scholarly journals Lost in Translation: population genomics and long-read sequencing reveals relaxation of concerted evolution of the ribosomal DNA cistron

2019 ◽  
Author(s):  
Keaton Tremble ◽  
Laura M. Suz ◽  
Bryn T.M. Dentinger
Keyword(s):  
Gene Flow ◽  
Dna Barcoding ◽  
Intraspecific Variation ◽  
Ribosomal Dna ◽  
Concerted Evolution ◽  
Population Genomics ◽  
Internal Transcribed Spacers ◽  
Rdna Genes ◽  
Rdna Array ◽  
Long Read

AbstractConcerted evolution of the ribosomal DNA array has been studied in numerous eukaryotic taxa, yet is still poorly understood. rDNA genes are repeated dozens to hundreds of times in the eukaryotic genome [1] and it is believed that these arrays are homogenized through concerted evolution [2, 3] preventing the accumulation of intragenomic, and intraspecific, variation. However, numerous studies have reported rampant intragenomic and intraspecific variation in the rDNA array [4–10], contradicting our current understanding of concerted evolution. The internal transcribed spacers (ITS) of the rDNA cistron are the most commonly used DNA barcoding region in Fungi [11], and rely on concerted evolution to homogenize the rDNA array leading to a “barcode gap” [12]. Here we show that in Boletus edulis Bull., ITS intragenomic variation persists at low allele frequencies throughout the rDNA array, this variation does not correlate with genomic relatedness between populations, and rDNA genes may not evolve in a strictly concerted fashion despite the presence of unequal recombination and gene conversion. Under normal assumptions, heterozygous positions found in ITS sequences represent hybridization between populations, yet through allelic mapping of the rDNA array we found numerous heterozygous alleles to be stochastically introgressed throughout, presenting a dishonest signal of gene flow. Moreover, despite the signal of gene flow in ITS, our organisms were highly inbred, indicating a disconnect between true gene flow and barcoding signals. In addition, we show that while the mechanisms of concerted evolution are ongoing in pseudo-heterozygous individuals, they are not fully homogenizing the ITS array. Concerted evolution of the rDNA array may insufficiently homogenize the ITS gene, allowing for misleading signals of gene flow to persist, vastly complicating the use of the ITS locus for DNA barcoding in Fungi.

Phylogenetic Analysis of Black Peper (Piper Spp.) Population Collected in Different Locations of Vietnam Based on the ITSU1-4 Gene Region

2021 ◽  
Author(s):  
Sonexay Rasphone ◽  
Long Thanh Dang ◽  
Hoan Nguyen ◽  
Ngoc Quang Nguyen ◽  
Oanh Thi Duong ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Ribosomal Dna ◽  
Maximum Likelihood Method ◽  
Dna Barcode ◽  
Population Expansion ◽  
Nuclear Ribosomal Dna ◽  
Likelihood Method ◽  
Gene Region ◽  
Universal Primers ◽  
Intraspecific Distance

Abstract Background: The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. To compare and find out the analysis genetic diversity difference some pepper individuals collected in different localities in Vietnam when using the ITS of nuclear ribosomal DNA. The ITS gene region from the nuclear genomes were tested for their suitability as DNA barcoding regions of thirty-nine pepper individuals. Universal primers were used, and sequenced products were analyzed using the Maximum Likelihood method and Tamura-Nei model in the MEGA X program.Results: We did not observe high variability in intraspecific distance within the ITSu1-4 gene region between individuals, ranged from 0.000 to 0.155 (mean = 0.033). The size of the gene region has fluctuated from 667 to 685 bp between different individuals with the percentage (G + C) contained in the ITSu1-4 gene region was ranged from 54.776% to 60.805%, mean = 60.174%. The values of Fu’s Fs, D, Fu and Li’s D* and F* were negative as well (Fs = -0.209, D = -1.824; P < 0.05, D* = -1.205; not significant, P > 0.10 and F* = -1.699; not significant, 0.10 > P > 0.05), indicating an excess of recently derived haplotypes and suggesting that either population expansion or background selection has occurred. The value Strobeck’s S the obtained between individuals in a population is high (S = 0.684). The results of evolutionary relationships of taxa obtained 3 groups with the highest value of Fst is shown in the pairs of groups II and III (Fst = 0.151), and the lowest is in groups II and I (Fst = 0.015). All of the new sequences have been deposited in GeneBank under the following accession numbers MZ636718 to MZ636756.Conclusions: This database is an important resource for researchers working on Species of pepper in Vietnam and also provides a tool to create ITSu1-4 databases for any given taxonomy.

scholarly journals Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study

2016 ◽  
Vol 7 ◽  
Author(s):  
Shangguo Feng ◽  
Mengying Jiang ◽  
Yujun Shi ◽  
Kaili Jiao ◽  
Chenjia Shen ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Ribosomal Dna ◽  
Phylogenetic Study ◽  
Its2 Region

scholarly journals Sequences of the second internal transcribed spacer of ribosomal DNA for three species of Trichostrongylus (Nematoda: Trichostrongylidae) from sheep in Russia

2007 ◽  
Vol 44 (2) ◽  
pp. 43-46 ◽  
Author(s):  
D. Kuznetsov ◽  
N. Kuznetsova
Keyword(s):  
Dna Sequence ◽  
Intraspecific Variation ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Moscow Region ◽  
Dna Sequence Data ◽  
Interspecific Differences ◽  
Second Internal Transcribed Spacer ◽  
First Time

AbstractFor the first time, DNA sequence data were obtained for three species of Trichostrongylus from Russia. Internal transcribed spacer (ITS-2) of ribosomal DNA was sequenced for T. axei, T. colubriformis and T. probolurus from sheep from the Moscow region. ITS-2 rDNA length was estimated as 238 nucleotides for T. colubriformis and T. probolurus and 237 nucleotides for T. axei. The G+C content of the ITS-2 sequences of T. colubriformis, T. axei and T. probolurus were 31 %, 32 % and 34 % respectively. The level of interspecific differences in ITS-2 of rDNA of T. axei, T. probolurus and T. colubriformis ranged from 3 to 4 %. The ITS-2 sequences from the Russian specimens were compared with those of T. axei, T. probolurus and T. colubriformis from Australia and Germany. Intraspecific variation ranged from 0 % in T. colubriformis to 3.0 % in T. axei.

Population genomics reveals high gene flow in grass rockfish ( Sebastes rastrelliger )

2017 ◽  
Vol 33 ◽  
pp. 57-63 ◽  
Author(s):  
Edith Martinez ◽  
Vincent Buonaccorsi ◽  
John R. Hyde ◽  
Andres Aguilar
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
High Gene Flow ◽  
High Gene

scholarly journals Spatial population genomics of a recent mosquito invasion

2020 ◽  
Author(s):  
Thomas L Schmidt ◽  
T. Swan ◽  
Jessica Chung ◽  
Stephan Karl ◽  
Samuel Demok ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Nucleotide Polymorphisms ◽  
Discrete Events ◽  
Long Distance ◽  
Population Genomic ◽  
Asian Tiger ◽  
Study Designs

AbstractPopulation genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232–577. Close kin dyads revealed recent movement between islands 31–203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

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