De novo gene birth

Oss, S. Branden Van; Carvunis, Anne‐Ruxandra

doi:10.1371/journal.pgen.1008160

Cited by 279 publications

(342 citation statements)

References 146 publications

(210 reference statements)

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“…7A-B), suggesting that these eliminated regions have recently evolved or are evolutionarily more flexible than the rest of the genome. These regions may more readily enable the birth of new genes, consistent with the observation that novel genes are often enriched in the testis and consistent with their propensity for elimination in Ascaris [51][52][53]. Overall, our comparative analysis of the C. elegans and Ascaris chromosomes reveals that many Ascaris sex chromosomes are the result of recent fusion events and that DNA elimination breaks re-subdivide the chromosomes into single chromosomes that are orthologous to individual C. elegans chromosomes.…”

Section: Chromosome Fusion In Ascaris Sex Chromosomessupporting

confidence: 82%

Comprehensive Chromosome End Remodeling During Programmed DNA Elimination

Wang

Veronezi

Zagoskin

et al. 2020

Preprint

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Germline and somatic genomes are typically the same in a multicellular organism. However, in some organisms including the parasitic nematode Ascaris, programmed DNA elimination leads to a reduced somatic genome compared to germline cells. Previous work on the parasitic nematode Ascaris demonstrated that programmed DNA elimination encompasses high fidelity chromosomal breaks at specific genome locations and loss of specific genome sequences including a major tandem repeat of 120 bp and ~1,000 germline-expressed genes. However, the precise chromosomal locations of the 120 bp repeats, the breaks regions, and the eliminated genes remained unknown. Here, we used PacBio longread sequencing and chromosome conformation capture (Hi-C) to obtain fully assembled chromosomes of Ascaris germline and somatic genomes, enabling a complete chromosomal view of DNA elimination.Surprisingly, we found that all 24 germline chromosomes undergo comprehensive chromosome end remodeling with DNA breaks in their subtelomeric regions and loss of distal sequences including the telomeres at both chromosome ends. All new Ascaris somatic chromosome ends are recapped by de novo telomere healing. We provide an ultrastructural analysis of DNA elimination and show that Ascaris eliminated DNA is incorporated into many double membrane-bound structures, similar to micronuclei, during telophase of a DNA elimination mitosis. These micronuclei undergo dynamic changes including loss of active histone marks and localize to the cytoplasm following daughter nuclei formation and cytokinesis where they form autophagosomes. Comparative analysis of nematode chromosomes suggests that germline chromosome fusions occurred forming Ascaris sex chromosomes that become independent chromosomes following DNA elimination breaks in somatic cells. These studies provide the first chromosomal view and define novel features and functions of metazoan programmed DNA elimination.

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Section: Chromosome Fusion In Ascaris Sex Chromosomessupporting

confidence: 82%

Comprehensive Chromosome End Remodeling During Programmed DNA Elimination

Wang

Veronezi

Zagoskin

et al. 2020

Preprint

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“…A large portion of these unannotated transcripts might be "transcriptional noise" 51 or, as suggested by 62 , fodder for de novo gene evolution. Other sequences may be on a continuum from protogene to gene to pseudogene and/or to oblivion 1,91 . No clear criteria have been established to assign these products of this "dark transcriptome" to any particular category.…”

Section: /14mentioning

confidence: 99%

Foster thy young: Enhanced prediction of orphan genes in assembled genomes

Singh

Bhandary

et al. 2019

Preprint

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The evolutionary rapid emergence of new genes gives rise to "orphan genes" that share no sequence homology to genes in closely related genomes. These genes provide organisms with a reservoir of genetic elements to quickly respond to changing selection pressures. Gene annotation pipelines that combine ab initio machine-learning with sequence homology-based searches are efficient in identifying basal genes with a long evolutionary history. However, their ability to identify orphan genes and other young genes has not been systematically evaluated. Here, we classify the phylostrata of curated Arabidopsis thaliana genes and use these to assess the ability of two of the most prevalent annotation pipelines, MAKER and BRAKER, to predict orphans and other young genes. MAKER predictions are highly dependent on the RNA-Seq evidence, predicting between 11% and 60% of the orphan-genes and 95% to 98% of basal-genes in the annotated genome of Arabidopsis. In contrast, BRAKER consistently predicts 33% of orphan-genes and 98% of basal-genes. A less used method to identify genes is by directly aligning RNA-Seq data to the genome sequence. We present a Findable, Accessible, Interoperable and Reusable (FAIR) approach, called BIND, that mitigates the under-prediction of orphan genes. BIND combines BRAKER predictions with direct evidence-based inference of transcripts based on RNA-Seq alignments to the genome. BIND increases the number and accuracy of orphan gene predictions, identifying 68% of Araport11-annotated orphan genes and 99% of the conserved genes.

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“…New protein-coding genes emerge over time, either through a combination of rearrangement, duplication and divergence from ancestrally coding sequences, or de novo from previously noncoding DNA (for a review see (Van Oss & Carvunis 2019)). Although genes clearly originated de novo during the emergence of life, de novo gene birth after this unique event was once believed to be vanishingly rare (Jacob 1977;Keese & Gibbs 1992;Zuckerkandl 1975).…”

Section: Introductionmentioning

confidence: 99%

“…Random sequences with high %GC tend to encode polypeptides with higher ISD (Ángyán et al 2012). Differences in genomic GC content between species might therefore shape disorder at the time of gene birth differently (Basile et al 2016;Van Oss & Carvunis 2019). Alternatively, the low disorder of young "protogenes" may be an artifact of including sequences that do not meet the evolutionary definition of functionality, which requires that the loss of the gene be deleterious, i.e.…”

Section: Introductionmentioning

confidence: 99%

Universal and taxon-specific trends in protein sequences as a function of age

James

Willis

Nelson

et al. 2020

Preprint

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Extant protein-coding sequences span a huge range of ages, from those that emerged only recently in particular lineages, to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be "phylostratigraphy" trends in any properties that evolve slowly with age. Indeed, a long-term reduction in hydrophobicity and in hydrophobic clustering has been found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced and dated eukaryotic species, using sensitive HMM methods to detect homology of protein domains (which may vary in age within the same gene), and applying a variety of quality filters. We find that the reduction in hydrophobic clustering is universal across diverse lineages, showing limited sign of saturation. But the tendency for young domains to have higher protein structural disorder, driven primarily by more hydrophilic amino acids, is found only among young animal domains, and not young plant domains, nor ancient domains predating the existence of the last eukaryotic common ancestor. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that events during the earliest stages of life on earth continue to have an impact on the composition of ancient sequences.

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De novo gene birth

Cited by 279 publications

References 146 publications

Comprehensive Chromosome End Remodeling During Programmed DNA Elimination

Comprehensive Chromosome End Remodeling During Programmed DNA Elimination

Foster thy young: Enhanced prediction of orphan genes in assembled genomes

Universal and taxon-specific trends in protein sequences as a function of age

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