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

Mapping Intimacies ◽

10.1101/797035 ◽

2019 ◽

Cited By ~ 2

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.

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

Molecular Biology and Evolution ◽

10.1093/molbev/msaa107 ◽

2020 ◽

Vol 37 (9) ◽

pp. 2549-2567 ◽

Cited By ~ 1

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.

Arabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation

Nature Communications ◽

10.1038/s41467-021-24553-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yan Xue ◽

Zhenhui Zhong ◽

C. Jake Harris ◽

Javier Gallego-Bartolomé ◽

Ming Wang ◽

...

Keyword(s):

Dna Methylation ◽

Arabidopsis Thaliana ◽

Transposable Element ◽

Zinc Finger ◽

Protein Function ◽

C Elegans ◽

Eukaryotic Organisms

AbstractThe Microrchidia (MORC) family of ATPases are required for transposable element (TE) silencing and heterochromatin condensation in plants and animals, and C. elegans MORC-1 has been shown to topologically entrap and condense DNA. In Arabidopsis thaliana, mutation of MORCs has been shown to reactivate silent methylated genes and transposons and to decondense heterochromatic chromocenters, despite only minor changes in the maintenance of DNA methylation. Here we provide the first evidence localizing Arabidopsis MORC proteins to specific regions of chromatin and find that MORC4 and MORC7 are closely co-localized with sites of RNA-directed DNA methylation (RdDM). We further show that MORC7, when tethered to DNA by an artificial zinc finger, can facilitate the establishment of RdDM. Finally, we show that MORCs are required for the efficient RdDM mediated establishment of DNA methylation and silencing of a newly integrated FWA transgene, even though morc mutations have no effect on the maintenance of preexisting methylation at the endogenous FWA gene. We propose that MORCs function as a molecular tether in RdDM complexes to reinforce RdDM activity for methylation establishment. These findings have implications for MORC protein function in a variety of other eukaryotic organisms.

Evolution of the Yeast Recombination Landscape

Molecular Biology and Evolution ◽

10.1093/molbev/msy233 ◽

2018 ◽

Vol 36 (2) ◽

pp. 412-422 ◽

Cited By ~ 4

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.

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

10.1101/786145 ◽

2019 ◽

Cited By ~ 4

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.

Genomic organization of the transposable element Tdd-3 from Dictyostelium discoideum

Nucleic Acids Research ◽

10.1093/nar/18.19.5751 ◽

1990 ◽

Vol 18 (19) ◽

pp. 5751-5757 ◽

Cited By ~ 7

Author(s):

Rolf Marschalek ◽

Gabi Borschet ◽

Theodor Dingermann

Keyword(s):

Transposable Element ◽

Dictyostelium Discoideum ◽

Genomic Organization

Terminal repeats of the drosophila transposable element copia: Nucleotide sequence and genomic organization

Cell ◽

10.1016/0092-8674(80)90496-1 ◽

1980 ◽

Vol 21 (2) ◽

pp. 581-588 ◽

Cited By ~ 88

Author(s):

Robert Levis ◽

Pamela Dunsmuir ◽

Gerald M. Rubin

Keyword(s):

Nucleotide Sequence ◽

Transposable Element ◽

Genomic Organization ◽

Terminal Repeats

Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans

Biology Direct ◽

10.1186/1745-6150-3-41 ◽

2008 ◽

Vol 3 (1) ◽

pp. 41 ◽

Cited By ~ 2

Author(s):

Noa Sela ◽

Adi Stern ◽

Wojciech Makalowski ◽

Tal Pupko ◽

Gil Ast

Keyword(s):

Transposable Element ◽

Protein Coding ◽

Coding Sequences ◽

C Elegans

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

Genetics ◽

10.1093/genetics/141.1.159 ◽

1995 ◽

Vol 141 (1) ◽

pp. 159-179 ◽

Cited By ~ 10

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.

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

10.1101/2021.01.15.426870 ◽

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.

A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress

10.1101/112847 ◽

2017 ◽

Author(s):

Alicia N. McMurchy ◽

Przemyslaw Stempor ◽

Tessa Gaarenstroom ◽

Brian Wysolmerski ◽

Yan Dong ◽

...

Keyword(s):

Small Rna ◽

Germ Line ◽

Large Fraction ◽

Repetitive Sequences ◽

Genotoxic Stress ◽

Repetitive Elements ◽

C Elegans ◽

Genes Encoding ◽

Rna Pathways ◽

Nuclear Rnai

AbstractRepetitive sequences derived from transposons make up a large fraction of eukaryotic genomes and must be silenced to protect genome integrity. Repetitive elements are often found in heterochromatin; however, the roles and interactions of heterochromatin proteins in repeat regulation are poorly understood. Here we show that a diverse set of C. elegans heterochromatin proteins act together with the piRNA and nuclear RNAi pathways to silence repetitive elements and prevent genotoxic stress in the germ line. Mutants in genes encoding HPL-2/HP1, LIN-13, LIN-61, LET-418/Mi-2, and H3K9me2 histone methyltransferase MET-2/SETDB1 also show functionally redundant sterility, increased germline apoptosis, DNA repair defects, and interactions with small RNA pathways. Remarkably, fertility of heterochromatin mutants could be partially restored by inhibiting cep-1/p53, endogenous meiotic double strand breaks, or the expression of MIRAGE1 DNA transposons. Functional redundancy among these factors and pathways underlies the importance of safeguarding the genome through multiple means.