Balancing selection on the number of repeats in the ribosomal intergenic spacer present in naturally occurring yellow perch (Perca flavescens) populations

Genome ◽  
2018 ◽  
Vol 61 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Frédérique Bélanger-Lépine ◽  
Christelle Leung ◽  
Hélène Glémet ◽  
Bernard Angers
Keyword(s):  
Microsatellite Loci ◽  
Yellow Perch ◽  
Balancing Selection ◽  
Natural Populations ◽  
Perca Flavescens ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
Length Variation ◽  
Repeat Units ◽  
Ribosomal Intergenic Spacer

The ribosomal intergenic spacer (IGS), responsible for the rate of transcription of rRNA genes, is associated with the growth and fecundity of individuals. A previous study of IGS length variants in a yellow perch (Perca flavescens) population revealed the presence of two predominant alleles differing by 1 kb due to variation in the number of repeat units. This study aims to assess whether length variation of IGS is the result of selection in natural populations. Length variation of IGS and 11 neutral microsatellite loci were assessed in geographically distant yellow perch populations. Most populations displayed the very same IGS alleles; they did not differ in frequencies among populations and the FST was not significantly different from zero. In contrast, diversity at microsatellite loci was high and differed among populations (FST = 0.18). Selection test based on FST identified IGS as a significant outlier from neutral expectations for population differentiation. Heterozygote excess was also detected in one specific cohort, suggesting temporal variation in the selection regime. While the exact mechanism remains to be specified, together the results of this study support the contention that balancing selection is acting to maintain two distinct IGS alleles in natural fish populations.

scholarly journals Extensive length variation in the ribosomal DNA intergenic spacer of yellow perch (Perca flavescens)

Genome ◽  
2016 ◽  
Vol 59 (3) ◽  
pp. 149-158 ◽  
Author(s):  
Bidénam Kakou ◽  
Bernard Angers ◽  
Hélène Glémet
Keyword(s):  
Growth Rate ◽  
Yellow Perch ◽  
Perca Flavescens ◽  
Gc Content ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Regulatory Elements ◽  
Rrna Gene ◽  
Length Variation ◽  
Repeat Region

The intergenic spacer (IGS) is located between ribosomal RNA (rRNA) gene copies. Within the IGS, regulatory elements for rRNA gene transcription are found, as well as a varying number of other repetitive elements that are at the root of IGS length heterogeneity. This heterogeneity has been shown to have a functional significance through its effect on growth rate. Here, we present the structural organization of yellow perch (Perca flavescens) IGS based on its entire sequence, as well as the IGS length variation within a natural population. Yellow perch IGS structure has four discrete regions containing tandem repeat elements. For three of these regions, no specific length class was detected as allele size was seemingly normally distributed. However, for one repeat region, PCR amplification uncovered the presence of two distinctive IGS variants representing a length difference of 1116 bp. This repeat region was also devoid of any CpG sites despite a high GC content. Balanced selection may be holding the alleles in the population and would account for the high diversity of length variants observed for adjacent regions. Our study is an important precursor for further work aiming to assess the role of IGS length variation in influencing growth rate in fish.

Description and phylogenetic analyses of ribosomal transcription units from species of Fasciolidae (Platyhelminthes: Digenea)

2020 ◽  
Vol 94 ◽  
Author(s):  
T.H. Le ◽  
K.L.T. Pham ◽  
H.T.T. Doan ◽  
T.K. Xuyen Le ◽  
K.T. Nguyen ◽  
...  
Keyword(s):  
Fasciola Hepatica ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Transcription Unit ◽  
Rrna Genes ◽  
28S Rrna ◽  
Intergenic Spacer Region ◽  
Repeat Units ◽  
Complete Sequences ◽  
Fasciolopsis Buski

Abstract Many members of Fasciolidae are common trematodes in cattle, buffaloes, sheep, elephants, pigs, with some capable of infecting humans also. In this study, the complete or near-complete sequences of ribosomal transcription unit (rTU or rDNA), each of Fasciola hepatica (Australia), Fascioloides jacksoni (Sri Lanka), Fasciolopsis buski (Vietnam) and three isolates of F. gigantica (Vietnam), were obtained and characterized. The full length of rDNA for each F. hepatica, ‘hybrid’ Fasciola sp., Fas. jacksoni and Fa. Buski, was 7657 bp, 7966 bp, 7781 bp and 8361 bp, with the complete intergenic spacer region (IGS) (862 bp, 1170 bp, 987 bp and 561 bp), respectively. The rDNA of two ‘pure’ F. gigantica isolates from Vietnam was 6794 bp with unsequenced IGS. For 28S rRNA genes the Fasciola spp. are equal, 1958 bp for 18S, 160 bp for 5.8S, 3863 bp and 454 bp for ITS1 but ITS2 differ by one nucleotide (Thymine) (359 or 360 bp). The ITS1 of the sensu lato Fa. buski has some distinguishable features, 286 bp for ITS2, 3862 bp for 28S and four repeat units of 356–361 bp each found in ITS1. The 28S rDNA analysis showed the lowest level of divergence (0–0.57%) between F. hepatica and F. gigantica and higher (2.23–2.62%) and highest (6–6.42%) for Fas. jacksoni and Fasciolopsis, respectively. The tree of 43 strains/species clearly produced a well-supported phylogeny, where 18 fasciolids consistently grouped, forming a discrete Fasciolidae clade, distinct from Philophthalmidae, Echinostomatidae and Echinochasmidae in Echinostomatoidea. Fascioloides jacksoni is outside Fasciola spp.: basal with Fas. magna, as previously demonstrated.

Length and sequence heterogeneity in 5S rDNA of Populus deltoides

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1181-1188 ◽  
Author(s):  
Madan S Negi ◽  
Jyothi Rajagopal ◽  
Neeti Chauhan ◽  
Richard Cronn ◽  
Malathi Lakshmikumaran
Keyword(s):  
Populus Deltoides ◽  
5S Rdna ◽  
Rrna Genes ◽  
Length Variation ◽  
Spacer Length ◽  
Sequence Heterogeneity ◽  
Distance Analysis ◽  
Repeat Units ◽  
Class 1 ◽  
Dna Microsatellite

The 5S rRNA genes and their associated non-transcribed spacer (NTS) regions are present as repeat units arranged in tandem arrays in plant genomes. Length heterogeneity in 5S rDNA repeats was previously identified in Populus deltoides and was also observed in the present study. Primers were designed to amplify the 5S rDNA NTS variants from the P. deltoides genome. The PCR-amplified products from the two accessions of P. deltoides (G3 and G48) suggested the presence of length heterogeneity of 5S rDNA units within and among accessions, and the size of the spacers ranged from 385 to 434 bp. Sequence analysis of the non-transcribed spacer (NTS) revealed two distinct classes of 5S rDNA within both accessions: class 1, which contained GAA trinucleotide microsatellite repeats, and class 2, which lacked the repeats. The class 1 spacer shows length variation owing to the microsatellite, with two clones exhibiting 10 GAA repeat units and one clone exhibiting 16 such repeat units. However, distance analysis shows that class 1 spacer sequences are highly similar inter se, yielding nucleotide diversity (π) estimates that are less than 0.15% of those obtained for class 2 spacers (π = 0.0183 vs. 0.1433, respectively). The presence of microsatellite in the NTS region leading to variation in spacer length is reported and discussed for the first time in P. deltoides.Key words: 5S rDNA, Populus, repetitive DNA, microsatellite, sequence heterogeneity.

Genomic organization of ribosomal RNA genes in Bromus (Poaceae)

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 198-205 ◽  
Author(s):  
M. Pillay
Keyword(s):  
Ribosomal Dna ◽  
Restriction Site ◽  
Intergenic Spacer ◽  
Molecular Data ◽  
Length Variation ◽  
Coding Region ◽  
Rdna Genes ◽  
Repeat Units ◽  
Site Mapping ◽  
Site Variation

Restriction site maps of the rDNA genes of nine Bromus species are described. The rDNA repeat units ranged from 8.2 to 11.1 kbp in length. Intraspecific length variation was observed in the BamHI digestions in three of the nine species. Restriction site variation was observed mainly in the intergenic spacer (IGS) but was also detected in the coding region. A unique KpnI site was present in the IGS of Bromus tectorum and Bromus sericeus (subgenus Stenobromus); in addition, B. sericeus contained an extra EcoRI site. An additional DraI site was observed in the IGS of Bromus trinii (subgenus Neobromus). A BstEII site in the IGS, common to seven of the species, was absent in B. tectorum and B. sericeus. In the coding region, a 2.1-kbp BstEII fragment was present in four subgenera represented by Bromus inermis and Bromus erectus (subgenus Festucaria), Bromus marginatus and Bromus carinatus (subgenus Ceratochloa), B. tectorum and B. sericeus (subgenus Stenobromus), and B. trinii (subgenus Neobromus); a similar fragment of only 1.1 kbp was present in Bromus mollis and Bromus arvensis (subgenus Bromus). An additional BamHI site was present in the coding region of B. erectus. Ribosomal DNA data suggested that B. mollis and B. arvensis (subgenus Bromus) are genetically isolated from the other subgenera, which showed a derived relationship. Restriction site mapping of the rDNA genes could provide useful molecular data for species identification and population and evolutionary studies in Bromus. Key words : Bromus, ribosomal DNA, restriction maps, evolutionary relationships.

scholarly journals Sequencing of the Ribosomal Intergenic Spacer Region for Strain Identification of Porphyromonas gingivalis

1999 ◽  
Vol 37 (8) ◽  
pp. 2723-2725 ◽  
Author(s):  
Robert W. Rumpf ◽  
Ann L. Griffen ◽  
Bo-Gui Wen ◽  
Eugene J. Leys
Keyword(s):  
Porphyromonas Gingivalis ◽  
Intergenic Spacer ◽  
Variable Region ◽  
Rrna Genes ◽  
23S Rrna ◽  
Clinical Samples ◽  
Strain Identification ◽  
Intergenic Spacer Region ◽  
Ribosomal Intergenic Spacer ◽  
23S Rrna Genes

The ribosomal intergenic spacer regions (ISRs) of 19 laboratory strains and 30 clinical samples of Porphyromonas gingivaliswere amplified by PCR and sequenced to provide a strain identifier. The ISR is a variable region of DNA located between the conserved 16S and 23S rRNA genes. This makes it an ideal locus for differentiation of strains within a species: primers specific for the conserved flanking genes were used to amplify the ISR, which was then sequenced to identify the strain. We have constructed a P. gingivalisISR sequence database to facilitate strain identification. ISR sequence analysis provides a strain identifier that can be easily reproduced among laboratories and catalogued for unambiguous comparison.

Sequence Length Variation of Internal Genic Space of 16S rDNA-23S rDNA in Bacterium with High Yield of Hydrogen Production

2011 ◽  
Vol 183-185 ◽  
pp. 1413-1416
Author(s):  
Yong Feng Li ◽  
Yi Xuan Wang ◽  
Lu Wang ◽  
Zhan Qing Wang
Keyword(s):  
16S Rdna ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
High Yield ◽  
23S Rrna ◽  
Sequence Length ◽  
Rrna Gene ◽  
Length Variation ◽  
Intergenic Spacer Region

To develop the identification of species for fermentative biohydrogen-producing bacterium, scholars have found a method which is based on PCR amplification of the 16S rRNA gene (rDNA)-23S rDNA intergenic regions. In the study, a large fragment of the rDNA operon, including the 16S rDNA, the intergenic spacer region (ISR) and approximately 2000 bases of the 23S rDNA, were polymerasechain reaction (PCR) amplified. The PCR amplification of the genomic DNA of Leptonema ilk strain 3055 using primers directed against conserved regions of the rRNA operon provided evidence that the 16S and 23S rRNA genes were linked via an intergenic spacer region. The sequencing of the intergenic spacer region indicated that it was 435 nucleotides in length and sequence similarity searches revealed that it bore no homology to any known sequences including tRNA available in databases.

Variation of nuclear ribosomal RNA genes in Eragrostis tef (Zucc.) Trotter

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 815-821 ◽  
Author(s):  
Michael Pillay
Keyword(s):  
Ribosomal Rna ◽  
Restriction Site ◽  
Ribosomal Rna Genes ◽  
Rrna Genes ◽  
Eragrostis Tef ◽  
Length Variation ◽  
Rdna Repeat ◽  
Spacer Length ◽  
Repeat Units ◽  
Rna Genes

Variation in the ribosomal RNA genes (rDNA) was examined to assess the genetic variability among 314 plants representing 28 accessions of Eragrostis tef, an important food crop. A restriction site map was constructed for the species by localization of the BamHI, BglII, DraI, EcoRI, EcoRV, NdeI, SacI, SpeI, XbaI, and XhoI sites. A comparison of this map with those of other grasses showed conservation of sites, especially in the coding region. However, a unique EcoRI site combined with a BamHI site in the 18S region may be of diagnostic value for the species. A BamHI fragment that spans the intergenic spacer was used as an indicator of length variation of rDNA repeat units. rDNA repeat units in E. tef ranged in size from 8.4 to 11.07 kbp. Considerable size variation of rDNA repeats was present among accessions, between individual plants within some accessions, and within single plants. A total of 19 spacer length (sl) phenotypes was observed in 16 accessions in which 11–42 plants were analyzed. A single restriction site polymorphism was detected in PI442115 that was also distinguished by having a single sl variant. Variation in the rRNA genes is a useful indicator of genetic diversity in E. tef germplasm.Key words: Eragrostis tef, ribosomal DNA, restriction map, genetic variation.

Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer

1992 ◽  
Vol 157 (2) ◽  
pp. 107-115 ◽  
Author(s):  
Elisabeth Navarro ◽  
Pascal Simonet ◽  
Philippe Normand ◽  
René Bardin
Keyword(s):  
Natural Populations ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Ribosomal Intergenic Spacer ◽  
Pcr Rflp

Correlations between Growth Traits and Heterozygosity, Allelic Distance (d2) at Microsatellite Loci in the Yellow Perch, Perca flavescens

2010 ◽  
Vol 150 ◽  
pp. 2-3
Author(s):  
Xiao-Juan Cao ◽  
Han-Ping Wang ◽  
Hong Yao ◽  
Wei-Min Wang ◽  
Paul O’Bryant ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Yellow Perch ◽  
Growth Traits ◽  
Perca Flavescens
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