Effects of environmental pollution on the rDNAomics of Amazonian fish

Silva, Francijara Araújo da; Feldberg, Eliana; Carvalho, Natália Dayane Moura; Rangel, Sandra Marcela Hernández; Schneider, Carlos Henrique; Carvalho‐Zilse, Gislene Almeida; Silva, Victor Fonsêca da; Gross, Maria Cláudia

doi:10.1016/j.envpol.2019.05.112

Cited by 19 publications

(12 citation statements)

References 46 publications

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“…Fluorescence in situ Hybridization (FISH) is a commonly used method to visualize genomic segments within intact cells. rDNA FISH has been done extensively, often to localize the rDNA or identify how many rDNA loci are present (Vitturi et al 1999;Fontana et al 2003;Garcia et al 2017;Araújo da Silva et al 2019). Others have used FISH to visualize 45S rDNA and thereby assess variability in rDNA content between cells (Rosato et al 2016).…”

Section: Molecular Inversion Probe-based Copy Number Estimation Yieldmentioning

confidence: 99%

Challenges and Approaches to Genotyping Repetitive DNA

Morton¹,

Hall

Kwan³

et al. 2020

G3 Genes|Genomes|Genetics

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Individuals within a species can exhibit vast variation in copy number of repetitive DNA elements. This variation may contribute to complex traits such as lifespan and disease, yet it is only infrequently considered in genotype-phenotype associations. Although the possible importance of copy number variation is widely recognized, accurate copy number quantification remains challenging. Here, we assess the technical reproducibility of several major methods for copy number estimation as they apply to the large repetitive ribosomal DNA array (rDNA). rDNA encodes the ribosomal RNAs and exists as a tandem gene array in all eukaryotes. Repeat units of rDNA are kilobases in size, often with several hundred units comprising the array, making rDNA particularly intractable to common quantification techniques. We evaluate pulsed-field gel electrophoresis, droplet digital PCR, and Nextera-based whole genome sequencing as approaches to copy number estimation, comparing techniques across model organisms and spanning wide ranges of copy numbers. Nextera-based whole genome sequencing, though commonly used in recent literature, produced high error. We explore possible causes for this error and provide recommendations for best practices in rDNA copy number estimation. We present a resource of high-confidence rDNA copy number estimates for a set of S. cerevisiae and C. elegans strains for future use. We furthermore explore the possibility for FISH-based copy number estimation, an alternative that could potentially characterize copy number on a cellular level.

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Section: Molecular Inversion Probe-based Copy Number Estimation Yieldmentioning

confidence: 99%

Challenges and Approaches to Genotyping Repetitive DNA

Morton¹,

Hall

Kwan³

et al. 2020

G3 Genes|Genomes|Genetics

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“…Additionally, methodological advances in molecular cytogenetics, namely diverse variants of fluorescence in situ hybridization (FISH), allow to decipher karyotype/genome evolution among related species, including the degree of preserved conserved synteny and the characterization of structural and functional organization of genomes [9–20]. These approaches already helped to document cryptic species diversification [21–29] as well as to track remarkable karyotype stability [30,31], the response of the genome dynamics to environmental cues [32] or its correlation with geographic distribution [33].…”

Section: Introductionmentioning

confidence: 99%

Cytogenetics of the small-sized fish, Copeina guttata (Characiformes, Lebiasinidae): Novel insights into the karyotype differentiation of the family

et al. 2019

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Lebiasinidae is a small fish family composed by miniature to small-sized fishes with few cytogenetic data (most of them limited to descriptions of diploid chromosome numbers), thus preventing any evolutionary comparative studies at the chromosomal level. In the present study, we are providing, the first cytogenetic data for the red spotted tetra, Copeina guttata, including the standard karyotype, C-banding, repetitive DNA mapping by fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH), providing chromosomal patterns and novel insights into the karyotype differentiation of the family. Males and females share diploid chromosome number 2n = 42 and karyotype composed of 2 metacentric (m), 4 submetacentric (sm) and 36 subtelocentric to acrocentric (st-a) chromosomes. Blocks of constitutive heterochromatin were observed in the centromeric and interstitial regions of several chromosomes, in addition to a remarkably large distal block, heteromorphic in size, which fully corresponded with the 18S rDNA sites in the fourth chromosomal pair. This overlap was confirmed by 5S/18S rDNA dual-color FISH. On the other hand, 5S rDNA clusters were situated in the long and short arms of the 2nd and 15th pairs, respectively. No sex-linked karyotype differences were revealed by male/female CGH experiments. The genomic probes from other two lebiasinid species, Lebiasina melanoguttata and Pyrrhulina brevis, showed positive hybridization signals only in the NOR region in the genome of C. guttata. We demonstrated that karyotype diversification in lebiasinids was accompanied by a series of structural and numeric chromosome rearrangements of different types, including particularly fusions and fissions.

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“…Chromosomal mapping of rDNA clusters has repeatedly helped to unveil diverse evolutionary issues (e.g., [82,83]). Particularly in fishes, it provided valuable clues about the incidence of cryptic, morphologically indistinguishable sibling species [5,6,8,10,84], polyploidization and interspecific hybridization events [85,86], a geographical gradient of genomic and morphological change [87], patterns of sex chromosome differentiation [80,[88][89][90], and the correlation of genome dynamics in response to environmental cues [91,92]. Among the Nannostomus species investigated here, chromosomal mapping revealed somewhat uniform patterns of distribution for both rDNA classes, with one to few sites of accumulation, as found in most fishes [93,94], as well as in some other lebiasinids [21,22] investigated to date.…”

Section: Discussionmentioning

confidence: 99%

Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective

Sember

Oliveira

Ráb

et al. 2020

Genes

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Lebiasinidae is a Neotropical freshwater family widely distributed throughout South and Central America. Due to their often very small body size, Lebiasinidae species are cytogenetically challenging and hence largely underexplored. However, the available but limited karyotype data already suggested a high interspecific variability in the diploid chromosome number (2n), which is pronounced in the speciose genus Nannostomus, a popular taxon in ornamental fish trade due to its remarkable body coloration. Aiming to more deeply examine the karyotype diversification in Nannostomus, we combined conventional cytogenetics (Giemsa-staining and C-banding) with the chromosomal mapping of tandemly repeated 5S and 18S rDNA clusters and with interspecific comparative genomic hybridization (CGH) to investigate genomes of four representative Nannostomus species: N. beckfordi, N. eques, N. marginatus, and N. unifasciatus. Our data showed a remarkable variability in 2n, ranging from 2n = 22 in N. unifasciatus (karyotype composed exclusively of metacentrics/submetacentrics) to 2n = 44 in N. beckfordi (karyotype composed entirely of acrocentrics). On the other hand, patterns of 18S and 5S rDNA distribution in the analyzed karyotypes remained rather conservative, with only two 18S and two to four 5S rDNA sites. In view of the mostly unchanged number of chromosome arms (FN = 44) in all but one species (N. eques; FN = 36), and with respect to the current phylogenetic hypothesis, we propose Robertsonian translocations to be a significant contributor to the karyotype differentiation in (at least herein studied) Nannostomus species. Interspecific comparative genome hybridization (CGH) using whole genomic DNAs mapped against the chromosome background of N. beckfordi found a moderate divergence in the repetitive DNA content among the species’ genomes. Collectively, our data suggest that the karyotype differentiation in Nannostomus has been largely driven by major structural rearrangements, accompanied by only low to moderate dynamics of repetitive DNA at the sub-chromosomal level. Possible mechanisms and factors behind the elevated tolerance to such a rate of karyotype change in Nannostomus are discussed.

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Effects of environmental pollution on the rDNAomics of Amazonian fish

Cited by 19 publications

References 46 publications

Challenges and Approaches to Genotyping Repetitive DNA

Challenges and Approaches to Genotyping Repetitive DNA

Cytogenetics of the small-sized fish, Copeina guttata (Characiformes, Lebiasinidae): Novel insights into the karyotype differentiation of the family

Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective

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