scholarly journals Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans

2020 ◽  
Vol 37 (9) ◽  
pp. 2549-2567 ◽  
Author(s):  
Gavin C Woodruff ◽  
Anastasia A Teterina
Keyword(s):  
Caenorhabditis Elegans ◽  
Recombination Rate ◽  
Genomic Organization ◽  
Reproductive Mode ◽  
Repetitive Elements ◽  
Repeat Content ◽  
Genomic Landscape ◽  
Chromosome Position ◽  
Caenorhabditis Species ◽  
Evolutionary Simulations

Abstract The abundance, diversity, and genomic distribution of repetitive elements is highly variable among species. These patterns are thought to be driven in part by reproductive mode and the interaction of selection and recombination, and recombination rates typically vary by chromosomal position. In the nematode Caenorhabditis elegans, repetitive elements are enriched at chromosome arms and depleted on centers, and this mirrors the chromosomal distributions of other genomic features such as recombination rate. How conserved is this genomic landscape of repeats, and what evolutionary forces maintain it? To address this, we compared the genomic organization of repetitive elements across five Caenorhabditis species with chromosome-level assemblies. As previously reported, repeat content is enriched on chromosome arms in most Caenorhabditis species, and no obvious patterns of repeat content associated with reproductive mode were observed. However, the fig-associated C. inopinata has experienced repetitive element expansion and reveals no association of global repeat density with chromosome position. Patterns of repeat superfamily specific distributions reveal this global pattern is driven largely by a few repeat superfamilies that in C. inopinata have expanded in number and have weak associations with chromosome position. Additionally, 15% of predicted protein-coding genes in C. inopinata align to transposon-related proteins. When these are excluded, C. inopinata has no enrichment of genes in chromosome centers, in contrast to its close relatives who all have such clusters. Forward evolutionary simulations reveal that chromosomal heterogeneity in recombination rate alone can generate structured repetitive genomic landscapes when insertions are weakly deleterious, whereas chromosomal heterogeneity in the fitness effects of transposon insertion can promote such landscapes across a variety of evolutionary scenarios. Thus, patterns of gene density along chromosomes likely contribute to global repetitive landscapes in this group, although other historical or genomic factors are needed to explain the idiosyncrasy of genomic organization of various transposable element taxa within C. inopinata. Taken together, these results highlight the power of comparative genomics and evolutionary simulations in testing hypotheses regarding the causes of genome organization.

scholarly journals Degradation of the repetitive genomic landscape in a close relative of C. elegans

2019 ◽  
Author(s):  
Gavin C. Woodruff ◽  
Anastasia A. Teterina
Keyword(s):  
Transposable Element ◽  
Recombination Rate ◽  
Genomic Organization ◽  
Reproductive Mode ◽  
Repetitive Elements ◽  
C Elegans ◽  
Repeat Content ◽  
Genomic Landscape ◽  
Chromosome Position ◽  
Evolutionary Simulations

AbstractThe abundance, diversity, and genomic distribution of repetitive elements is highly variable among species. These patterns are thought to be driven in part by reproductive mode and the interaction of selection and recombination, and recombination rates typically vary by chromosomal position. In the nematode C. elegans, repetitive elements are enriched at chromosome arms and depleted on centers, and this mirrors the chromosomal distributions of other genomic features such as recombination rate. How conserved is this genomic landscape of repeats, and what evolutionary forces maintain it? To address this, we compared the genomic organization of repetitive elements across five Caenorhabditis species with chromosome-level assemblies. As previously reported, repeat content is enriched on chromosome arms in most Caenorhabditis species, and no obvious patterns of repeat content associated with reproductive mode were observed. However, the fig-associated Caenorhabditis inopinata has experienced rampant repetitive element expansion and reveals no association of global repeat content with chromosome position. Patterns of transposable element superfamily-specific distributions reveal this global pattern is driven largely by a few transposable element superfamilies that in C. inopinata have expanded in number and have weak associations with chromosome position. Additionally, 15% of predicted protein-coding genes in C. inopinata align to transposon-related proteins. When these are excluded, C. inopinata has no enrichment of genes in chromosome centers, in contrast to its close relatives who all have such clusters. Forward evolutionary simulations reveal that chromosomal heterogeneity in recombination rate is insufficient for generating structured genomic repetitive landscapes. Instead, heterogeneity in the fitness effects of transposable element insertion is needed to promote heterogeneity in repetitive landscapes. Thus, patterns of gene density along chromosomes are likely drivers of global repetitive landscapes in this group, although other historical or genomic factors are needed to explain the idiosyncrasy of genomic organization of various transposable element taxa within C. inopinata. Taken together, these results highlight the power of comparative genomics and evolutionary simulations in testing hypotheses regarding the causes of genome organization.

scholarly journals Evolution of the Yeast Recombination Landscape

2018 ◽  
Vol 36 (2) ◽  
pp. 412-422 ◽  
Author(s):  
Haoxuan Liu ◽  
Calum J Maclean ◽  
Jianzhi Zhang
Keyword(s):  
Recombination Rate ◽  
Yeast Species ◽  
Evolutionary Conservation ◽  
Double Strand Breaks ◽  
Strand Breaks ◽  
Crossover Interference ◽  
Recombination Hotspots ◽  
Genomic Landscape ◽  
Evolutionarily Conserved ◽  
Cold Spots

Abstract Meiotic recombination comprises crossovers and noncrossovers. Recombination, crossover in particular, shuffles mutations and impacts both the level of genetic polymorphism and the speed of adaptation. In many species, the recombination rate varies across the genome with hot and cold spots. The hotspot paradox hypothesis asserts that recombination hotspots are evolutionarily unstable due to self-destruction. However, the genomic landscape of double-strand breaks (DSBs), which initiate recombination, is evolutionarily conserved among divergent yeast species, casting doubt on the hotspot paradox hypothesis. Nonetheless, because only a subset of DSBs are associated with crossovers, the evolutionary conservation of the crossover landscape could differ from that of DSBs. Here, we investigate this possibility by generating a high-resolution recombination map of the budding yeast Saccharomyces paradoxus through whole-genome sequencing of 50 meiotic tetrads and by comparing this recombination map with that of S. cerevisiae. We observe a 40% lower recombination rate in S. paradoxus than in S. cerevisiae. Compared with the DSB landscape, the crossover landscape is even more conserved. Further analyses indicate that the elevated conservation of the crossover landscape is explained by a near-subtelomeric crossover preference in both yeasts, which we find to be attributable at least in part to crossover interference. We conclude that the yeast crossover landscape is highly conserved and that the evolutionary conservation of this landscape can differ from that of the DSB landscape.

scholarly journals A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

2019 ◽  
Author(s):  
Lillian K. Padgitt-Cobb ◽  
Sarah B. Kingan ◽  
Jackson Wells ◽  
Justin Elser ◽  
Brent Kronmiller ◽  
...  
Keyword(s):  
Large Scale ◽  
Humulus Lupulus ◽  
Plant Genome ◽  
Repeat Content ◽  
Haplotype Variation ◽  
Genomic Landscape ◽  
Cannabidiolic Acid ◽  
Long Read ◽  
History Of ◽  
Insight Into

AbstractHop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing, and around the world, hop has been used in traditional medicine to treat a variety of ailments. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large, repetitive, and heterozygous genome of hop. We present the first report of a haplotype-phased assembly of a large plant genome. Our assembly and annotation of the Cascade cultivar genome is the most extensive to date. PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. Previous studies estimated repeat content at around 60%. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. Our quantification of repeat content provides context for the size of the hop genome, and supports the hypothesis of whole genome duplication (WGD), rather than expansion due to LTRs. With our more complete assembly, we have identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze a phased, diploid assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

scholarly journals Intron Size Correlates Positively With Recombination Rate in Caenorhabditis elegans

Genetics ◽  
2004 ◽  
Vol 166 (3) ◽  
pp. 1585-1590 ◽  
Author(s):  
Anuphap Prachumwat ◽  
Laura DeVincentis ◽  
Michael F. Palopoli
Keyword(s):  
Caenorhabditis Elegans ◽  
Recombination Rate ◽  
Intron Size

Molecular and genomic organization of clusters of repetitive DNA sequences in Caenorhabditis elegans

1992 ◽  
Vol 226 (1) ◽  
pp. 159-168 ◽  
Author(s):  
Gino Naclerio ◽  
Giuseppina Cangiano ◽  
Alan Coulson ◽  
Alexandra Levitt ◽  
Vivian Ruvolo ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Genomic Organization ◽  
Repetitive Dna Sequences

scholarly journals Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans.

Genetics ◽  
1995 ◽  
Vol 141 (1) ◽  
pp. 159-179 ◽  
Author(s):  
T M Barnes ◽  
Y Kohara ◽  
A Coulson ◽  
S Hekimi
Keyword(s):  
Caenorhabditis Elegans ◽  
Genetic Map ◽  
Recombination Rate ◽  
Physical Map ◽  
Gene Density ◽  
Cdna Clones ◽  
Recombination Rates ◽  
Noncoding Dna ◽  
Physical Size ◽  
C Elegans

Abstract The genetic map of each Caenorhabditis elegans chromosome has a central gene cluster (less pronounced on the X chromosome) that contains most of the mutationally defined genes. Many linkage group termini also have clusters, though involving fewer loci. We examine the factors shaping the genetic map by analyzing the rate of recombination and gene density across the genome using the positions of cloned genes and random cDNA clones from the physical map. Each chromosome has a central gene-dense region (more diffuse on the X) with discrete boundaries, flanked by gene-poor regions. Only autosomes have reduced rates of recombination in these gene-dense regions. Cluster boundaries appear discrete also by recombination rate, and the boundaries defined by recombination rate and gene density mostly, but not always, coincide. Terminal clusters have greater gene densities than the adjoining arm but similar recombination rates. Thus, unlike in other species, most exchange in C. elegans occurs in gene-poor regions. The recombination rate across each cluster is constant and similar; and cluster size and gene number per chromosome are independent of the physical size of chromosomes. We propose a model of how this genome organization arose.

scholarly journals Chromosome size affects sequence divergence between species through the interplay of recombination and selection

2021 ◽  
Author(s):  
Anna Tigano ◽  
Ruqayya Khan ◽  
Arina D. Omer ◽  
David Weisz ◽  
Olga Dudchenko ◽  
...  
Keyword(s):  
Recombination Rate ◽  
Chromosomal Rearrangements ◽  
Genome Structure ◽  
Sequence Divergence ◽  
Great Apes ◽  
Integrative Approach ◽  
Chromosome Size ◽  
Recombination Rates ◽  
Evolutionary Simulations ◽  
The Relationship

AbstractThe structure of the genome, including the architecture, number, and size of its chromosomes, shapes the distribution of genetic diversity and sequence divergence. Importantly, smaller chromosomes experience higher recombination rates than larger ones. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we adopted an integrative approach that combines empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different Mammalian clades - Peromyscus rodents, Mus mice, and great apes - from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades, but not the Mus clade, demonstrating that the dramatic chromosomal rearrangements among Mus species masked the ancestral genomic landscape of divergence in many comparisons. Moreover, our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different size is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge and eventually speciate, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations also revealed other factors that affect the relationship between chromosome size and divergence, including chromosomal rearrangements, demography, and divergence times, and deepen our understanding of the role of genome structure on the evolution of species divergence.

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