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Adams AN, Denton RD, Mueller RL. Gigantic genomes of salamanders indicate that body temperature, not genome size, is the driver of global methylation and 5-methylcytosine deamination in vertebrates. Evolution 2022; 76:1052-1061. [PMID: 35275604 DOI: 10.1111/evo.14468] [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: 10/01/2021] [Revised: 12/29/2021] [Accepted: 01/14/2022] [Indexed: 01/21/2023]
Abstract
Transposable elements (TEs) are sequences that replicate and move throughout genomes, and they can be silenced through methylation of cytosines at CpG dinucleotides. TE abundance contributes to genome size, but TE silencing variation across genomes of different sizes remains underexplored. Salamanders include most of the largest C-values - 9 to 120 Gb. We measured CpG methylation levels in salamanders with genomes ranging from 2N = ∼58 Gb to 4N = ∼116 Gb. We compared these levels to results from endo- and ectothermic vertebrates with more typical genomes. Salamander methylation levels are approximately 90%, higher than all endotherms. However, salamander methylation does not differ from other ectotherms, despite an approximately 100-fold difference in nuclear DNA content. Because methylation affects the nucleotide compositional landscape through 5-methylcytosine deamination to thymine, we quantified salamander CpG dinucleotide levels and compared them to other vertebrates. Salamanders and other ectotherms have comparable CpG levels, and ectotherm levels are higher than endotherms. These data show no shift in global methylation at the base of salamanders, despite a dramatic increase in TE load and genome size. This result is reconcilable with previous studies that considered endothermy and ectothermy, which may be more important drivers of methylation in vertebrates than genome size.
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Affiliation(s)
| | - Robert Daniel Denton
- Department of Biology, Marian University, Indianapolis, IN, 46222.,Division of Science and Math, University of Minnesota Morris, Morris, MN, 56267
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Tu Z, Liu M, Wang Y, Xu S, Song N, Gao T, Han Z. The low mitochondrial diversities in lizardfish Saurida elongate: Recent population expansion and selection. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Costantini M. An overview on genome organization of marine organisms. Mar Genomics 2015; 24 Pt 1:3-9. [PMID: 25899406 DOI: 10.1016/j.margen.2015.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/17/2015] [Accepted: 03/17/2015] [Indexed: 11/16/2022]
Abstract
In this review we will concentrate on some general genome features of marine organisms and their evolution, ranging from vertebrate to invertebrates until unicellular organisms. Before genome sequencing, the ultracentrifugation in CsCl led to high resolution of mammalian DNA (without seeing at the sequence). The analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong in a small number of families characterized by different GC levels. The recent availability of a number of fully sequenced genomes allowed mapping very precisely the isochores, based on DNA sequences. Since isochores are tightly linked to biological properties such as gene density, replication timing and recombination, the new level of detail provided by the isochore map helped the understanding of genome structure, function and evolution. This led the current level of knowledge and to further insights.
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Affiliation(s)
- Maria Costantini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.
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Bernardi G. Speciation in fishes. Mol Ecol 2013; 22:5487-502. [PMID: 24118417 DOI: 10.1111/mec.12494] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/08/2013] [Accepted: 08/14/2013] [Indexed: 12/27/2022]
Abstract
The field of speciation has seen much renewed interest in the past few years, with theoretical and empirical advances that have moved it from a descriptive field to a predictive and testable one. The goal of this review is to provide a general background on research on speciation as it pertains to fishes. Three major components to the question are first discussed: the spatial, ecological and sexual factors that influence speciation mechanisms. We then move to the latest developments in the field of speciation genomics. Affordable and rapidly available, massively parallel sequencing data allow speciation studies to converge into a single comprehensive line of investigation, where the focus has shifted to the search for speciation genes and genomic islands of speciation. We argue that fish present a very diverse array of scenarios, making them an ideal model to study speciation processes.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA, 95076, USA
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Matsubara K, Kuraku S, Tarui H, Nishimura O, Nishida C, Agata K, Kumazawa Y, Matsuda Y. Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC(3) profiling in snake. BMC Genomics 2012; 13:604. [PMID: 23140509 PMCID: PMC3549455 DOI: 10.1186/1471-2164-13-604] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 10/24/2012] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Extant sauropsids (reptiles and birds) are divided into two major lineages, the lineage of Testudines (turtles) and Archosauria (crocodilians and birds) and the lineage of Lepidosauria (tuatara, lizards, worm lizards and snakes). Karyotypes of these sauropsidan groups generally consist of macrochromosomes and microchromosomes. In chicken, microchromosomes exhibit a higher GC-content than macrochromosomes. To examine the pattern of intra-genomic GC heterogeneity in lepidosaurian genomes, we constructed a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 183 cDNA clones by fluorescence in situ hybridization, and examined the correlation between the GC-content of exonic third codon positions (GC3) of the genes and the size of chromosomes on which the genes were localized. RESULTS Although GC3 distribution of snake genes was relatively homogeneous compared with those of the other amniotes, microchromosomal genes showed significantly higher GC3 than macrochromosomal genes as in chicken. Our snake cytogenetic map also identified several conserved segments between the snake macrochromosomes and the chicken microchromosomes. Cross-species comparisons revealed that GC3 of most snake orthologs in such macrochromosomal segments were GC-poor (GC3 < 50%) whereas those of chicken orthologs in microchromosomes were relatively GC-rich (GC3 ≥ 50%). CONCLUSION Our results suggest that the chromosome size-dependent GC heterogeneity had already occurred before the lepidosaur-archosaur split, 275 million years ago. This character was probably present in the common ancestor of lepidosaurs and but lost in the lineage leading to Anolis during the diversification of lepidosaurs. We also identified several genes whose GC-content might have been influenced by the size of the chromosomes on which they were harbored over the course of sauropsid evolution.
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Affiliation(s)
- Kazumi Matsubara
- Department of Information and Biological Sciences, Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan.
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Fadhlaoui-Zid K, Knittweis L, Aurelle D, Nafkha C, Ezzeddine S, Fiorentino F, Ghmati H, Ceriola L, Jarboui O, Maltagliati F. Genetic structure of Octopus vulgaris (Cephalopoda, Octopodidae) in the central Mediterranean Sea inferred from the mitochondrial COIII gene. C R Biol 2012. [DOI: 10.1016/j.crvi.2012.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Seebacher F, Holmes S, Roosen NJ, Nouvian M, Wilson RS, Ward AJW. Capacity for thermal acclimation differs between populations and phylogenetic lineages within a species. Funct Ecol 2012. [DOI: 10.1111/j.1365-2435.2012.02052.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frank Seebacher
- School of Biological Sciences A08; University of Sydney; Sydney NSW 2006 Australia
| | - Sebastian Holmes
- Water & Wildlife Ecology Group (WWEG); The School of Natural Sciences; The University of Western Sydney; Penrith NSW 2751 Australia
| | - Nicholas J. Roosen
- School of Biological Sciences A08; University of Sydney; Sydney NSW 2006 Australia
| | - Morgane Nouvian
- School of Biological Sciences A08; University of Sydney; Sydney NSW 2006 Australia
| | - Robbie S. Wilson
- School of Biological Sciences; University of Queensland; Brisbane QLD 4072 Australia
| | - Ashley J. W. Ward
- School of Biological Sciences A08; University of Sydney; Sydney NSW 2006 Australia
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Agorreta A, Rüber L. A standardized reanalysis of molecular phylogenetic hypotheses of Gobioidei. SYST BIODIVERS 2012. [DOI: 10.1080/14772000.2012.699477] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Tattersall GJ, Sinclair BJ, Withers PC, Fields PA, Seebacher F, Cooper CE, Maloney SK. Coping with Thermal Challenges: Physiological Adaptations to Environmental Temperatures. Compr Physiol 2012; 2:2151-202. [DOI: 10.1002/cphy.c110055] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Smarda P, Bureš P, Smerda J, Horová L. Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability. THE NEW PHYTOLOGIST 2012; 193:513-21. [PMID: 22050640 DOI: 10.1111/j.1469-8137.2011.03942.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
• Knowledge of the phylogenetic pattern and biological relevance of the base composition of large eukaryotic genomes (including those of plants) is poor. With the use of flow cytometry (FCM), the amount of available data on the guanine + cytosine (GC) content of plants has nearly doubled in the last decade. However, skepticism exists concerning the reliability of the method because of uncertainty in some input parameters. • Here, we tested the reliability of FCM for estimating GC content by comparison with the biochemical method of DNA temperature melting analysis (TMA). We conducted measurements in 14 plant species with a maximum currently known GC content range (33.6-47.5% as measured by FCM). We also compared the estimations of the GC content by FCM with genomic sequences in 11 Oryza species. • FCM and TMA data exhibited a high degree of correspondence which remained stable over the relatively wide range of binding lengths (3.39-4.09) assumed for the base-specific dye used. A high correlation was also observed between FCM results and the sequence data in Oryza, although the latter GC contents were consistently lower. • Reliable estimates of the genomic base composition in plants by FCM are comparable with estimates obtained using other methods, and so wider application of FCM in future plant genomic research, although it would pose a challenge, would be supported by these findings.
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Affiliation(s)
- Petr Smarda
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic.
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Costantini M, Auletta F, Bernardi G. The distributions of "new" and "old" Alu sequences in the human genome: the solution of a "mystery". Mol Biol Evol 2011; 29:421-7. [PMID: 22057813 DOI: 10.1093/molbev/msr242] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The distribution in the human genome of the largest family of mobile elements, the Alu sequences, has been investigated for the past 30 years, and the vast majority of Alu sequences were shown to have the highest density in GC-rich isochores. Ten years ago, it was discovered, however, that the small "youngest" (most recently transposed) Alu families had a strikingly different distribution compared with the "old" families. This raised the question as to how this change took place in evolution. We solved what was considered to be a "mystery" by 1) revisiting our previous results on the integration and stability of retroviral sequences, and 2) assessing the densities of acceptor sites TTTT/AA in isochore families. We could conclude 1) that the open state of chromatin structure plays a crucial role in allowing not only the initial integration of retroviral sequences but also that of the youngest Alu sequences, and 2) that the distribution of old Alus can be explained as due to Alu sequences being unstable in the GC-poor isochores but stable in the compositionally matching GC-rich isochores, again in line with what happens in the case of retroviral sequences.
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Affiliation(s)
- Maria Costantini
- Laboratory of Cellular and Developmental Biology, Stazione Zoologica Anton Dohrn, Naples, Italy
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Liu M, Lu ZC, Gao TX, Yanagimoto T, Sakurai Y. Remarkably low mtDNA control-region diversity and shallow population structure in Pacific cod Gadus macrocephalus. JOURNAL OF FISH BIOLOGY 2010; 77:1071-1082. [PMID: 21039491 DOI: 10.1111/j.1095-8649.2010.02743.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
To investigate the genetic diversity and describe the population structure in Gadus macrocephalus, a 452 base pair (bp) fragment of the mitochondrial DNA control region was analysed in 259 individuals. The results showed remarkably low nucleotide diversity and a lack of genealogical structure. Small but significant genetic differentiations, however, were detected among north-western Pacific populations, but no large-scale regional differences were detected. These results indicate that populations of G. macrocephalus in the north-western Pacific are genetically subdivided and represent evolutionary lineages that should be managed individually.
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Affiliation(s)
- M Liu
- Fisheries College, Ocean University of China, Qingdao, Shandong 266003, China Liaoning Marine Fisheries Research Institute, Dalian, Liaoning 116023, China
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von der Heyden S, Lipinski MR, Matthee CA. Remarkably low mtDNA control region diversity in an abundant demersal fish. Mol Phylogenet Evol 2009; 55:1183-8. [PMID: 19761857 DOI: 10.1016/j.ympev.2009.09.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 09/09/2009] [Indexed: 10/20/2022]
Abstract
Cape hake, Merluccius paradoxus, is a valuable commercially exploited demersal species. Using the 5' mtDNA control region we show that 96% of 1013 fishes sampled over a three-year period share one of two dominant haplotypes; 19 haplotypes were recovered in total, suggesting a genetically homogenous population of fish. Accordingly, haplotype and nucleotide diversities are low (h = 0.53, pi = 0.0014); an asymptotic haplotype accumulation curve suggests that few additional haplotypes exist. Comparing h and pi with other fish species shows that M. paradoxus and other southern African fish species have remarkably low genetic diversity values compared with other global marine fishes. Despite low genetic variability, frequency differences among M. paradoxus haplotypes suggest weakly structured populations between Namibia and South Africa. However, given the remarkably homogeneous mtDNA population genetic structure between fishes sampled along 1800 km, it is clear that faster evolving markers such a microsatellites are also needed before inferences can be made regarding stock identification and management of this species.
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Affiliation(s)
- Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
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Costantini M, Cammarano R, Bernardi G. The evolution of isochore patterns in vertebrate genomes. BMC Genomics 2009; 10:146. [PMID: 19344507 PMCID: PMC2678159 DOI: 10.1186/1471-2164-10-146] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 04/03/2009] [Indexed: 01/23/2023] Open
Abstract
Background Previous work from our laboratory showed that (i) vertebrate genomes are mosaics of isochores, typically megabase-size DNA segments that are fairly homogeneous in base composition; (ii) isochores belong to a small number of families (five in the human genome) characterized by different GC levels; (iii) isochore family patterns are different in fishes/amphibians and mammals/birds, the latter showing GC-rich isochore families that are absent or very scarce in the former; (iv) there are two modes of genome evolution, a conservative one in which isochore patterns basically do not change (e.g., among mammalian orders), and a transitional one, in which they do change (e.g., between amphibians and mammals); and (v) isochores are tightly linked to a number of basic biological properties, such as gene density, gene expression, replication timing and recombination. Results The present availability of a number of fully sequenced genomes ranging from fishes to mammals allowed us to carry out investigations that (i) more precisely quantified our previous conclusions; (ii) showed that the different isochore families of vertebrate genomes are largely conserved in GC levels and dinucleotide frequencies, as well as in isochore size; and (iii) isochore family patterns can be either conserved or change within both warm- and cold-blooded vertebrates. Conclusion On the basis of the results presented, we propose that (i) the large conservation of GC levels and dinucleotide frequencies may reflect the conservation of chromatin structures; (ii) the conservation of isochore size may be linked to the role played by isochores in chromosome structure and replication; (iii) the formation, the maintainance and the changes of isochore patterns are due to natural selection.
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