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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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Identification of candidate genes from androgenic gland in Macrobrachium nipponense regulated by eyestalk ablation. Sci Rep 2021; 11:19855. [PMID: 34615913 PMCID: PMC8494903 DOI: 10.1038/s41598-021-99022-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/17/2021] [Indexed: 11/28/2022] Open
Abstract
The eyestalk of crustaceans, such as Macrobrachium nipponense, contains many neurosecretory hormones affecting the process of reproduction, molting, metabolism of glucose, and other functions. In this study, important metabolic pathways and candidate genes involved in male sexual development were selected from M. nipponense. The methodology involved performing long-read and next generation transcriptome sequencing of genes from the androgenic gland after eyestalk ablation. qPCR analysis revealed that the mRNA expression of Mn-IAG was significantly increased after ablation of both the single-side (SS) and double-side (DS) eyestalk, compared with the control group (CG). The long-read transcriptome generated 49,840 non-redundant transcripts. A total of 1319, 2092 and 4351 differentially expressed genes (DEGs) were identified between CG versus SS, SS versus DS and CG versus DS, respectively. These data indicated that ablation of the double-sided eyestalk played stronger regulatory roles than the single-side ablation on male sexual development in M. nipponense. This was consistent with the qPCR analysis. Cell Cycle, Cellular Senescence, Oxidative Phosphorylation, Glycolysis/Gluconeogenesis and Steroid Hormone Biosynthesis were the primary enriched metabolic pathways in all three comparisons, and the important genes from these metabolic pathways were also selected. qPCR permitted secondary confirmation of ten DEGs identified through RNA-seq. RNAi-mediated silencing analyses of Hydroxysteroid dehydrogenase like 1 (HSDL1) revealed that HSDL1 has a positive regulatory effect on testes development. This study provides valuable insight into male sexual development in M. nipponense, including metabolic pathways and genes, paving the way for advanced studies on male sexual development in this species and in other crustaceans.
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Drozdova P, Kizenko A, Saranchina A, Gurkov A, Firulyova M, Govorukhina E, Timofeyev M. The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae). BMC Ecol Evol 2021; 21:81. [PMID: 33971810 PMCID: PMC8108468 DOI: 10.1186/s12862-021-01806-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/20/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Vision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species. RESULTS We evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning. CONCLUSIONS This repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.
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Affiliation(s)
- Polina Drozdova
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | | | | | - Anton Gurkov
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | - Maria Firulyova
- Computer Technologies Department, ITMO University, St. Petersburg, Russia
| | | | - Maxim Timofeyev
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
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Neuparth T, Machado AM, Montes R, Rodil R, Barros S, Alves N, Ruivo R, Castro LFC, Quintana JB, Santos MM. Transcriptomic data on the transgenerational exposure of the keystone amphipod Gammarus locusta to simvastatin. Data Brief 2020; 32:106248. [PMID: 32944603 PMCID: PMC7481811 DOI: 10.1016/j.dib.2020.106248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/20/2020] [Accepted: 08/25/2020] [Indexed: 11/17/2022] Open
Abstract
The use of transcriptomics data brings new insights and works as a powerful tool to explore the molecular mode of action (MoA) of transgenerational inheritance effects of contaminants of emerging concern. Therefore, in this dataset, we present the transcriptomic data of the transgenerational effects of environmentally relevant simvastatin levels, one of the most prescribed human pharmaceuticals, in the keystone amphipod species Gammarus locusta. In summary, G. locusta juveniles were maintained under simvastatin exposure up to adulthood (exposed group - F0E) and the offspring of F0E were transferred to control water for the three subsequent generations (transgenerational group - F1T, F2T and F3T). To gain insights into the biological functions and canonical pathways transgenerationally disrupted by simvastatin, a G. locusta de novo transcriptome assembly was produced and the transcriptomic profiles of three individual G. locusta females, per group, over the four generations (F0 to F3) - solvent control groups (F0.C, F1.C, F2.C and F3.C), F0 320 ng/L simvastatin exposed group (F0.320E) and F1 to F3 320 transgenerational group (F1.320T; F2.320T and F3.320T) - were analyzed. Briefly, Illumina HiSeq™ 2500 platform was used to perform RNA sequencing, and due to the unavailability of G. locusta genome, the RNA-seq datasets were assembled de novo using Trinity and annotated with Trinotate software. After assembly and post-processing steps, 106093 transcripts with N50 of 2371 bp and mean sequence length of 1343.98 bp was produced. BUSCO analyses showed a transcriptome with gene completeness of 97.5 % Arthropoda library profile. The Bowtie2, RSEM and edgeR tools were used for the differential gene expression (DEGs) analyses that allowed the identification of a high quantity of genes differentially expressed in all generations. Finally, to identify the main metabolic pathways affected by the transgenerational effects of SIM across all generations, the DGEs genes were blasted onto KEGG pathways database using the KAAS webserver. The data furnished in this article allows a better molecular understanding of the transgenerational effects produced by simvastatin in the keystone amphipod G. locusta and has major implications for hazard and risk assessment of pharmaceuticals and other emerging contaminants. This article is related to the research article entitled "Transgenerational inheritance of chemical-induced signature: a case study with simvastatin [1].
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Affiliation(s)
- Teresa Neuparth
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
- Corresponding authors.
| | - André M. Machado
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Rosa Montes
- Department of Analytical Chemistry, Nutrition and Food Sciences, IAQBUS - Institute of Research on Chemical and Biological Analysis, Universidade de Santiago de Compostela, R. Constantino Candeira S/N, 15782 Santiago de Compostela, Spain
| | - Rosario Rodil
- Department of Analytical Chemistry, Nutrition and Food Sciences, IAQBUS - Institute of Research on Chemical and Biological Analysis, Universidade de Santiago de Compostela, R. Constantino Candeira S/N, 15782 Santiago de Compostela, Spain
| | - Susana Barros
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Nélson Alves
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Raquel Ruivo
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Luis Filipe C. Castro
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - José B. Quintana
- Department of Analytical Chemistry, Nutrition and Food Sciences, IAQBUS - Institute of Research on Chemical and Biological Analysis, Universidade de Santiago de Compostela, R. Constantino Candeira S/N, 15782 Santiago de Compostela, Spain
| | - Miguel M. Santos
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- Corresponding authors at: CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.
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Drozdova P, Madyarova E, Dimova M, Gurkov A, Vereshchagina K, Adelshin R, Timofeyev M. The diversity of microsporidian parasites infecting the Holarctic amphipod Gammarus lacustris from the Baikal region is dominated by the genus Dictyocoela. J Invertebr Pathol 2020; 170:107330. [PMID: 31978415 DOI: 10.1016/j.jip.2020.107330] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/13/2020] [Accepted: 01/18/2020] [Indexed: 11/18/2022]
Abstract
Microsporidia are a highly diverse group of single-celled eukaryotic parasites related to fungi and infecting hosts belonging to all groups of eukaryotes, including some protists, invertebrate and vertebrate animals. We investigated the diversity of microsporidia in the Holarctic amphipod species Gammarus lacustris from mostly, but not limited to, water bodies in the Lake Baikal region. Ribosomal DNA sequencing and host transcriptome sequencing data from various works show that this species is predominantly infected by representatives of the genus Dictyocoela and probably has some features underlying this specific interaction.
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Affiliation(s)
- Polina Drozdova
- Irkutsk State University, Karl Marx str. 1, 664003 Irkutsk, Russia
| | - Ekaterina Madyarova
- Irkutsk State University, Karl Marx str. 1, 664003 Irkutsk, Russia; Baikal Research Centre, Lenin str. 21, 664003 Irkutsk, Russia
| | - Mariya Dimova
- Irkutsk State University, Karl Marx str. 1, 664003 Irkutsk, Russia
| | - Anton Gurkov
- Irkutsk State University, Karl Marx str. 1, 664003 Irkutsk, Russia; Baikal Research Centre, Lenin str. 21, 664003 Irkutsk, Russia
| | - Kseniya Vereshchagina
- Irkutsk State University, Karl Marx str. 1, 664003 Irkutsk, Russia; Baikal Research Centre, Lenin str. 21, 664003 Irkutsk, Russia
| | - Renat Adelshin
- Irkutsk State University, Karl Marx str. 1, 664003 Irkutsk, Russia; Irkutsk Anti-Plague Research Institute of Siberia and Far East, Trilissera str. 78, 664047 Irkutsk, Russia
| | - Maxim Timofeyev
- Irkutsk State University, Karl Marx str. 1, 664003 Irkutsk, Russia; Baikal Research Centre, Lenin str. 21, 664003 Irkutsk, Russia.
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Cogne Y, Degli-Esposti D, Pible O, Gouveia D, François A, Bouchez O, Eché C, Ford A, Geffard O, Armengaud J, Chaumot A, Almunia C. De novo transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups. Sci Data 2019; 6:184. [PMID: 31562330 PMCID: PMC6764967 DOI: 10.1038/s41597-019-0192-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/13/2019] [Indexed: 11/17/2022] Open
Abstract
Gammarids are amphipods found worldwide distributed in fresh and marine waters. They play an important role in aquatic ecosystems and are well established sentinel species in ecotoxicology. In this study, we sequenced the transcriptomes of a male individual and a female individual for seven different taxonomic groups belonging to the two genera Gammarus and Echinogammarus: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni, and Echinogammarus marinus. These taxa were chosen to explore the molecular diversity of transcribed genes of genotyped individuals from these groups. Transcriptomes were de novo assembled and annotated. High-quality assembly was confirmed by BUSCO comparison against the Arthropod dataset. The 14 RNA-Seq-derived protein sequence databases proposed here will be a significant resource for proteogenomics studies of these ecotoxicologically relevant non-model organisms. These transcriptomes represent reliable reference sequences for whole-transcriptome and proteome studies on other gammarids, for primer design to clone specific genes or monitor their specific expression, and for analyses of molecular differences between gammarid species. Measurement(s) | transcription profiling assay | Technology Type(s) | RNA sequencing | Factor Type(s) | sex • species | Sample Characteristic - Organism | Gammarus • Echinogammarus | Sample Characteristic - Environment | habitat |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9777905
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Affiliation(s)
- Yannick Cogne
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Davide Degli-Esposti
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Olivier Pible
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Duarte Gouveia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Adeline François
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, F-31320, Castanet-Tolosan, France
| | - Camille Eché
- GeT-PlaGe, Genotoul, INRA Auzeville, F-31320, Castanet-Tolosan, France
| | - Alex Ford
- School of Biological Sciences, Institute of Marine Sciences Laboratories, P04 9LY, Portsmouth, United Kingdom
| | - Olivier Geffard
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France.
| | - Arnaud Chaumot
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Christine Almunia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
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Ma Q, Bu D, Zhang J, Wu Y, Pei D. The Transcriptome Landscape of Walnut Interspecies Hybrid ( Juglans hindsii × Juglans regia) and Regulation of Cambial Activity in Relation to Grafting. Front Genet 2019; 10:577. [PMID: 31293615 PMCID: PMC6598599 DOI: 10.3389/fgene.2019.00577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/03/2019] [Indexed: 12/18/2022] Open
Abstract
Walnuts (Juglans, Juglandaceae) are known throughout the world as economically important trees that provide fat, protein, vitamins, and minerals as a food source, and produce high-quality timber. We have amended the purpose section to say "However," the omics resources are limited, which hampered the elucidation of molecular mechanisms resulting in their economically important traits (such as yield, fertility alternation, oil synthesis, and wood formation). To enrich the omics database of walnut, there is great need for analyses of its genomic and transcriptomic characteristics. In this study, we reported for the first time of the transcriptome landscape of six important organs or tissues in walnut interspecies hybrid using next-generation sequencing technology. Over 338 million clean reads were obtained. This yielded 74,072 unigenes with an average length of 782.71 bp. To develop an understanding of gene functions and regulatory pathways, 66,355 of the unigenes were identified as homologs of annotated genes and classified into three general categories with 61 functional subcategories. 2,288 out of 2,549 unmapped unigenes had at least one BLAST hit against the public databases. A total of 1,237 transcription factor-encoding genes (TFs) and 2,297 tissue-specific unigenes were identified. Interestingly, in the new shoot between an adult seedling and a grafted tree, the expression of 9,494 unigenes were significantly different, among which 4,388 were up-regulated and 5,106 were down-regulated. Of these, 195, 177, 232, 75, 114, and 68 unigenes were related to transcription factors, cell wall, defense response, transport, plant hormone biosynthesis, and other cambial activity-related functions, respectively. The obtained sequences and putative functional data constitute a resource for future functional analyses in walnut and other woody plants. These findings will be useful in further studies addressing the molecular mechanisms underlying grafting-related cambial activity.
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Affiliation(s)
- Qingguo Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Dechao Bu
- Key Laboratory of Intelligent Information Processing, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Junpei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yang Wu
- Key Laboratory of Intelligent Information Processing, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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