Evolution of Eukaryote Genome Complexity

The dynamic nature of the nuclear envelope (NE) is often underestimated. The NE protects, regulates, and organizes the eukaryote genome and adapts to epigenetic changes and to its environment. The NE morphology is characterized by a wide range of diversity and abnormality such as invagination and blebbing, and it is a diagnostic factor for pathologies such as cancer. Recently, the micronuclei, a small nucleus that contains a full chromosome or a fragment thereof, has gained much attention. The NE of micronuclei is prone to collapse, leading to DNA release into the cytoplasm with consequences ranging from the activation of the cGAS/STING pathway, an innate immune response, to the creation of chromosomal instability. The discovery of those mechanisms has revolutionized the understanding of some inflammation-related diseases and the origin of complex chromosomal rearrangements, as observed during the initiation of tumorigenesis. Herein, we will highlight the complexity of the NE biology and discuss the clinical symptoms observed in NE-related diseases. The interplay between innate immunity, genomic instability, and nuclear envelope leakage could be a major focus in future years to explain a wide range of diseases and could lead to new classes of therapeutics.

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Fine-tuning the performance of ddRAD-seq in the peach genome

Scientific Reports ◽

10.1038/s41598-021-85815-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Maximiliano Martín Aballay ◽

Natalia Cristina Aguirre ◽

Carla Valeria Filippi ◽

Gabriel Hugo Valentini ◽

Gerardo Sánchez

Keyword(s):

Germplasm Collection ◽

In Silico Analysis ◽

Genotyping By Sequencing ◽

Fine Tuning ◽

The Novel ◽

Peach Genome ◽

Genome Complexity ◽

Next Generation Sequencing Ngs ◽

Sample Set ◽

Silico Analysis

AbstractThe advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach.

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Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes

Scientific Reports ◽

10.1038/s41598-021-93257-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Weitao Chen ◽

Ming Zou ◽

Yuefei Li ◽

Shuli Zhu ◽

Xinhui Li ◽

...

Keyword(s):

De Novo ◽

Parental Species ◽

F1 Hybrids ◽

Pelteobagrus Fulvidraco ◽

F1 Hybrid ◽

Short Reads ◽

Final Assembly ◽

Genome Complexity ◽

Hybrid Genome ◽

Silurus Asotus

AbstractGenome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.

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Humanizing the yeast origin recognition complex

Nature Communications ◽

10.1038/s41467-020-20277-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Clare S. K. Lee ◽

Ming Fung Cheung ◽

Jinsen Li ◽

Yongqian Zhao ◽

Wai Hei Lam ◽

...

Keyword(s):

Amino Acid ◽

Protein Complex ◽

Origin Recognition Complex ◽

Specific Binding ◽

Life Cycles ◽

Amino Acid Insertion ◽

Evolutionarily Conserved ◽

Transcriptional Start Sites ◽

Eukaryote Genome ◽

Origin Recognition

AbstractThe Origin Recognition Complex (ORC) is an evolutionarily conserved six-subunit protein complex that binds specific sites at many locations to coordinately replicate the entire eukaryote genome. Though highly conserved in structure, ORC’s selectivity for replication origins has diverged tremendously between yeasts and humans to adapt to vastly different life cycles. In this work, we demonstrate that the selectivity determinant of ORC for DNA binding lies in a 19-amino acid insertion helix in the Orc4 subunit, which is present in yeast but absent in human. Removal of this motif from Orc4 transforms the yeast ORC, which selects origins based on base-specific binding at defined locations, into one whose selectivity is dictated by chromatin landscape and afforded with plasticity, as reported for human. Notably, the altered yeast ORC has acquired an affinity for regions near transcriptional start sites (TSSs), which the human ORC also favors.

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