1
|
Fodor E, Okendo J, Szabó N, Szabó K, Czimer D, Tarján-Rácz A, Szeverényi I, Low BW, Liew JH, Koren S, Rhie A, Orbán L, Miklósi Á, Varga M, Burgess SM. The reference genome of Macropodus opercularis (the paradise fish). Sci Data 2024; 11:540. [PMID: 38796485 PMCID: PMC11127978 DOI: 10.1038/s41597-024-03277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/18/2024] [Indexed: 05/28/2024] Open
Abstract
Amongst fishes, zebrafish (Danio rerio) has gained popularity as a model system over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such as behavior. By embracing other, less conventional experimental organisms, opportunities arise to gain broader insights into evolution and development, as well as studying behavioral aspects not available in current popular model systems. The anabantoid paradise fish (Macropodus opercularis), an "air-breather" species has a highly complex behavioral repertoire and has been the subject of many ethological investigations but lacks genomic resources. Here we report the reference genome assembly of M. opercularis using long-read sequences at 150-fold coverage. The final assembly consisted of 483,077,705 base pairs (~483 Mb) on 152 contigs. Within the assembled genome we identified and annotated 20,157 protein coding genes and assigned ~90% of them to orthogroups.
Collapse
Affiliation(s)
- Erika Fodor
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Javan Okendo
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Nóra Szabó
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Kata Szabó
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dávid Czimer
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Anita Tarján-Rácz
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ildikó Szeverényi
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Keszthely, Hungary
| | - Bi Wei Low
- Science Unit, Lingnan University, Hong Kong, China
| | | | - Sergey Koren
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Arang Rhie
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - László Orbán
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Keszthely, Hungary
| | - Ádám Miklósi
- Department of Ethology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary.
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
| |
Collapse
|
2
|
Zuo B, Nneji LM, Sun YB. Comparative genomics reveals insights into anuran genome size evolution. BMC Genomics 2023; 24:379. [PMID: 37415107 PMCID: PMC10324214 DOI: 10.1186/s12864-023-09499-8] [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: 03/06/2023] [Accepted: 06/30/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types. RESULTS Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats. CONCLUSIONS Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.
Collapse
Affiliation(s)
- Bin Zuo
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China
| | - Lotanna Micah Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Yan-Bo Sun
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China.
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, 650091, China.
| |
Collapse
|
3
|
Zhou J, Liu A, He F, Zhang Y, Shen L, Yu J, Zhang X. Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:501-514. [PMID: 36470576 PMCID: PMC10787021 DOI: 10.1016/j.gpb.2022.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 11/03/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
The white-blotched river stingray (Potamotrygon leopoldi) is a cartilaginous fish native to the Xingu River, a tributary of the Amazon River system. As a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family in which no member has the genome sequencing information available, P. leopoldi provides the evolutionary details in fish phylogeny, niche adaptation, and skeleton formation. In this study, we present its draft genome of 4.11 Gb comprising 16,227 contigs and 13,238 scaffolds, with contig N50 of 3937 kb and scaffold N50 of 5675 kb in size. Our analysis shows that P. leopoldi is a slow-evolving fish that diverged from elephant sharks about 96 million years ago. Moreover, two gene families related to the immune system (immunoglobulin heavy constant delta genes and T-cell receptor alpha/delta variable genes) exhibit expansion in P. leopoldi only. We also identified the Hox gene clusters in P. leopoldi and discovered that seven Hox genes shared by five representative fish species are missing in P. leopoldi. The RNA sequencing data from P. leopoldi and other three fish species demonstrate that fishes have a more diversified tissue expression spectrum when compared to mammals. Our functional studies suggest that lack of the gc gene encoding vitamin D-binding protein in cartilaginous fishes (both P. leopoldi and Callorhinchus milii) could partly explain the absence of hard bone in their endoskeleton. Overall, this genome resource provides new insights into the niche adaptation, body plan, and skeleton formation of P. leopoldi, as well as the genome evolution in cartilaginous fishes.
Collapse
Affiliation(s)
- Jingqi Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Funan He
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Yunbin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Libing Shen
- International Human Phenome Institutes (Shanghai), Shanghai 200433, China; Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Jun Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiang Zhang
- Shanghai Nanmulin Biotechnology Company Limited, Shanghai 200031, China.
| |
Collapse
|
4
|
de Moraes RLR, Sassi FDMC, Marinho MMF, Ráb P, Porto JIR, Feldberg E, Cioffi MDB. Small Body, Large Chromosomes: Centric Fusions Shaped the Karyotype of the Amazonian Miniature Fish Nannostomus anduzei (Characiformes, Lebiasinidae). Genes (Basel) 2023; 14:192. [PMID: 36672933 PMCID: PMC9858914 DOI: 10.3390/genes14010192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Miniature refers to species with extraordinarily small adult body size when adult and can be found within all major metazoan groups. It is considered that miniature species have experienced severe alteration of numerous morphological traits during evolution. For a variety of reasons, including severe labor concerns during collecting, chromosomal acquisition, and taxonomic issues, miniature fishes are neglected and understudied. Since some available studies indicate possible relationship between diploid chromosome number (2n) and body size in fishes, we aimed to study one of the smallest Neotropical fish Nannostomus anduzei (Teleostei, Characiformes, Lebiasinidae), using both conventional (Giemsa staining, C-banding) and molecular cytogenetic methods (FISH mapping of rDNAs, microsatellites, and telomeric sequences). Our research revealed that N. anduzei possesses one of the lowest diploid chromosome numbers (2n = 22) among teleost fishes, and its karyotype is entirely composed of large metacentric chromosomes. All chromosomes, except for pair number 11, showed an 18S rDNA signal in the pericentromeric region. 5S rDNA signals were detected in the pericentromeric regions of chromosome pair number 1 and 6, displaying synteny to 18S rDNA signals. Interstitial telomeric sites (ITS) were identified in the centromeric region of pairs 6 and 8, indicating that centric fusions played a significant role in karyotype evolution of studied species. Our study provides further evidence supporting the trend of diploid chromosome number reduction along with miniaturization of adult body size in fishes.
Collapse
Affiliation(s)
- Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
| | - Francisco de Menezes Cavalcante Sassi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
| | - Manoela Maria Ferreira Marinho
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Cidade Universitária, Castelo Branco, João Pessoa 58051-900, PB, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Jorge Ivan Rebelo Porto
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
| |
Collapse
|
5
|
Wang J, Yuan L, Tang J, Liu J, Sun C, Itgen MW, Chen G, Sessions SK, Zhang G, Mueller RL. Transposable element and host silencing activity in gigantic genomes. Front Cell Dev Biol 2023; 11:1124374. [PMID: 36910142 PMCID: PMC9998948 DOI: 10.3389/fcell.2023.1124374] [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: 12/15/2022] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
Transposable elements (TEs) and the silencing machinery of their hosts are engaged in a germline arms-race dynamic that shapes TE accumulation and, therefore, genome size. In animal species with extremely large genomes (>10 Gb), TE accumulation has been pushed to the extreme, prompting the question of whether TE silencing also deviates from typical conditions. To address this question, we characterize TE silencing via two pathways-the piRNA pathway and KRAB-ZFP transcriptional repression-in the male and female gonads of Ranodon sibiricus, a salamander species with a ∼21 Gb genome. We quantify 1) genomic TE diversity, 2) TE expression, and 3) small RNA expression and find a significant relationship between the expression of piRNAs and TEs they target for silencing in both ovaries and testes. We also quantified TE silencing pathway gene expression in R. sibiricus and 14 other vertebrates with genome sizes ranging from 1 to 130 Gb and find no association between pathway expression and genome size. Taken together, our results reveal that the gigantic R. sibiricus genome includes at least 19 putatively active TE superfamilies, all of which are targeted by the piRNA pathway in proportion to their expression levels, suggesting comprehensive piRNA-mediated silencing. Testes have higher TE expression than ovaries, suggesting that they may contribute more to the species' high genomic TE load. We posit that apparently conflicting interpretations of TE silencing and genomic gigantism in the literature, as well as the absence of a correlation between TE silencing pathway gene expression and genome size, can be reconciled by considering whether the TE community or the host is currently "on the attack" in the arms race dynamic.
Collapse
Affiliation(s)
- Jie Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Liang Yuan
- School of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Jiaxing Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.,College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Jiongyu Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Michael W Itgen
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Guiying Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | | | - Guangpu Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.,College of Life Sciences, Sichuan Normal University, Chengdu, China
| | | |
Collapse
|
6
|
Schedel FDB, Musilova Z, Indermaur A, Bitja‐Nyom AR, Salzburger W, Schliewen UK. Towards the phylogenetic placement of the enigmatic African genus Prolabeops Schultz, 1941. JOURNAL OF FISH BIOLOGY 2022; 101:1333-1342. [PMID: 36053860 PMCID: PMC9826184 DOI: 10.1111/jfb.15205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
The small cyprinid genus Prolabeops Schultz, 1941 is restricted to the Nyong and Sanaga River systems in Cameroon. In the past, the genus had been suggested to be either a member of the Labeoninae, Torinae or the Smiliogastrinae mainly on the basis of morphological similarities, and it is nowadays considered as incertae sedis within the Cypriniformes. This study provides the first attempt to reveal the phylogenetic position of Prolabeops using molecular data. For this purpose, the authors sequenced a large fraction of the mitochondrial genome (c. 13,600 bp), including all mitochondrial protein coding genes, of two Prolabeops melanhypopterus specimens and an additional four Enteromius specimens. The large-scale phylogenetic analysis was based on an alignment including all mitochondrial protein coding genes of 902 specimens representing c. 899 cypriniform species. Prolabeops was clearly recovered within the African Smiliogastrinae, forming a weakly supported clade together with Enteromius jae, Enteromius hulstaerti and Barboides gracilis. The study data underline the urgent need of a thorough taxonomic revision of the small African barbs collectively placed in the genus Enteromius.
Collapse
Affiliation(s)
- Frederic D. B. Schedel
- Zoological InstituteUniversity of BaselBaselSwitzerland
- Faculty of Biology, Division of Evolutionary BiologyLMU MunichMartinsriedGermany
| | - Zuzana Musilova
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Arnold Roger Bitja‐Nyom
- Department of Biological SciencesUniversity of NgaoundéréNgaoundéréCameroon
- Department of Management of Fisheries and Aquatic EcosystemsUniversity of DoualaDoualaCameroon
| | | | - Ulrich K. Schliewen
- Department of IchthyologySNSB‐Bavarian State Collection Zoology (ZSM)MunichGermany
| |
Collapse
|
7
|
Sam KK, Lau NS, Kuah MK, Lading EA, Shu-Chien AC. A complete inventory of long-chain polyunsaturated fatty acid biosynthesis pathway enzymes in the miniaturized cyprinid Paedocypris micromegethes. FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:817-838. [PMID: 35643977 DOI: 10.1007/s10695-022-01082-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
The capacity for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis activity in a species depends on the enzymatic activities of fatty acyl desaturase (Fads) and elongation of very long-chain fatty acid (Elovl). The miniaturized fish Paedocypris micromegethes is a developmentally truncated cyprinid living in highly acidic water conditions in tropical peat swamps. The capacity for LC-PUFA biosynthesis in this species, which has a reduced genome size, is unknown. A high-quality de novo transcriptome assembly enabled the identification of a putative Fads2 and four Elovl. The Fads2 was verified as a P. micromegethes Fads2 ortholog with in vitro Δ5 and Δ6 activities. The Elovl sequences were established as an Elovl5, Elovl2, and two Elovl4 paralogs, namely Elovl4a and Elovl4b. These Elovl enzymes, mainly Elovl5 and Elovl2, fulfill the necessary C18, C20, and C22 PUFA elongation steps for LC-PUFA biosynthesis. Collectively, these results validate the presence of a complete repertoire of LC-PUFA biosynthesis enzymes in a peat swamp miniatured freshwater fish.
Collapse
Affiliation(s)
- Ka-Kei Sam
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900, Bayan Lepas, Penang, Malaysia
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900, Bayan Lepas, Penang, Malaysia
| | - Meng-Kiat Kuah
- Lab-Ind Resource Sdn. Bhd, 48300, Bukit Beruntung, Selangor, Malaysia
| | - Engkamat Anak Lading
- Forest Department Sarawak, Forest Department HQ, Level 11, Baitul Makmur II, Medan Raya, Petra Jaya, 93050, Kuching, Sarawak, Malaysia
| | - Alexander Chong Shu-Chien
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900, Bayan Lepas, Penang, Malaysia.
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia.
| |
Collapse
|
8
|
Lika K, Augustine S, Kooijman SALM. The comparative energetics of the ray-finned fish in an evolutionary context. CONSERVATION PHYSIOLOGY 2022; 10:coac039. [PMID: 35811597 PMCID: PMC9258789 DOI: 10.1093/conphys/coac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/13/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
To address challenges in management and conservation of fishes and fisheries it is essential to understand their life histories and energetics. The Add-my-Pet (AmP) collection of data on energetics and Dynamic Energy Budget (DEB) parameters currently contains 1150 of the 40000 extant species of fish. It gives 250-280 traits per species, depending on the model type that was applied, such as maximum reserve capacity, lifespan, specific respiration and precociality index, based on which the ray-finned fish (Actinopterygii) was compared with the four other fish classes (Cyclostomata, Chondrichthyes, Actinistia, Dipnoi) and the Tetrapoda. The Actinopterygii are the only vertebrate class that shows metabolic acceleration, and clearly so in only three sub-clades. Different from chondrichthyans, quite a few species follow the waste-to-hurry strategy, especially small bodied freshwater fish such as tropical annual killifish, but also in small minnows and darters in continental climates. We briefly discuss links between waste-to-hurry, which is associated with a large specific somatic maintenance, and sensitivity for pesticides. We discuss why this interferes with the physical co-variation between maximum reserve capacity and ultimate structural length or weight and explains why maximum reserve capacity increases with body length in chondrichthyans, but not in actinopterygians. Reserve capacity has relevance, e.g. mass-specific maintenance, starvation and the kinetics of lipophyllic compounds (such as pesticides), since reserve is relatively rich in lipids in fish. Also, unlike chondrichthyans, the size at birth is very small and not linked to ultimate size; we discuss the implications. Actinopterygians allocate more to soma, compared with chondrichthyans; the latter allocate more to maturity or reproduction. Actinopterygians, Actinistia and Dipnoi are near the supply-end of the supply-demand spectrum, while chondrichthyans clearly show demand properties.
Collapse
Affiliation(s)
- Konstadia Lika
- Department of Biology, University of Crete, Voutes University Campus, 70013, Heraklion, Greece
| | - Starrlight Augustine
- Akvaplan-niva, Fram High North Research Centre for Climate and the Environment, Postboks 6606, 9296 Tromsø, Norway
| | - Sebastiaan A L M Kooijman
- Department of Theoretical Biology, VU University Amsterdam, de Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| |
Collapse
|
9
|
Arbour JH, Stanchak KE. The little fishes that could: smaller fishes demonstrate slow body size evolution but faster speciation in the family Percidae. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab125] [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]
Abstract
Abstract
Body size affects numerous aspects of organismal biology and many factors have been invoked to explain body size distributions in a macroecological and macroevolutionary context. Body size in the freshwater fish family Percidae is strongly right-skewed (i.e. dominated by small sizes), with small body size potentially being associated with fast water habitats. We constructed a new species-level, multi-locus, time-calibrated phylogeny of Percidae, and used it to test for changes in the rate and pattern of maximum body size evolution. We also tested whether speciation rates varied as a function of body size. We found that Etheostomatinae evolved towards a smaller adaptive optimum in body size compared to the other subfamilies of Percidae, and that this shift was associated with a reduction in the rate of body size evolution. Speciation rates were associated with body size across percids, showing a peak around small to medium body size. Small body size appears to partially, but not fully, explain the diversity of small percids, as many darters fall well below the “optimum” body size. Reinforcement of selection for small body size via selection for novel morphologies or via sexual selection may help to fully explain the remarkable diversity of darter radiation.
Collapse
Affiliation(s)
- Jessica H Arbour
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | | |
Collapse
|
10
|
Britz R, Conway KW, Rüber L. The emerging vertebrate model species for neurophysiological studies is Danionella cerebrum, new species (Teleostei: Cyprinidae). Sci Rep 2021; 11:18942. [PMID: 34556691 PMCID: PMC8460714 DOI: 10.1038/s41598-021-97600-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/26/2021] [Indexed: 11/09/2022] Open
Abstract
The four described species of Danionella are tiny, transparent fishes that mature at sizes between 10–15 mm, and represent some of the most extreme cases of vertebrate progenesis known to date. The miniature adult size and larval appearance of Danionella, combined with a diverse behavioral repertoire linked to sound production by males, have established Danionella as an important model for neurophysiological studies. The external similarity between the different species of Danionella has offered an important challenge to taxonomic identification using traditional external characters, leading to confusion over the identity of the model species. Using combined morphological and molecular taxonomic approaches, we show here that the most extensively studied species of Danionella is not D. translucida, but represents an undescribed species, D. cerebrum n. sp. that is externally almost identical to D. translucida, but differs trenchantly in several internal characters. Molecular analyses confirm the distinctiveness of D. cerebrum and D. translucida and suggest that the two species are not even sister taxa. Analysis of the evolution of sexual dimorphisms associated with the Weberian apparatus reveals significant increases in complexity from the simpler condition found in D. dracula, to most complex conditions in D. cerebrum, D. mirifica and D. translucida.
Collapse
Affiliation(s)
- Ralf Britz
- Senckenberg Natural History Collections Dresden, Museum of Zoology, 01109, Dresden, Germany. .,Research Associate, Department of Life Sciences, Natural History Museum, London, SW75BD, UK.
| | - Kevin W Conway
- Department of Ecology and Conservation, Biology and Biodiversity Research and Teaching Collections, Texas A&M University, College Station, College Station, TX, 77543, USA.,Research Associate, Ichthyology, Australian Museum Research Institute, 1 William Street, Sydney, NSW, 2010, Australia
| | - Lukas Rüber
- Naturhistorisches Museum Bern, 3005, Bern, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland
| |
Collapse
|
11
|
Adams RH, Blackmon H, DeGiorgio M. Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data. Syst Biol 2021; 70:660-680. [PMID: 33587145 PMCID: PMC8208806 DOI: 10.1093/sysbio/syab009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/01/2021] [Indexed: 12/03/2022] Open
Abstract
Stochastic models of character trait evolution have become a cornerstone of evolutionary biology in an array of contexts. While probabilistic models have been used extensively for statistical inference, they have largely been ignored for the purpose of measuring distances between phylogeny-aware models. Recent contributions to the problem of phylogenetic distance computation have highlighted the importance of explicitly considering evolutionary model parameters and their impacts on molecular sequence data when quantifying dissimilarity between trees. By comparing two phylogenies in terms of their induced probability distributions that are functions of many model parameters, these distances can be more informative than traditional approaches that rely strictly on differences in topology or branch lengths alone. Currently, however, these approaches are designed for comparing models of nucleotide substitution and gene tree distributions, and thus, are unable to address other classes of traits and associated models that may be of interest to evolutionary biologists. Here, we expand the principles of probabilistic phylogenetic distances to compute tree distances under models of continuous trait evolution along a phylogeny. By explicitly considering both the degree of relatedness among species and the evolutionary processes that collectively give rise to character traits, these distances provide a foundation for comparing models and their predictions, and for quantifying the impacts of assuming one phylogenetic background over another while studying the evolution of a particular trait. We demonstrate the properties of these approaches using theory, simulations, and several empirical data sets that highlight potential uses of probabilistic distances in many scenarios. We also introduce an open-source R package named PRDATR for easy application by the scientific community for computing phylogenetic distances under models of character trait evolution.[Brownian motion; comparative methods; phylogeny; quantitative traits.].
Collapse
Affiliation(s)
- Richard H Adams
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| |
Collapse
|
12
|
Lamichhaney S, Catullo R, Keogh JS, Clulow S, Edwards SV, Ezaz T. A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum. Proc Natl Acad Sci U S A 2021; 118:e2011649118. [PMID: 33836564 PMCID: PMC7980411 DOI: 10.1073/pnas.2011649118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements (TEs) or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms driving or constraining genome size are poorly understood. Here, we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog (Platyplectrum ornatum) from Australia, and compare it to other published frog and vertebrate genomes to examine the forces driving reduction in genome size. At ∼1.06 gigabases (Gb), the P. ornatum genome is like that of birds, revealing four major mechanisms underlying TE dynamics: reduced abundance of all major classes of TEs; increased net deletion bias in TEs; drastic reduction in intron lengths; and expansion via gene duplication of the repertoire of TE-suppressing Piwi genes, accompanied by increased expression of Piwi-interacting RNA (piRNA)-based TE-silencing pathway genes in germline cells. Transcriptomes from multiple tissues in both sexes corroborate these results and provide insight into sex-differentiation pathways in Platyplectrum Genome skimming of two closely related frog species (Lechriodus fletcheri and Limnodynastes fletcheri) confirms a reduction in TEs as a major driver of genome reduction in Platyplectrum and supports a macroevolutionary scenario of small genome size in frogs driven by convergence in life history, especially rapid tadpole development and tadpole diet. The P. ornatum genome offers a model for future comparative studies on mechanisms of genome size reduction in amphibians and vertebrates generally.
Collapse
Affiliation(s)
- Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Renee Catullo
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia 2601
- Australian National Insect Collection and Future Science Platform Environomics, Commonwealth Scientific and Industrial Research Organization, Acton, ACT, Australia 2601
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia 2601
| | - Simon Clulow
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia 2109
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Tariq Ezaz
- Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia 2617
| |
Collapse
|
13
|
Strong CRC, Palci A, Caldwell MW. Insights into skull evolution in fossorial snakes, as revealed by the cranial morphology of Atractaspis irregularis (Serpentes: Colubroidea). J Anat 2021; 238:146-172. [PMID: 32815172 PMCID: PMC7755084 DOI: 10.1111/joa.13295] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 01/03/2023] Open
Abstract
Comparative osteological analyses of extant organisms provide key insight into major evolutionary transitions and phylogenetic hypotheses. This is especially true for snakes, given their unique morphology relative to other squamates and the persistent controversy regarding their evolutionary origins. However, the osteology of several major snake groups remains undescribed, thus hindering efforts to accurately reconstruct the phylogeny of snakes. One such group is the Atractaspididae, a family of fossorial colubroids. We herein present the first detailed description of the atractaspidid skull, based on fully segmented micro-computed tomography (micro-CT) scans of Atractaspis irregularis. The skull of Atractaspis presents a highly unique morphology influenced by both fossoriality and paedomorphosis. This paedomorphosis is especially evident in the jaws, palate, and suspensorium, the major elements associated with macrostomy (large-gaped feeding in snakes). Comparison to scolecophidians-a group of blind, fossorial, miniaturized snakes-in turn sheds light on current hypotheses of snake phylogeny. Features of both the naso-frontal joint and the morphofunctional system related to macrostomy refute the traditional notion that scolecophidians are fundamentally different from alethinophidians (all other extant snakes). Instead, these features support the controversial hypothesis of scolecophidians as "regressed alethinophidians," in contrast to their traditional placement as the earliest-diverging snake lineage. We propose that Atractaspis and scolecophidians fall along a morphological continuum, characterized by differing degrees of paedomorphosis. Altogether, a combination of heterochrony and miniaturization provides a mechanism for the derivation of the scolecophidian skull from an ancestral fossorial alethinophidian morphotype, exemplified by the nonminiaturized and less extreme paedomorph Atractaspis.
Collapse
Affiliation(s)
| | - Alessandro Palci
- Earth Sciences SectionSouth Australian MuseumAdelaideSAAustralia,College of Science and EngineeringFlinders UniversityBedford ParkSAAustralia
| | - Michael W. Caldwell
- Department of Biological SciencesUniversity of AlbertaEdmontonABCanada,Department of Earth and Atmospheric SciencesUniversity of AlbertaEdmontonABCanada
| |
Collapse
|
14
|
Giorgetti OB, Shingate P, O'Meara CP, Ravi V, Pillai NE, Tay BH, Prasad A, Iwanami N, Tan HH, Schorpp M, Venkatesh B, Boehm T. Antigen receptor repertoires of one of the smallest known vertebrates. SCIENCE ADVANCES 2021; 7:7/1/eabd8180. [PMID: 33523858 PMCID: PMC7775753 DOI: 10.1126/sciadv.abd8180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/04/2020] [Indexed: 05/06/2023]
Abstract
The rules underlying the structure of antigen receptor repertoires are not yet fully defined, despite their enormous importance for the understanding of adaptive immunity. With current technology, the large antigen receptor repertoires of mice and humans cannot be comprehensively studied. To circumvent the problems associated with incomplete sampling, we have studied the immunogenetic features of one of the smallest known vertebrates, the cyprinid fish Paedocypris sp. "Singkep" ("minifish"). Despite its small size, minifish has the key genetic facilities characterizing the principal vertebrate lymphocyte lineages. As described for mammals, the frequency distributions of immunoglobulin and T cell receptor clonotypes exhibit the features of fractal systems, demonstrating that self-similarity is a fundamental property of antigen receptor repertoires of vertebrates, irrespective of body size. Hence, minifish achieve immunocompetence via a few thousand lymphocytes organized in robust scale-free networks, thereby ensuring immune reactivity even when cells are lost or clone sizes fluctuate during immune responses.
Collapse
Affiliation(s)
- Orlando B Giorgetti
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Prashant Shingate
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Connor P O'Meara
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Vydianathan Ravi
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Nisha E Pillai
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Boon-Hui Tay
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Aravind Prasad
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore 117377, Singapore
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
| |
Collapse
|
15
|
Conway KW, Kubicek K, Britz R. Extreme evolutionary shifts in developmental timing establish the miniature
Danionella
as a novel model in the neurosciences. Dev Dyn 2020; 250:601-611. [DOI: 10.1002/dvdy.280] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 01/01/2023] Open
Affiliation(s)
- Kevin W. Conway
- Department of Ecology and Conservation Biology and Biodiversity Research and Teaching Collections Texas A&M University College Station Texas USA
| | - Kole Kubicek
- Department of Ecology and Conservation Biology and Biodiversity Research and Teaching Collections Texas A&M University College Station Texas USA
| | - Ralf Britz
- Sektionsleiter Ichthyologie Senckenberg Naturhistorische Sammlungen, Dresden, Museum für Tierkunde Dresden Germany
| |
Collapse
|
16
|
Matschiner M, Böhne A, Ronco F, Salzburger W. The genomic timeline of cichlid fish diversification across continents. Nat Commun 2020; 11:5895. [PMID: 33208747 PMCID: PMC7674422 DOI: 10.1038/s41467-020-17827-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/15/2020] [Indexed: 11/23/2022] Open
Abstract
Cichlid fishes are celebrated for their vast taxonomic, phenotypic, and ecological diversity; however, a central aspect of their evolution - the timeline of their diversification - remains contentious. Here, we generate draft genome assemblies of 14 species representing the global cichlid diversity and integrate these into a new phylogenomic hypothesis of cichlid and teleost evolution that we time-calibrate with 58 re-evaluated fossil constraints and a new Bayesian model accounting for fossil-assignment uncertainty. Our results support cichlid diversification long after the breakup of the supercontinent Gondwana and lay the foundation for precise temporal reconstructions of the exceptional continental cichlid adaptive radiations.
Collapse
Affiliation(s)
- Michael Matschiner
- Zoological Institute, University of Basel, Basel, Switzerland.
- Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Astrid Böhne
- Zoological Institute, University of Basel, Basel, Switzerland
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Fabrizia Ronco
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Walter Salzburger
- Zoological Institute, University of Basel, Basel, Switzerland.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| |
Collapse
|
17
|
EDITORIAL NOTES AND NEWS. COPEIA 2020. [DOI: 10.1643/ct2020113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
18
|
Qu Z, Nong W, Yu Y, Baril T, Yip HY, Hayward A, Hui JHL. Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae). BMC Genomics 2020; 21:726. [PMID: 33076831 PMCID: PMC7574432 DOI: 10.1186/s12864-020-07145-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/12/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Teleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries and aquaculture. Additionally, the four-finger threadfin Eleutheronema tetradactylum is of conservation relevance since its populations are considered to be in rapid decline and it is classified as endangered. However, no genomic resources are currently available for the threadfin family Polynemidae. RESULTS We sequenced and assembled the first threadfin fish genome, the four-finger threadfin E. tetradactylum. We provide a genome assembly for E. tetradactylum with high contiguity (scaffold N50 = 56.3 kb) and high BUSCO completeness at 96.5%. The assembled genome size of E. tetradactylum is just 610.5 Mb, making it the second smallest perciform genome assembled to date. Just 9.07-10.91% of the genome sequence was found to consist of repetitive elements (standard RepeatMasker analysis vs custom analysis), making this the lowest repeat content identified to date for any perciform fish. A total of 37,683 protein-coding genes were annotated, and we include analyses of developmental transcription factors, including the Hox, ParaHox, and Sox families. MicroRNA genes were also annotated and compared with other chordate lineages, elucidating the gains and losses of chordate microRNAs. CONCLUSIONS The four-finger threadfin E. tetradactylum genome presented here represents the first available genome sequence for the ecologically, biologically, and commercially important clade of threadfin fish. Our findings provide a useful genomic resource for future research into the interesting biology and evolution of this valuable group of food fish.
Collapse
Affiliation(s)
- Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yifei Yu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, Exeter, TR10 9FE, UK
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, Exeter, TR10 9FE, UK.
| | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|
19
|
Zhang J, Qi J, Shi F, Pan H, Liu M, Tian R, Geng Y, Li H, Qu Y, Chen J, Seim I, Li M. Insights into the Evolution of Neoteny from the Genome of the Asian Icefish Protosalanx chinensis. iScience 2020; 23:101267. [PMID: 32593955 PMCID: PMC7327861 DOI: 10.1016/j.isci.2020.101267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/28/2020] [Accepted: 06/08/2020] [Indexed: 12/23/2022] Open
Abstract
Salangids, known as Asian icefishes, represent a peculiar radiation within the bony fish order Protacanthopterygii where adult fish retain larval characteristics such as transparent and miniaturized bodies and a cartilaginous endoskeleton into adulthood. Here, we report a de novo genome of Protosalanx chinensis, the most widely distributed salangid lineage. The P. chinensis genome assembly is more contiguous and complete than a previous assembly. We estimate that P. chinensis, salmons, trouts, and pikes diverged from a common ancestor 185 million years ago. A juxtaposition with other fish genomes revealed loss of the genes encoding ectodysplasin-A receptor (EDAR), SCPP1, and four Hox proteins and likely lack of canonical fibroblast growth factor 5 (FGF5) function. We also report genomic variations of P. chinensis possibly reflecting the immune system repertoire of a species with a larval phenotype in sexually mature individuals. The new Asian icefish reference genome provides a solid foundation for future studies.
Collapse
Affiliation(s)
- Jie Zhang
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.
| | - Jiwei Qi
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
| | - Fanglei Shi
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huijuan Pan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Ran Tian
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Huaying Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Yujie Qu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource, Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou 510260, China.
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, QLD 4102, Australia.
| | - Ming Li
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| |
Collapse
|
20
|
Giribet G. Genomes: Miniaturization Taken to Extremes. Curr Biol 2020; 30:R314-R316. [DOI: 10.1016/j.cub.2020.02.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
21
|
Slyusarev GS, Starunov VV, Bondarenko AS, Zorina NA, Bondarenko NI. Extreme Genome and Nervous System Streamlining in the Invertebrate Parasite Intoshia variabili. Curr Biol 2020; 30:1292-1298.e3. [PMID: 32084405 DOI: 10.1016/j.cub.2020.01.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/21/2019] [Accepted: 01/17/2020] [Indexed: 11/19/2022]
Abstract
Orthonectida is a small, rare, and in many aspects enigmatic group of organisms with a unique life cycle and a highly simplified adult free-living stage parasitizing various marine invertebrates [1, 2]. Phylogenetic relationships of Orthonectida have remained controversial for a long time. According to recent data, they are close to Annelida, specifically to Clitellata [3-5]. Several studies have shown that parasitism can not only lead to a dramatic reduction of the body plan and morphological structures but also affect organisms at the genomic level [6, 7]. Comparative studies of parasites and closely related non-parasitic species could clarify the genome reduction degree and evolution of parasitism. Here, we report on the morphology, genome structure, and content of the smallest known Orthonectida species Intoshia variabili, inhabiting the flatworm Graffiellus croceus. This orthonectid with an extremely simplified nervous system demonstrates the smallest known genome (15.3 Mbp) and one of the lowest reported so far gene numbers (5,120 protein-coding genes) among metazoans. The genome is extremely compact, due to a significant reduction of gene number, intergenic regions, intron length, and repetitive elements. The small genome size is probably a result of extreme genome reduction due to their parasitic lifestyle, as well as of simplification and miniaturization of the free-living stages. Our data could provide further insights into the evolution of parasitism and could help to define a minimal bilaterian gene set.
Collapse
Affiliation(s)
- George S Slyusarev
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Viktor V Starunov
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia; Zoological Institute RAS, Universitetskaya nab. 1, 199034 St. Petersburg, Russia
| | - Anton S Bondarenko
- Faculty of Physics, Saint-Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Natalia A Zorina
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Natalya I Bondarenko
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia.
| |
Collapse
|
22
|
Kadobianskyi M, Schulze L, Schuelke M, Judkewitz B. Hybrid genome assembly and annotation of Danionella translucida. Sci Data 2019; 6:156. [PMID: 31451709 PMCID: PMC6710283 DOI: 10.1038/s41597-019-0161-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/26/2019] [Indexed: 11/09/2022] Open
Abstract
Studying neuronal circuits at cellular resolution is very challenging in vertebrates due to the size and optical turbidity of their brains. Danionella translucida, a close relative of zebrafish, was recently introduced as a model organism for investigating neural network interactions in adult individuals. Danionella remains transparent throughout its life, has the smallest known vertebrate brain and possesses a rich repertoire of complex behaviours. Here we sequenced, assembled and annotated the Danionella translucida genome employing a hybrid Illumina/Nanopore read library as well as RNA-seq of embryonic, larval and adult mRNA. We achieved high assembly continuity using low-coverage long-read data and annotated a large fraction of the transcriptome. This dataset will pave the way for molecular research and targeted genetic manipulation of this novel model organism.
Collapse
Affiliation(s)
- Mykola Kadobianskyi
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Lisanne Schulze
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Markus Schuelke
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
| | - Benjamin Judkewitz
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
| |
Collapse
|
23
|
Feiner N, Wood NJ. Lizards possess the most complete tetrapod Hox gene repertoire despite pervasive structural changes in Hox clusters. Evol Dev 2019; 21:218-228. [PMID: 31298799 DOI: 10.1111/ede.12300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/26/2019] [Accepted: 06/08/2019] [Indexed: 01/21/2023]
Abstract
Hox genes are a remarkable example of conservation in animal development and their nested expression along the head-to-tail axis orchestrates embryonic patterning. Early in vertebrate history, two duplications led to the emergence of four Hox clusters (A-D) and redundancy within paralog groups has been partially accommodated with gene losses. Here we conduct an inventory of squamate Hox genes using the genomes of 10 lizard and 7 snake species. Although the HoxC1 gene has been hypothesized to be lost in the amniote ancestor, we reveal that it is retained in lizards. In contrast, all snakes lack functional HoxC1 and -D12 genes. Varying levels of degradation suggest differences in the process of gene loss between the two genes. The vertebrate HoxC1 gene is prone to gene loss and its functional domains are more variable than those of other Hox1 genes. We describe for the first time the HoxC1 expression patterns in tetrapods. HoxC1 is broadly expressed during development in the diencephalon, the neural tube, dorsal root ganglia, and limb buds in two lizard species. Our study emphasizes the value of revisiting Hox gene repertoires by densely sampling taxonomic groups and its feasibility owing to growing sequence resources in evaluating gene repertoires across taxa.
Collapse
Affiliation(s)
- Nathalie Feiner
- Department of Zoology, University of Oxford, Oxford, United Kingdom.,Department of Biology, Lund University, Lund, Sweden
| | - Natalie J Wood
- Department of Zoology, University of Oxford, Oxford, United Kingdom.,Centre for Life's Origins and Evolution, Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| |
Collapse
|
24
|
McGrath C. Highlight: Big Surprises from the World's Smallest Fish. Genome Biol Evol 2018; 10:1104-1105. [PMID: 29718209 PMCID: PMC5906955 DOI: 10.1093/gbe/evy065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2018] [Indexed: 11/12/2022] Open
|