1
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Zuo B, Nneji LM, Sun YB. Comparative genomics reveals insights into anuran genome size evolution. BMC Genomics 2023; 24:379. [PMID: 37415107 DOI: 10.1186/s12864-023-09499-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
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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.
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2
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Miller KE, Cadart C, Heald R. Dodecaploid Xenopus longipes provides insight into the emergence of size scaling relationships during development. Curr Biol 2023; 33:1327-1336.e4. [PMID: 36889317 PMCID: PMC10115129 DOI: 10.1016/j.cub.2023.02.021] [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: 08/15/2022] [Revised: 01/12/2023] [Accepted: 02/06/2023] [Indexed: 03/09/2023]
Abstract
Genome and cell size are strongly correlated across species1,2,3,4,5,6 and influence physiological traits like developmental rate.7,8,9,10,11,12 Although size scaling features such as the nuclear-cytoplasmic (N/C) ratio are precisely maintained in adult tissues,13 it is unclear when during embryonic development size scaling relationships are established. Frogs of the genus Xenopus provide a model to investigate this question, since 29 extant Xenopus species vary in ploidy from 2 to 12 copies (N) of the ancestral frog genome, ranging from 20 to 108 chromosomes.14,15 The most widely studied species, X. laevis (4N = 36) and X. tropicalis (2N = 20), scale at all levels, from body size to cellular and subcellular levels.16 Paradoxically, the rare, critically endangered dodecaploid (12N = 108) Xenopus longipes (X. longipes) is a small frog.15,17 We observed that despite some morphological differences, X. longipes and X. laevis embryogenesis occurred with similar timing, with genome to cell size scaling emerging at the swimming tadpole stage. Across the three species, cell size was determined primarily by egg size, whereas nuclear size correlated with genome size during embryogenesis, resulting in different N/C ratios in blastulae prior to gastrulation. At the subcellular level, nuclear size correlated more strongly with genome size, whereas mitotic spindle size scaled with cell size. Our cross-species study indicates that scaling of cell size to ploidy is not due to abrupt changes in cell division timing, that different size scaling regimes occur during embryogenesis, and that the developmental program of Xenopus is remarkably consistent across a wide range of genome and egg sizes.
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Affiliation(s)
- Kelly E Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Clotilde Cadart
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA.
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3
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Mueller RL, Cressler CE, Schwartz RS, Chong RA, Butler M. Metamorphosis Imposes Variable Constraints on Genome Expansion through Effects on Development. Integr Org Biol 2023; 5:obad015. [PMID: 37143961 PMCID: PMC10153748 DOI: 10.1093/iob/obad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/25/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023] Open
Abstract
Genome size varies ∼100,000-fold across eukaryotes and has long been hypothesized to be influenced by metamorphosis in animals. Transposable element accumulation has been identified as a major driver of increase, but the nature of constraints limiting the size of genomes has remained unclear, even as traits such as cell size and rate of development co-vary strongly with genome size. Salamanders, which possess diverse metamorphic and non-metamorphic life histories, join the lungfish in having the largest vertebrate genomes-3 to 40 times that of humans-as well as the largest range of variation in genome size. We tested 13 biologically-inspired hypotheses exploring how the form of metamorphosis imposes varying constraints on genome expansion in a broadly representative phylogeny containing 118 species of salamanders. We show that metamorphosis during which animals undergo the most extensive and synchronous remodeling imposes the most severe constraint against genome expansion, with the severity of constraint decreasing with reduced extent and synchronicity of remodeling. More generally, our work demonstrates the potential for broader interpretation of phylogenetic comparative analysis in exploring the balance of multiple evolutionary pressures shaping phenotypic evolution.
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Affiliation(s)
| | - C E Cressler
- School of Biological Sciences, University of Nebraska Lincoln, Lincoln, NE 68588, USA
| | - R S Schwartz
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - R A Chong
- School of Life Sciences, University of Hawai'i, Honolulu, HI 96822, USA
| | - M Butler
- School of Life Sciences, University of Hawai'i, Honolulu, HI 96822, USA
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4
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Carducci F, Carotti E, Gerdol M, Greco S, Canapa A, Barucca M, Biscotti MA. Investigation of the activity of transposable elements and genes involved in their silencing in the newt Cynops orientalis, a species with a giant genome. Sci Rep 2021; 11:14743. [PMID: 34285310 PMCID: PMC8292531 DOI: 10.1038/s41598-021-94193-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
Caudata is an order of amphibians with great variation in genome size, which can reach enormous dimensions in salamanders. In this work, we analysed the activity of transposable elements (TEs) in the transcriptomes obtained from female and male gonads of the Chinese fire-bellied newt, Cynops orientalis, a species with a genome about 12-fold larger than the human genome. We also compared these data with genomes of two basal sarcopterygians, coelacanth and lungfish. In the newt our findings highlighted a major impact of non-LTR retroelements and a greater total TE activity compared to the lungfish Protopterus annectens, an organism also characterized by a giant genome. This difference in TE activity might be due to the presence of young copies in newt in agreement also with the increase in the genome size, an event that occurred independently and later than lungfish. Moreover, the activity of 33 target genes encoding proteins involved in the TE host silencing mechanisms, such as Ago/Piwi and NuRD complex, was evaluated and compared between the three species analysed. These data revealed high transcriptional levels of the target genes in both newt and lungfish and confirmed the activity of NuRD complex genes in adults. Finally, phylogenetic analyses performed on PRDM9 and TRIM28 allowed increasing knowledge about the evolution of these two key genes of the NuRD complex silencing mechanism in vertebrates. Our results confirmed that the gigantism of the newt genomes may be attributed to the activity and accumulation of TEs.
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Affiliation(s)
- Federica Carducci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Elisa Carotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Marco Gerdol
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via L. Giorgieri, 5, 34127, Trieste, Italy
| | - Samuele Greco
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via L. Giorgieri, 5, 34127, Trieste, Italy
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
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5
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Park IS. The Nuclear DNA Content Determination of 31 Endemic Freshwater Fishes in Korea. Dev Reprod 2021; 25:25-32. [PMID: 33977172 PMCID: PMC8087261 DOI: 10.12717/dr.2021.25.1.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 11/17/2022]
Abstract
The main purpose of the current study was to obtain nuclear DNA content data
among the representatives of the families and subfamilies of 31 endemic fishes
that inhabit river of Korea. DNA contents of 31 endemic species were observed to
rang from 1.5 to 4.8 pg DNA/nucleus. In Cyprinidae, DNA content of
Abbottina springeri (1.5±0.03 pg DNA/nucleus) was
the lowest value and DNA content of Carassius cuvieri
(4.5±0.32 pg DNA/nucleus) was the highest value in all experimental
groups. In Cobitidae, DNA content of Iksookimia longicorpa
(3.9±0.17 pg DNA/nucleus) was the highest value and DNA content of
Orthrias toni (1.5±0.18 pg DNA/nucleus) was the
lowest value in all experimental groups. This study provides new information for
a better understanding of the process of genomic evolution in 31 endemic species
in river of Korea.
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Affiliation(s)
- In-Seok Park
- Division of Convergence on Marine Science, College of Ocean Science and Engineering, Korea Maritime & Ocean University, Busan 49112, Korea
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6
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Miller KE, Brownlee C, Heald R. The power of amphibians to elucidate mechanisms of size control and scaling. Exp Cell Res 2020; 392:112036. [PMID: 32343955 PMCID: PMC7246146 DOI: 10.1016/j.yexcr.2020.112036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/19/2020] [Accepted: 04/22/2020] [Indexed: 01/26/2023]
Abstract
Size is a fundamental feature of biology that affects physiology at all levels, from the organism to organs and tissues to cells and subcellular structures. How size is determined at these different levels, and how biological structures scale to fit together and function properly are important open questions. Historically, amphibian systems have been extremely valuable to describe scaling phenomena, as they occupy some of the extremes in biological size and are amenable to manipulations that alter genome and cell size. More recently, the application of biochemical, biophysical, and embryological techniques to amphibians has provided insight into the molecular mechanisms underlying scaling of subcellular structures to cell size, as well as how perturbation of normal size scaling impacts other aspects of cell and organism physiology.
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Affiliation(s)
- Kelly E Miller
- Department of Molecular and Cell Biology, University of California, CA, 94720, Berkeley, USA
| | - Christopher Brownlee
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794-8651, USA.
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, CA, 94720, Berkeley, USA.
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7
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Canapa A, Barucca M, Biscotti MA, Forconi M, Olmo E. Transposons, Genome Size, and Evolutionary Insights in Animals. Cytogenet Genome Res 2016; 147:217-39. [PMID: 26967166 DOI: 10.1159/000444429] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.
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Affiliation(s)
- Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Universitx00E0; Politecnica delle Marche, Ancona, Italy
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8
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Maciak S, Janko K, Kotusz J, Choleva L, Boroń A, Juchno D, Kujawa R, Kozłowski J, Konarzewski M. Standard Metabolic Rate (SMR) is inversely related to erythrocyte and genome size in allopolyploid fish of the Cobitis taenia hybrid complex. Funct Ecol 2011. [DOI: 10.1111/j.1365-2435.2011.01870.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Abstract
Reptiles are a karyologically heterogeneous group, where some orders and suborders exhibit characteristics similar to those of anamniotes and others share similarities with homeotherms. The class also shows different evolutionary trends, for instance in genome and chromosome size and composition. The turtle DNA base composition is similar to that of mammals, whereas that of lizards and snakes is more similar to that of anamniotes. The major karyological differences between turtles and squamates are the size and composition of the genome and the rate at which chromosomes change. Turtles have larger and more variable genome sizes, and a greater amount of middle repetitive DNA that differs even among related species. In lizards and snakes size of the genome are smaller, single-copy DNA is constant within each suborder, and differences in repetitive DNA involve fractions that become increasingly heterogeneous with widening phylogenetic distance. With regard to variation in karyotype morphology, turtles and crocodiles show low variability in chromosome number, morphology, and G-banding pattern. Greater variability is found among squamates, which have a similar degree of karyotypic change-as do some mammals, such as carnivores and bats-and in which there are also differences among congeneric species. An interesting relationship has been highlighted in the entire class Reptilia between rates of change in chromosomes, number of living species, and rate of extinction. However, different situations obtain in turtles and crocodiles on the one hand, and squamates on the other. In the former, the rate of change in chromosomes is lower and the various evolutionary steps do not seem to have entailed marked chromosomal variation, whereas squamates have a higher rate of change in chromosomes clearly related to the number of living species, and chromosomal variation seems to have played an important role in the evolution of several taxa. The different evolutionary trends in chromosomes observed between turtles and crocodiles on the one hand and squamates on the other might depend on their different patterns of G-banding.
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Affiliation(s)
- Ettore Olmo
- Istituto di Biologia e Genetica, Università Politecnica delle Marche and Istituto Nazionale di Biosistemi e Biostrutture, Via Brecce Bianche, 60131 Ancona, Italy
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10
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Redi CA, Zacharias H, Merani S, Oliveira-Miranda M, Aguilera M, Zuccotti M, Garagna S, Capanna E. Genome Sizes in Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria. J Hered 2005; 96:485-93. [PMID: 15994420 DOI: 10.1093/jhered/esi080] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Topical literature and Web site databases provide genome sizes for approximately 4,000 animal species, invertebrates and vertebrates, 330 of which are mammals. We provide the genome size for 67 mammalian species, including 51 never reported before. Knowledge of genome size facilitates sequencing projects. The data presented here encompassed 5 Metatheria (order Didelphimorphia) and 62 Eutheria: 15 Xenarthra, 24 Euarchontoglires (Rodentia), as well as 23 Laurasiatheria (22 Chiroptera and 1 species from Perissodactyla). Already available karyotypes supplement the haploid nuclear DNA contents of the respective species. Thus, we established the first comprehensive set of genome size measurements for 15 Xenarthra species (armadillos) and for 12 house-mouse species; each group was previously represented by only one species. The Xenarthra exhibited much larger genomes than the modal 3 pg DNA known for mammals. Within the genus Mus, genome sizes varied between 2.98 pg and 3.68 pg. The 22 bat species we measured support the low 2.63 pg modal value for Chiroptera. In general, the genomes of Euarchontoglires and Laurasiatheria were found being smaller than those of (Afrotheria and) Xenarthra. Interspecific variation in genome sizes is discussed with particular attention to repetitive elements, which probably promoted the adaptation of extant mammals to their environment.
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Affiliation(s)
- C A Redi
- Laboratorio di Biologia dello Sviluppo e Centro di Eccellenza di Biologia Applicata, Università di Pavia, Pavia, Italy.
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11
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Abstract
Sauropsids form a complex group of vertebrates including squamates (lizards and snakes), turtles, crocodiles, sphenodon and birds (which are often considered as a separate class). Although avian genomes have been relatively well studied, the genomes of the other groups have remained only sparsely characterized. Moreover, the nuclear sequences available in databanks are still very limited. In the present study, we have analysed the compositional patterns, i.e. the GC (molar fraction of guanine and cytosine in DNA) distributions, of 31 reptilian (particularly snake) genomes by analytical ultracentrifugation of DNAs in CsCl gradients. The profiles were characterized by their modal buoyant density rho(o), mean buoyant density < rho>, asymmetry < rho>- rho(o), and heterogeneity H. The modal buoyant density distribution of reptilian DNAs clearly distinguishes two groups. The snakes fall in the same range of modal densities as most mammals, whereas crocodiles, turtles and lizards show higher values (>1.700 g/cm(3)). As far as the more important compositional properties of asymmetry and heterogeneity are concerned, previous studies showed that amphibians and fishes share relatively low values, whereas birds and mammals are characterized by highly heterogeneous and asymmetric patterns (with the exception of Muridae, which have a lower heterogeneity). The present results show that the snake genomes cover a broad range of asymmetry and heterogeneity values, whereas the genomes of crocodiles and turtles cover a narrow range that is intermediate between those of fishes/amphibians and those of mammals/birds.
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Affiliation(s)
- Sandrine Hughes
- Laboratorio di Evoluzione Molecolare, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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12
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Chipman AD, Khaner O, Haas A, Tchernov E. The evolution of genome size: what can be learned from anuran development? THE JOURNAL OF EXPERIMENTAL ZOOLOGY 2001; 291:365-74. [PMID: 11754015 DOI: 10.1002/jez.1135] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Differences in nuclear DNA content in vertebrates have been shown to be correlated with cell size, cell division rate, and embryonic developmental rate. We compare seven species of anuran amphibians with a three-fold range of genome sizes. Parameters examined include the number and density of cells in a number of embryonic structures, and the change in cell number in the CNS during development. We show that genome size is correlated with cell proliferation rate and with developmental rate at different stages of embryonic development, but that the correlation between genome size and cell size is only evident at later stages. We discuss the evolution of genome size in amphibians. Our discussion takes into account data that reportedly support two conflicting hypotheses: the "skeletal DNA" hypothesis, which claims a selective role for differences in genome size, and the "junk DNA" hypothesis, which claims that differences in genome size are a random result of the accumulation of noncoding DNA sequences. We show that these supposedly conflicting hypotheses can be integrated into a more complex and inclusive model for the evolution of genome size.
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Affiliation(s)
- A D Chipman
- The Department for Cell and Animal Biology, The Hebrew University, Jerusalem 91904, Israel.
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13
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Porter CA. Organization and chromosomal location of repetitive DNA sequences in three species of squamate reptiles. Chromosome Res 1994; 2:263-73. [PMID: 7921642 DOI: 10.1007/bf01552720] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Repetitive DNA sequences were isolated from the genomes of species representing three major clades of squamate reptiles. A repetitive sequence (Cn4C7) was isolated from the New Mexican whiptail lizard, Cnemidophorus neomexicanus. This sequence is distributed throughout the chromosomes, but is more concentrated in the telomeric region. Cn4C7 also hybridizes to the chromosomes of other Cnemidophorus. Some evidence was found for concerted evolution of this repeat in hybrid unisexual lineages. In the lesser earless lizard, Holbrookia maculata, the predominant repeat in the genome is represented by a sequence (Hm1E11) which is restricted to the area flanking the centromere in all species of Holbrookia. Two families of repetitive sequences (one dispersed, and the other telomeric) were isolated from the western diamondback rattlesnake, Crotalus atrox. The type and distribution of repetitive sequences in squamates is often taxon-specific, and may be useful as characters for elucidating taxonomic relationships.
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Affiliation(s)
- C A Porter
- Department of Biological Sciences, Texas Tech University, Lubbock 79409
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14
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Ono H, Figueroa F, O'hUigin C, Klein J. Cloning of the beta 2-microglobulin gene in the zebrafish. Immunogenetics 1993; 38:1-10. [PMID: 8462988 DOI: 10.1007/bf00216384] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The beta 2-microglobulin (beta 2m) is a protein found in the serum in a free form and on the cell surface in a form noncovalently associated with the alpha chain of the class I major histocompatibility complex (Mhc) molecules. In mammals, the beta 2m-encoding gene (B2m) is found on a chromosome different from the Mhc proper. We have isolated and characterized the B2m gene of the zebrafish, Brachydanio rerio, family Cyprinidae. We obtained both cDNA and genomic clones of the Brre-B2m gene. The cDNA clones contained the entire coding sequence, the entire 3' untranslated (UT) region, and at least part of the 5'UT region. The genomic clone contained the entire Brre-B2m gene. The coding sequence specifies 97 amino acid residues of the mature protein so that the zebrafish beta 2m is two residues shorter than human and one residue shorter than cattle, fowl, or turkey beta 2m (codons at positions 85 and 86 have been deleted in the Brre-B2m gene). The amino acid and nucleotide sequence similarities between zebrafish and human beta 2m (B2m) are 45% and 59%, respectively. Approximately 24% of the positions are invariant and an additional 9% show only conservative substitutions in comparisons which include all known beta 2m sequences (fish, avian, and mammalian). Most of the conserved positions are in the beta strands (some 47% of the beta-strand positions are conserved in the three vertebrate classes). The Brre-B2m gene consists of four exons separated by three introns. All of the introns are considerably shorter than the corresponding introns in the mammalian B2m genes. The coding sequences of the cDNA and the genomic clones are almost identical but the sequences of the 3'UT regions differ at 1.7% of the sites, suggesting that the genes borne by these clones might have diverged at least 0.7 million years (my) ago. In contrast to the human B2m gene, the Brre-B2m gene shows no bias in the distribution of the CpG dinucleotides: the dinucleotides are distributed evenly along the entire available sequence. The haploid genome of the zebrafish contains only one copy of the B2m gene.
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Affiliation(s)
- H Ono
- Max-Planck-Institut für Biologie, Abteilung Immungenetik, Tübingen, Germany
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15
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Bernardi G, Bernardi G. Compositional patterns in the nuclear genome of cold-blooded vertebrates. J Mol Evol 1990; 31:265-81. [PMID: 2124275 DOI: 10.1007/bf02101122] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA preparations obtained from 122 species of fishes, 5 species of amphibians, and 13 species of reptiles were investigated in their compositional properties by analytical equilibrium centrifugation in CsCl density gradients. These species represented 21 orders of Osteichthyes, 3 orders of Chondrichthyes, 2 orders of amphibians, and 3 orders of reptiles. Modal buoyant densities of fish DNAs ranged from 1.696 to 1.707 g/cm3, the vast majority of values falling, however, between 1.699 and 1.704 g/cm3, which is the range covered by the DNAs of amphibians and reptiles. In all cases, DNA bands in CsCl were only weakly asymmetrical and only very rarely were accompanied by separate satellite bands (mostly on the GC-rich side). Intermolecular compositional heterogeneities were low in the vast majority of cases, and, like CsCl band asymmetries, at least partially due to cryptic or poorly resolved satellites. The present findings indicate, therefore, that DNAs from cold-blooded vertebrates are characterized by a number of common properties, namely a very wide spectrum of modal buoyant densities, low intermolecular compositional heterogeneities, low CsCl band asymmetries, and, in most cases, small amounts of satellite DNAs. In the case of fish DNAs a negative correlation was found between the GC level and the haploid size (c value) of the genome. If polyploidization is neglected, this phenomenon appears to be mainly due to the fact that increases and decreases in GC are associated with contraction and expansion phenomena, respectively, of intergenic noncoding sequences, which are GC poor relative to coding sequences.
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Affiliation(s)
- G Bernardi
- Laboratoire de Génétique Moléculaire, Institut Jacques Monod, Paris, France
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