucosus. These results provide new data for investigating genome evolution and highlight the need for precise tracking of the sample origin in any studies in this morphospecies.
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Affiliation(s)
- Polina Drozdova
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia
- Baikal Research Centre, 664011 Irkutsk, Russia
- Correspondence: (P.D.); (M.T.)
| | | | | | - Anton Gurkov
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia
- Baikal Research Centre, 664011 Irkutsk, Russia
| | - Maxim Timofeyev
- Institute of Biology, Irkutsk State University, 664025 Irkutsk, Russia
- Baikal Research Centre, 664011 Irkutsk, Russia
- Correspondence: (P.D.); (M.T.)
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