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

2020 ◽  
Vol 148 ◽  
pp. 106804
Author(s):  
Keaton Tremble ◽  
Laura M. Suz ◽  
Bryn T.M. Dentinger
Keyword(s):  
Ribosomal Dna ◽  
Concerted Evolution ◽  
Population Genomics ◽  
Long Read ◽  
Lost In Translation

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.

scholarly journals The population genomics of structural variation in a songbird genus

2019 ◽  
Author(s):  
Matthias H. Weissensteiner ◽  
Ignas Bunikis ◽  
Ana Catalán ◽  
Kees-Jan Francoijs ◽  
Ulrich Knief ◽  
...  
Keyword(s):  
Structural Variation ◽  
Population Genomics ◽  
De Novo ◽  
Natural Populations ◽  
Evolutionary Significance ◽  
Substantial Part ◽  
Sequencing Data ◽  
Premating Isolation ◽  
Population Genetic Analysis ◽  
Long Read

AbstractStructural variation (SV) accounts for a substantial part of genetic mutations segregating across eukaryotic genomes with important medical and evolutionary implications. Here, we characterized SV across evolutionary time scales in the songbird genus Corvus using de novo assembly and read mapping approaches. Combining information from short-read (N = 127) and long-read re-sequencing data (N = 31) as well as from optical maps (N = 16) revealed a total of 201,738 insertions, deletions and inversions. Population genetic analysis of SV in the Eurasian crow speciation model revealed an evolutionary young (~530,000 years) cis-acting 2.25-kb retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth of SV segregating in natural populations and demonstrate its evolutionary significance.

scholarly journals Draft Genome Resource for Macrophomina phaseolina Associated With Charcoal Rot in Sorghum

2020 ◽  
Vol 33 (5) ◽  
pp. 724-726 ◽  
Author(s):  
Neeraj Purushotham ◽  
Ashley Jones ◽  
Barsha Poudel ◽  
Jamila Nasim ◽  
Dante Adorada ◽  
...  
Keyword(s):  
Population Genomics ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Single Copy ◽  
Macrophomina Phaseolina ◽  
Phytopathogenic Fungus ◽  
Molecular Diagnostic ◽  
Charcoal Rot ◽  
Future Studies ◽  
Long Read

Macrophomina phaseolina is a soil-borne phytopathogenic fungus that causes charcoal rot in several plant species, including sorghum. We constructed a draft genome of M. phaseolina isolate BRIP 70780a from sorghum, using long-read native DNA from MinION sequencing, which was error-corrected using short-read Illumina MiSeq reads. The draft genome, consisting of 22 contigs with an N50 of 4,257,441 bp, 99.3% complete benchmarking universal single-copy orthologs, and 14,471 genes, is a valuable resource to aid future studies in population genomics and molecular diagnostic marker development for rapid detection of the pathogen.

scholarly journals Ribosomal DNA in the Grasshopper Podisma pedestris: Escape From Concerted Evolution

Genetics ◽  
2006 ◽  
Vol 174 (2) ◽  
pp. 863-874 ◽  
Author(s):  
Irene Keller ◽  
Ioana C. Chintauan-Marquier ◽  
Paris Veltsos ◽  
Richard A. Nichols
Keyword(s):  
Ribosomal Dna ◽  
Concerted Evolution

scholarly journals Rapid Concerted Evolution of Nuclear Ribosomal DNA in Two Tragopogon Allopolyploids of Recent and Recurrent Origin

Genetics ◽  
2005 ◽  
Vol 169 (2) ◽  
pp. 931-944 ◽  
Author(s):  
A. Kovarik ◽  
J. C. Pires ◽  
A. R. Leitch ◽  
K. Y. Lim ◽  
A. M. Sherwood ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Concerted Evolution ◽  
Nuclear Ribosomal Dna

scholarly journals Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 186 ◽  
Author(s):  
Charlotte J. Houldcroft
Keyword(s):  
Epstein Barr Virus ◽  
Population Genomics ◽  
Human Herpesvirus ◽  
Mixed Genotype ◽  
Barr Virus ◽  
Childhood Infections ◽  
Sequencing Technologies ◽  
Long Read ◽  
Epstein Barr ◽  
Human Herpesviruses

The nine human herpesviruses are some of the most ubiquitous pathogens worldwide, causing life-long latent infection in a variety of different tissues. Human herpesviruses range from mild childhood infections to known tumour viruses and ‘trolls of transplantation’. Epstein-Barr virus was the first human herpesvirus to have its whole genome sequenced; GenBank now includes thousands of herpesvirus genomes. This review will cover some of the recent advances in our understanding of herpesvirus diversity and disease that have come about as a result of new sequencing technologies, such as target enrichment and long-read sequencing. It will also look at the problem of resolving mixed-genotype infections, whether with short or long-read sequencing methods; and conclude with some thoughts on the future of the field as herpesvirus population genomics becomes a reality.

scholarly journals Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication

2020 ◽  
Vol 37 (12) ◽  
pp. 3507-3524 ◽  
Author(s):  
Yixuan Kou ◽  
Yi Liao ◽  
Tuomas Toivainen ◽  
Yuanda Lv ◽  
Xinmin Tian ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Population Genomics ◽  
Indica Rice ◽  
Population Sample ◽  
Mobile Element ◽  
Plant Genome ◽  
Rice Varieties ◽  
Data Set ◽  
Asian Rice ◽  
Long Read

Abstract Structural variants (SVs) are a largely unstudied feature of plant genome evolution, despite the fact that SVs contribute substantially to phenotypes. In this study, we discovered SVs across a population sample of 347 high-coverage, resequenced genomes of Asian rice (Oryza sativa) and its wild ancestor (O. rufipogon). In addition to this short-read data set, we also inferred SVs from whole-genome assemblies and long-read data. Comparisons among data sets revealed different features of genome variability. For example, genome alignment identified a large (∼4.3 Mb) inversion in indica rice varieties relative to japonica varieties, and long-read analyses suggest that ∼9% of genes from the outgroup (O. longistaminata) are hemizygous. We focused, however, on the resequencing sample to investigate the population genomics of SVs. Clustering analyses with SVs recapitulated the rice cultivar groups that were also inferred from SNPs. However, the site-frequency spectrum of each SV type—which included inversions, duplications, deletions, translocations, and mobile element insertions—was skewed toward lower frequency variants than synonymous SNPs, suggesting that SVs may be predominantly deleterious. Among transposable elements, SINE and mariner insertions were found at especially low frequency. We also used SVs to study domestication by contrasting between rice and O. rufipogon. Cultivated genomes contained ∼25% more derived SVs and mobile element insertions than O. rufipogon, indicating that SVs contribute to the cost of domestication in rice. Peaks of SV divergence were enriched for known domestication genes, but we also detected hundreds of genes gained and lost during domestication, some of which were enriched for traits of agronomic interest.

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