Intraspecific <i>de novo</i> gene birth revealed by presence–absence variant genes in <i>Caenorhabditis elegans</i>

Lee, Bo Yun; Kim, Jun; Lee, Junho

doi:10.1093/nargab/lqac031

Cited by 9 publications

(4 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Indeed, even though TE insertions are not the main events enabling neORF emergence, their presence in genomes may promote other mutations that contribute to neORFs emergence. This has also been suggested by ( Lee et al 2022 ), who studied presence-absence variants of genes in C.elegans , and showed that some of these de novo genes have signatures of active transposons. Concerning the 25%–30% of neORFs which emerged inside TEs, the question is whether to consider them as de novo genes.…”

Section: Discussionsupporting

confidence: 64%

Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inDrosophila melanogaster

et al. 2023

View full text Add to dashboard Cite

Novel genes are essential for evolutionary innovations and differ substantially even between closely related species. Recently, multiple studies across many taxa showed that some novel genes arise de novo, that is, from previously noncoding DNA. To characterize the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within noncoding sequences in closely related sister genomes. So far, most studies do not detect noncoding homologs of de novo genes because of incomplete assemblies and annotations, and long evolutionary distances separating genomes. Here, we overcome these issues by searching for de novo expressed open reading frames (neORFs), the not-yet fixed precursors of de novo genes that emerged within a single species. We sequenced and assembled genomes with long-read technology and the corresponding transcriptomes from inbred lines ofDrosophila melanogaster, derived from seven geographically diverse populations. We found line-specific neORFs in abundance but few neORFs shared by lines, suggesting a rapid turnover. Gain and loss of transcription is more frequent than the creation of ORFs, for example, by forming new start and stop codons. Consequently, the gain of ORFs becomes rate limiting and is frequently the initial step in neORFs emergence. Furthermore, transposable elements (TEs) are major drivers for intragenomic duplications of neORFs, yet TE insertions are less important for the emergence of neORFs. However, highly mutable genomic regions around TEs provide new features that enable gene birth. In conclusion, neORFs have a high birth-death rate, are rapidly purged, but surviving neORFs spread neutrally through populations and within genomes.

show abstract

Section: Discussionsupporting

confidence: 64%

Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inDrosophila melanogaster

et al. 2023

View full text Add to dashboard Cite

show abstract

“…These include Illumina paired-end data of over 600 wild isolates by CeNDR, which also obtained first-generation PacBio long-read data of 14 wild isolates. Second-generation PacBio HiFi data 20 and Oxford Nanopore Technologies (ONT) long-read data 21 are available with CB4856 HA from Hawaii, which is the most intensively studied C. elegans wild isolate aside from the standard wild type strain N2. Illumina, PacBio, and ONT data is available with an N2-derivative with no known history of mutagenesis called VC2010 or PD1074 22 , 23 and is called CGC1 at Caenorhabditis elegans genetics center.…”

Section: Resultsmentioning

confidence: 99%

Effect of recombination on genetic diversity of Caenorhabditis elegans

Hwang,

Wang

2023

Sci Rep

View full text Add to dashboard Cite

Greater molecular divergence and genetic diversity are present in regions of high recombination in many species. Studies describing the correlation between variant abundance and recombination rate have long focused on recombination in the context of linked selection models, whereby interference between linked sites under positive or negative selection reduces genetic diversity in regions of low recombination. Here, we show that indels, especially those of intermediate sizes, are enriched relative to single nucleotide polymorphisms in regions of high recombination in C. elegans. To explain this phenomenon, we reintroduce an alternative model that emphasizes the mutagenic effect of recombination. To extend the analysis, we examine the variants with a phylogenetic context and discuss how different models could be examined together. The number of variants generated by recombination in natural populations could be substantial including possibly the majority of some indel subtypes. Our work highlights the potential importance of a mutagenic effect of recombination, which could have a significant role in the shaping of natural genetic diversity.

show abstract

“…Long-read DNA sequencing and short-read RNA sequencing of LJ2284, LJ2285, LJ2400, and LJ2406 were conducted as previously described ( Kim et al 2019a ; Lee et al 2022a ). In summary, genomic DNA was extracted from mixed-stage worms using phenol/chloroform/isoamyl alcohol (25:24:1) and sequenced using the HiFi mode of the PacBio Sequel II platform by Macrogen.…”

Section: Methodsmentioning

confidence: 99%

Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures

Lim,

Kim,

Kim

et al. 2023

Genome Res.

Self Cite

View full text Add to dashboard Cite

Telomeres are composed of tandem arrays of telomeric-repeat motifs (TRMs) and telomere-binding proteins (TBPs), which are responsible for ensuring end-protection and end-replication of chromosomes. TRMs are highly conserved due to the sequence specificity of TBPs, although significant alterations in TRM have been observed in several taxa, except Nematoda. We used public whole-genome sequencing datasets to analyze putative TRMs of 100 nematode species and determined that three distinct branches included specific novel TRMs, suggesting that evolutionary alterations in TRMs occurred in Nematoda. We focused on one of the three branches, the Panagrolaimidae family, and performed a de novo assembly of four high-quality draft genomes of the canonical (TTAGGC) and novel TRM (TTAGAC) isolates; the latter genomes revealed densely clustered arrays of the novel TRM. We then comprehensively analyzed the subtelomeric regions of the genomes to infer how the novel TRM evolved. We identified DNA damage-repair signatures in subtelomeric sequences that were representative of consequences of telomere maintenance mechanisms by alternative lengthening of telomeres. We propose a hypothetical scenario in which TTAGAC-containing units are clustered in subtelomeric regions and pre-existing TBPs capable of binding both canonical and novel TRMs aided the evolution of the novel TRM in the Panagrolaimidae family.

show abstract

Intraspecific de novo gene birth revealed by presence–absence variant genes in Caenorhabditis elegans

Cited by 9 publications

References 74 publications

Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inDrosophila melanogaster

Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inDrosophila melanogaster

Effect of recombination on genetic diversity of Caenorhabditis elegans

Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures

Contact Info

Product

Resources

About