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Li W, Song J, Tu H, Jiang S, Pan B, Li J, Zhao Y, Chen L, Xu Q. Genome sequencing of Coryphaenoides yaquinae reveals convergent and lineage-specific molecular evolution in deep-sea adaptation. Mol Ecol Resour 2024; 24:e13989. [PMID: 38946220 DOI: 10.1111/1755-0998.13989] [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: 02/18/2024] [Revised: 05/30/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
Abyssal (3501-6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome-level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal-living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep-sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep-sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin-containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep-sea species shed new light on the common genetic innovations required for deep-sea adaptation by the fishes.
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Affiliation(s)
- Wenhao Li
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Jie Song
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Huaming Tu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Binbin Pan
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jiazhen Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Yongpeng Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Qianghua Xu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
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Qi Y, Zhong Z, Liu X, He X, Zhou Y, Zhang L, Chen C, Linse K, Qiu JW, Sun J. Phylogenomic analyses reveal a single deep-water colonisation in Patellogastropoda. Mol Phylogenet Evol 2024; 190:107968. [PMID: 38000707 DOI: 10.1016/j.ympev.2023.107968] [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: 09/27/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Patellogastropoda, the true limpets, is a major group of gastropods widely distributed in marine habitats from the intertidal to deep sea. Though important for understanding their evolutionary radiation, the phylogenetic relationships among the patellogastropod families have always been challenging to reconstruct, with contradictory results likely due to insufficient sampling. Here, we obtained mitogenomic and phylogenomic data (transcriptomic or genomic) from six species representing the three predominantly deep-water patellogastropod families: Lepetidae, Neolepetopsidae, and Pectinodontidae. By using various phylogenetic methods, we show that mitogenome phylogeny recovers monophyly of eight families in most of the trees, though the relationships among families remain contentious. Meanwhile, a more robust family-level topology consistent with morphology was achieved by phylogenomics. This also reveals that these mainly deep-water families are monophyletic, suggesting a single colonisation of the deep water around the Jurassic. We also found a lack of significant correlation between genome size and habitat depth, despite some deep-water species exhibiting larger genome sizes. Our phylogenomic tree provides a stable phylogenetic backbone for Patellogastropoda that includes seven of the nine recognized families and paves the way for future evolutionary analyses in this major group of molluscs.
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Affiliation(s)
- Ying Qi
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Zhaoyan Zhong
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Xu Liu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Xing He
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Yadong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 311005, China
| | - Lili Zhang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Katrin Linse
- British Antarctic Survey, Cambridge, United Kingdom
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Jin Sun
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China.
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Saha A, Bellucci A, Fratini S, Cannicci S, Ciofi C, Iannucci A. Ecological factors and parity mode correlate with genome size variation in squamate reptiles. BMC Ecol Evol 2023; 23:69. [PMID: 38053023 PMCID: PMC10696768 DOI: 10.1186/s12862-023-02180-4] [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: 05/16/2023] [Accepted: 11/25/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Evidence of correlation between genome size, the nuclear haploid DNA content of a cell, environmental factors and life-history traits have been reported in many animal species. Genome size, however, spans over three orders of magnitude across taxa and such a correlation does not seem to follow a universal pattern. In squamate reptiles, the second most species-rich order of vertebrates, there are currently no studies investigating drivers of genome size variability. We run a series of phylogenetic generalized least-squares models on 227 species of squamates to test for possible relationships between genome size and ecological factors including latitudinal distribution, bioclimatic variables and microhabitat use. We also tested whether genome size variation can be associated with parity mode, a highly variable life history trait in this order of reptiles. RESULTS The best-fitting model showed that the interaction between microhabitat use and parity mode mainly accounted for genome size variation. Larger genome sizes were found in live-bearing species that live in rock/sand ecosystems and in egg-laying arboreal taxa. On the other hand, smaller genomes were found in fossorial live-bearing species. CONCLUSIONS Environmental factors and species parity mode appear to be among the main parameters explaining genome size variation in squamates. Our results suggest that genome size may favour adaptation of some species to certain environments or could otherwise result from the interaction between environmental factors and parity mode. Integration of genome size and genome sequencing data could help understand the role of differential genome content in the evolutionary process of genome size variation in squamates.
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Affiliation(s)
- Anik Saha
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Arianna Bellucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Sara Fratini
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- National Biodiversity Future Center, 90133, Palermo, Italy
| | - Stefano Cannicci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- National Biodiversity Future Center, 90133, Palermo, Italy
| | - Claudio Ciofi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
| | - Alessio Iannucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
- National Biodiversity Future Center, 90133, Palermo, Italy.
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He X, Wang H, Xu T, Zhang Y, Chen C, Sun Y, Qiu JW, Zhou Y, Sun J. Genomic Analysis of a Scale Worm Provides Insights into Its Adaptation to Deep-Sea Hydrothermal Vents. Genome Biol Evol 2023; 15:evad125. [PMID: 37401460 PMCID: PMC10348049 DOI: 10.1093/gbe/evad125] [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: 05/09/2023] [Revised: 06/24/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023] Open
Abstract
Deep-sea polynoid scale worms endemic to hydrothermal vents have evolved an adaptive strategy to the chronically hypoxic environment, but its underlying molecular mechanisms remain elusive. Here, we assembled a chromosome-scale genome of the vent-endemic scale worm Branchipolynoe longqiensis (the first annotated genome in the subclass Errantia) and annotated two shallow-water polynoid genomes, aiming to elucidate the adaptive mechanisms. We present a genome-wide molecular phylogeny of Annelida which calls for extensive taxonomy revision by including more genomes from key lineages. The B. longqiensis genome with a genome size of 1.86 Gb and 18 pseudochromosomes is larger than the genomes of two shallow-water polynoids, possibly due to the expansion of various transposable elements (TEs) and transposons. We revealed two interchromosomal rearrangements in B. longqiensis when compared with the two shallow-water polynoid genomes. The intron elongation and interchromosomal rearrangement can influence a number of biological processes, such as vesicle transport, microtubules, and transcription factors. Furthermore, the expansion of cytoskeleton-related gene families may favor the cell structure maintenance of B. longqiensis in the deep ocean. The expansion of synaptic vesicle exocytosis genes has possibly contributed to the unique complex structure of the nerve system in B. longqiensis. Finally, we uncovered an expansion of single-domain hemoglobin and a unique formation of tetra-domain hemoglobin via tandem duplications, which may be related to the adaptation to a hypoxic environment.
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Affiliation(s)
- Xing He
- Institute of Evolution and Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Hui Wang
- Institute of Evolution and Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Ting Xu
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yanjie Zhang
- School of Life Sciences, Hainan University, Haikou, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yanan Sun
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jian-Wen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yadong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Jin Sun
- Institute of Evolution and Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, China
- Laoshan Laboratory, Qingdao, China
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Piertney SB, Wenzel M, Jamieson AJ. Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench. Mol Ecol 2023; 32:2206-2218. [PMID: 36808786 DOI: 10.1111/mec.16887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/20/2023]
Abstract
The examination of genetic structure in the deep-ocean hadal zone has focused on divergence between tectonic trenches to understand how environment and geography may drive species divergence and promote endemism. There has been little attempt to examine localized genetic structure within trenches, partly because of logistical challenges associated with sampling at an appropriate scale, and the large effective population sizes of species that can be sampled adequately may mask underlying genetic structure. Here we examine genetic structure in the superabundant amphipod Hirondellea gigas in the Mariana Trench at depths of 8126-10,545 m. RAD sequencing was used to identify 3182 loci containing 43,408 single nucleotide polymorphisms (SNPs) across individuals after stringent pruning of loci to prevent paralogous multicopy genomic regions being erroneously merged. Principal components analysis of SNP genotypes resolved no genetic structure between sampling locations, consistent with a signature of panmixia. However, discriminant analysis of principal components identified divergence between all sites driven by 301 outlier SNPs in 169 loci and significantly associated with latitude and depth. Functional annotation of loci identified differences between singleton loci used in analysis and paralogous loci pruned from the data set and also between outlier and nonoutlier loci, all consistent with hypotheses explaining the role of transposable elements driving genome dynamics. This study challenges the traditional perspective that highly abundant amphipods within a trench form a single panmictic population. We discuss the findings in relation to eco-evolutionary and ontogenetic processes operating in the deep sea, and highlight key challenges associated with population genetic analysis in nonmodel systems with inherent large effective population sizes and genomes.
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Affiliation(s)
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Alan J Jamieson
- Minderoo-UWA Deep-Sea Research Centre, School of Biological Sciences and Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia
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6
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Weston JNJ, Jensen EL, Hasoon MSR, Kitson JJN, Stewart HA, Jamieson AJ. Barriers to gene flow in the deepest ocean ecosystems: Evidence from global population genomics of a cosmopolitan amphipod. SCIENCE ADVANCES 2022; 8:eabo6672. [PMID: 36288308 PMCID: PMC9604539 DOI: 10.1126/sciadv.abo6672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The deepest marine ecosystem, the hadal zone, hosts endemic biodiversity resulting from geographic isolation and environmental selection pressures. However, the pan-ocean distribution of some fauna challenges the concept that the hadal zone is a series of isolated island-like habitats. Whether this remains true at the population genomic level is untested. We investigated phylogeographic patterns of the amphipod, Bathycallisoma schellenbergi, from 12 hadal features across the Pacific, Atlantic, Indian, and Southern oceans and analyzed genome-wide single-nucleotide polymorphism markers and two mitochondrial regions. Despite a cosmopolitan distribution, populations were highly restricted to individual features with only limited gene flow between topographically connected features. This lack of connectivity suggests that populations are on separate evolutionary trajectories, with evidence of potential cryptic speciation at the Atacama Trench. Together, this global study demonstrates that the shallower ocean floor separating hadal features poses strong barriers to dispersal, driving genetic isolation and creating pockets of diversity to conserve.
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Affiliation(s)
- Johanna N J Weston
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | - Evelyn L Jensen
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | - Megan S R Hasoon
- Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | - James J N Kitson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | - Heather A Stewart
- British Geological Survey, Lyell Centre, Research Avenue South, Edinburgh EH14 4AP, UK
- School of Energy, Geoscience, Infrastructure and Society, Institute of Life and Earth Sciences, Heriot-Watt University, Edinburgh, UK, EH14 4AS, UK
| | - Alan J Jamieson
- Minderoo-UWA Deep-Sea Research Centre, School of Biological Sciences and Oceans Institute, The University of Western Australia (M090), 35 Stirling Highway, Perth, WA 6009
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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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Iannucci A, Saha A, Cannicci S, Bellucci A, Cheng CLY, Ng KH, Fratini S. Ecological, physiological and life-history traits correlate with genome sizes in decapod crustaceans. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.930888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Crustaceans are characterized by some of the most variable genome sizes among animals. Significant relationships between genome size and specific eco-physiological and morphological features have been described in many crustacean taxa, such as Amphipoda, Ostracoda, Cladocera, and Copepoda. A consistent pattern of genome size variation is yet to be found, however, in one of the most specious order of crustaceans, the Decapoda. We investigated how genome size is related to selected eco-physiological and life-history traits in species belonging to this order. We analyzed the respiratory, excretory, and developmental adaptations of 179 decapod species inhabiting shallow marine, deep marine, freshwater, intertidal, and terrestrial habitats. Our results show that the genome size is significantly larger in decapods that have a direct development. Moreover, in Anomura, Astacidea, and Brachyura we found larger genome sizes in species (i) living in freshwater habitats, (ii) using gills as a strictly water-breathing organs, and (iii) presenting a direct development. While species that (i) live in shallow waters, and intertidal and terrestrial habitats, (ii) have some degrees of air-breathing adaptations, namely gills that can exchange oxygen with air if wet or branchiostegal lungs, and (iii) possess an indirect or extended development are characterized by significantly smaller genomes. Our analyses show that developmental complexity affects genome size in decapods, and that multiple eco-physiological and life-history traits correlate with genome size in Anomura, Astacidea, and Brachyura.
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Li Y, Liu Y, Yu H, Liu F, Han W, Zeng Q, Zhang Y, Zhang L, Hu J, Bao Z, Wang S. Adaptive Bird-like Genome Miniaturization During the Evolution of Scallop Swimming Lifestyle. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1066-1077. [PMID: 35905893 DOI: 10.1016/j.gpb.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/08/2022] [Accepted: 07/20/2022] [Indexed: 10/16/2022]
Abstract
Genome miniaturization drives key evolutionary innovations of adaptive traits in vertebrates, such as the flight evolution of birds. However, whether similar evolutionary processes exist in invertebrates remains poorly understood. Derived from the second-largest animal phylum, scallops are a special group of bivalve molluscs and acquire the evolutionary novelty of the swimming lifestyle, providing excellent models for investigating the coordinated genome and lifestyle evolution. Here, we show for the first time that genome sizes of scallops exhibit a generally negative correlation with locomotion activity. To elucidate the co-evolution of genome size and swimming lifestyle, we focus on the Asian moon scallop (Amusium pleuronectes) that possesses the smallest known scallop genome while being among scallops with the highest swimming activity. Whole-genome sequencing of A. pleuronectes reveals highly conserved chromosomal macrosynteny and microsynteny, suggestive of a highly contracted but not degenerated genome. Genome reduction of A. pleuronectes is facilitated by significant inactivation of transposable elements, leading to reduced gene length, elevated expression of genes involved in energy-producing pathways, and decreased copy numbers and expression levels of biomineralization-related genes. Similar evolutionary changes of relevant pathways are also observed for bird genome reduction with flight evolution. The striking mimicry of genome miniaturization underlying the evolution of bird flight and scallop swimming unveils the potentially common, pivotal role of genome size fluctuation in the evolution of novel lifestyles in the animal kingdom.
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Affiliation(s)
- Yuli Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yaran Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Hongwei Yu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Fuyun Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Wentao Han
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Qifan Zeng
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Yuehuan Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Lingling Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jingjie Hu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Zhenmin Bao
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Shi Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China.
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Yuan J, Zhang X, Kou Q, Sun Y, Liu C, Li S, Yu Y, Zhang C, Jin S, Xiang J, Li X, Li F. Genome of a giant isopod, Bathynomus jamesi, provides insights into body size evolution and adaptation to deep-sea environment. BMC Biol 2022; 20:113. [PMID: 35562825 PMCID: PMC9107163 DOI: 10.1186/s12915-022-01302-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/21/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The deep-sea may be regarded as a hostile living environment, due to low temperature, high hydrostatic pressure, and limited food and light. Isopods, a species-rich group of crustaceans, are widely distributed across different environments including the deep sea and as such are a useful model for studying adaptation, migration, and speciation. Similar to other deep-sea organisms, giant isopods have larger body size than their shallow water relatives and have large stomachs and fat bodies presumably to store organic reserves. In order to shed light on the genetic basis of these large crustaceans adapting to the oligotrophic environment of deep-sea, the high-quality genome of a deep-sea giant isopod Bathynomus jamesi was sequenced and assembled. RESULTS B. jamesi has a large genome of 5.89 Gb, representing the largest sequenced crustacean genome to date. Its large genome size is mainly attributable to the remarkable proliferation of transposable elements (84%), which may enable high genome plasticity for adaptive evolution. Unlike its relatives with small body size, B. jamesi has expanded gene families related to pathways of thyroid and insulin hormone signaling that potentially contribute to its large body size. Transcriptomic analysis showed that some expanded gene families related to glycolysis and vesicular transport were specifically expressed in its digestive organs. In addition, comparative genomics and gene expression analyses in six tissues suggested that B. jamesi has inefficient lipid degradation, low basal metabolic rate, and bulk food storage, suggesting giant isopods adopt a more efficient mechanism of nutrient absorption, storage, and utilization to provide sustained energy supply for their large body size. CONCLUSIONS Taken together, the giant isopod genome may provide a valuable resource for understanding body size evolution and adaptation mechanisms of macrobenthic organisms to deep-sea environments.
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Affiliation(s)
- Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qi Kou
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yamin Sun
- Research Center for Functional Genomics and Biochip, Tianjin, 300457, China
| | - Chengzhang Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Chengsong Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Songjun Jin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Xinzheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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11
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Christiansen H, Heindler FM, Hellemans B, Jossart Q, Pasotti F, Robert H, Verheye M, Danis B, Kochzius M, Leliaert F, Moreau C, Patel T, Van de Putte AP, Vanreusel A, Volckaert FAM, Schön I. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 2021; 22:625. [PMID: 34418978 PMCID: PMC8380342 DOI: 10.1186/s12864-021-07917-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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Affiliation(s)
- Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.
| | - Franz M Heindler
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Quentin Jossart
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Henri Robert
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Marie Verheye
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Bruno Danis
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Camille Moreau
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Université de Bourgogne Franche-Comté (UBFC) UMR CNRS 6282 Biogéosciences, Dijon, France
| | - Tasnim Patel
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Anton P Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Isa Schön
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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12
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Weng YM, Francoeur CB, Currie CR, Kavanaugh DH, Schoville SD. A high-quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation. Mol Ecol Resour 2021; 21:2145-2165. [PMID: 33938156 DOI: 10.1111/1755-0998.13409] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022]
Abstract
The hyperdiverse order Coleoptera comprises a staggering ~25% of known species on Earth. Despite recent breakthroughs in next generation sequencing, there remains a limited representation of beetle diversity in assembled genomes. Most notably, the ground beetle family Carabidae, comprising more than 40,000 described species, has not been studied in a comparative genomics framework using whole genome data. Here we generate a high-quality genome assembly for Nebria riversi, to examine sources of novelty in the genome evolution of beetles, as well as genetic changes associated with specialization to high-elevation alpine habitats. In particular, this genome resource provides a foundation for expanding comparative molecular research into mechanisms of insect cold adaptation. Comparison to other beetles shows a strong signature of genome compaction, with N. riversi possessing a relatively small genome (~147 Mb) compared to other beetles, with associated reductions in repeat element content and intron length. Small genome size is not, however, associated with fewer protein-coding genes, and an analysis of gene family diversity shows significant expansions of genes associated with cellular membranes and membrane transport, as well as protein phosphorylation and muscle filament structure. Finally, our genomic analyses show that these high-elevation beetles have endosymbiotic Spiroplasma, with several metabolic pathways (e.g., propanoate biosynthesis) that might complement N. riversi, although its role as a beneficial symbiont or as a reproductive parasite remains equivocal.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin - Madison, Madison, WI, USA
| | - Charlotte B Francoeur
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, WI, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, WI, USA
| | - David H Kavanaugh
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin - Madison, Madison, WI, USA
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13
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Weston JNJ, Espinosa-Leal L, Wainwright JA, Stewart ECD, González CE, Linley TD, Reid WDK, Hidalgo P, Oliva ME, Ulloa O, Wenzhöfer F, Glud RN, Escribano R, Jamieson AJ. Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean. MARINE BIODIVERSITY : A JOURNAL OF THE SENCKENBERG RESEARCH INSTITUTE 2021; 51:51. [PMID: 34007343 PMCID: PMC8120496 DOI: 10.1007/s12526-021-01182-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Eurythenes S.I. Smith in Scudder, 1882 (Crustacea: Amphipoda) are prevalent scavengers of the benthopelagic community from bathyal to hadal depths. While a well-studied genus, molecular systematic studies have uncovered cryptic speciation and multiple undescribed lineages. Here, we apply an integrative taxonomic approach and describe the tenth species, Eurythenes atacamensis sp. nov., based on specimens from the 2018 Atacamex and RV Sonne SO261 Expeditions to the southern sector of the Peru-Chile Trench, the Atacama Trench (24-21°S). Eurythenes atacamensis sp. nov. is a large species, max. observed length 83.2 mm, possesses diagnostic features, including a short gnathopod 1 palm and a chelate gnathopod 2 palm, and a distinct genetic lineage based on a 16S rRNA and COI phylogeny. This species is a dominant bait-attending fauna with an extensive bathymetric range, spanning from 4974 to 8081 m. The RV Sonne SO261 specimens were recovered along a 10-station transect from abyssal to hadal depths and further examined for demographic and bathymetric-related patterns. Ontogenetic vertical stratification was evident across the trench axis, with only juveniles present at abyssal depths (4974-6025 m). Total length-depth analysis revealed that the size of females was unrelated to depth, whereas juveniles followed a sigmoidal relationship with a step-up in size at depths >7200 m. Thus, these bathymetric trends suggest that juveniles and females employ differing ecological strategies in subduction trench environments. This study highlights that even dominant and ecologically important species are still being discovered within the abyssal and hadal environments. Continued systematic expeditions will lead to an improved understanding of the eco-evolutionary drivers of speciation in the world's largest ecosystem.
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Affiliation(s)
- Johanna N. J. Weston
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
| | - Liliana Espinosa-Leal
- Programa de Doctorado en Oceanografía, Departamento de Oceanografía, Universidad de Concepción, P.O. Box 160 C, Concepción, Chile
- Departamento de Oceanografía and Instituto Milenio de Oceanografía, Universidad de Concepción, P.O. Box 160 C, Concepción, Chile
| | - Jennifer A. Wainwright
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
| | - Eva C. D. Stewart
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
- Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Carolina E. González
- Departamento de Oceanografía and Instituto Milenio de Oceanografía, Universidad de Concepción, P.O. Box 160 C, Concepción, Chile
| | - Thomas D. Linley
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
| | - William D. K. Reid
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
| | - Pamela Hidalgo
- Departamento de Oceanografía and Instituto Milenio de Oceanografía, Universidad de Concepción, P.O. Box 160 C, Concepción, Chile
| | - Marcelo E. Oliva
- Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Osvaldo Ulloa
- Departamento de Oceanografía and Instituto Milenio de Oceanografía, Universidad de Concepción, P.O. Box 160 C, Concepción, Chile
| | - Frank Wenzhöfer
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research, 27570 Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, 28358 Bremen, Germany
- Department of Biology, Nordcee and HADAL, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ronnie N. Glud
- Department of Biology, Nordcee and HADAL, University of Southern Denmark, 5230 Odense M, Denmark
- Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477 Japan
| | - Rubén Escribano
- Departamento de Oceanografía and Instituto Milenio de Oceanografía, Universidad de Concepción, P.O. Box 160 C, Concepción, Chile
| | - Alan J. Jamieson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
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14
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Glazier DS. Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem. BIOLOGY 2021; 10:270. [PMID: 33810583 PMCID: PMC8067107 DOI: 10.3390/biology10040270] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.
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15
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Molina WF, Costa GWWF, Cunha IMC, Bertollo LAC, Ezaz T, Liehr T, Cioffi MB. Molecular Cytogenetic Analysis in Freshwater Prawns of the Genus Macrobrachium (Crustacea: Decapoda: Palaemonidae). Int J Mol Sci 2020; 21:ijms21072599. [PMID: 32283616 PMCID: PMC7178241 DOI: 10.3390/ijms21072599] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 01/18/2023] Open
Abstract
Freshwater prawns of the genus Macrobrachium are one of the important components of circumtropical marine, estuarine, and freshwater environments. They have been extensively exploited for human consumption for many years. More than 250 species reflect the evolutionary success of this highly diversified group, with a complex and challenging taxonomy due to morphological variations and vast geographical distribution. Although genetic approaches have been used to clarify phylogenetic and taxonomic aspects of Macrobrachium species, cytogenetic information is still very scarce and mostly focused on chromosome number and morphology. Here, we present chromosome data for three species from the Neotropical region, M. carcinus,M. acanthurus, and M. amazonicum, and one species from the Oriental region, M. rosenbergii. Using conventional cytogenetic approaches and chromosome mapping of repetitive DNAs by fluorescence in situ hybridization (FISH), we identified numerical diversification of the diploid set, within and between both zoogeographic regions. These included M. acanthurus and M. amazonicum sharing diploid chromosomes of 98, while M. carcinus has 94, and M. rosenbergii has 118 chromosomes. Argentophilic sites are also variable in number, but they occur in a much higher number than 18S rDNA, representing two to 10 sites within the study species. Microsatellites repeat motifs are also abundant in the chromosomes, with a co-localization and uniform distribution along the chromosome arms, but completely absent in the AT-rich centromeric regions. As a whole, our study suggests that the 2n divergence was followed by a considerable rDNA diversification. The abundance of the exceptional amount of microsatellite sequences in the chromosomes also suggests that they are essential components of the Macrobrachium genome and, therefore, maintained as a shared feature by the species, the reason for which is yet unknown.
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Affiliation(s)
- Wagner F. Molina
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59078970, Brazil; (W.F.M.); (G.W.W.F.C.); (I.M.C.C.)
| | - Gideão W. W. F. Costa
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59078970, Brazil; (W.F.M.); (G.W.W.F.C.); (I.M.C.C.)
| | - Inailson M. C. Cunha
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59078970, Brazil; (W.F.M.); (G.W.W.F.C.); (I.M.C.C.)
| | - Luiz A. C. Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP C.P. 676, Brazil; (L.A.C.B.); (M.B.C.)
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia;
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 7747 Jena, Germany
- Correspondence:
| | - Marcelo B. Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP C.P. 676, Brazil; (L.A.C.B.); (M.B.C.)
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16
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Kwan YH, Zhang D, Mestre NC, Wong WC, Wang X, Lu B, Wang C, Qian PY, Sun J. Comparative Proteomics on Deep-Sea Amphipods after in Situ Copper Exposure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:13981-13991. [PMID: 31638389 DOI: 10.1021/acs.est.9b04503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interest in deep-sea mining increased along with the environmental concerns of these activities to the deep-sea fauna. The discovery of optimal biomarkers of deep-sea mining activities in deep-sea species is a crucial step toward the supply of important ecological information for environmental impact assessment. In this study, an in situ copper exposure experiment was performed on deep-sea scavenging amphipods. Abyssorchomene distinctus individuals were selected among all the exposed amphipods for molecular characterization. Copper concentration within the gut was assessed, followed by a tandem mass tag-based coupled with two-dimensional liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) applied to identify and quantify the protein expression changes after 48 h of exposure. 2937 proteins were identified and annotated, and 1918 proteins among all identified proteins were assigned by at least two nonambiguous peptides. The screening process was performed based on the differences in protein abundance and the specific correlation between the proteins and copper in previous studies. These differentially produced proteins include Na+/K+ ATPase, cuticle, chitinase, and proteins with unknown function. Their abundances showed correlation with copper and had high sensitivity to indicate the copper level, being here proposed as biomarker candidates for deep-sea mining activities in the future. This is a key step in the development of environmental impact assessment of deep-sea mining activities integrating ecotoxicological data.
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Affiliation(s)
- Yick Hang Kwan
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
| | - Dongsheng Zhang
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Nélia C Mestre
- CIMA - Centro de Investigação Marinha e Ambiental , Universidade do Algarve , Campus de Gambelas, 8005-139 Faro , Portugal
| | - Wai Chuen Wong
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
| | - Xiaogu Wang
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Bo Lu
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Chunsheng Wang
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Pei-Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
| | - Jin Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
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17
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Hultgren KM, Jeffery NW, Moran A, Gregory TR. Latitudinal variation in genome size in crustaceans. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx153] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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