Size evolution of gigantic genomes suggests stochastic outcomes of transposable element/host silencing interactions DOI Creative Commons
Jie Wang, Guangpu Zhang, Cheng Sun

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 23, 2024

Abstract Size evolution among gigantic genomes involves gain and loss of many gigabases transposable elements (TEs), sequences that parasitize host genomes. Animals suppress TEs using piRNA KRAB-ZFP pathways. hosts coevolve in an arms race, where suppression strength reflects TE fitness costs. In enormous genomes, additional costs become miniscule. How, then, do invoke further addition massive DNA amounts? We analyzed proliferation histories, deletion rates, community diversities six salamander (21.3 - 49.9 Gb), alongside gonadal expression activity is higher testes than ovaries, attributable to lower suppression. Unexpectedly, genome size/expansion uncorrelated with rate, history, expression, Also, diversity increases size, contrasting theoretical predictions. TE/host antagonism likely produces stochastic accumulation, determined by noisy intermolecular interactions huge genomes/cells.

Language: Английский

The First Genome-Wide Survey Analysis of the Tibetan Plateau Tetraploid Schizothorax curvilabiatus Reveals Its Microsatellite Characteristics and Phylogenetic Relationships DOI Open Access
Bingjian Liu,

Lizhi Gao,

Y Liu

et al.

Genes, Journal Year: 2025, Volume and Issue: 16(5), P. 491 - 491

Published: April 25, 2025

Background/Objectives: Schizothorax curvilabiatus, a typical highland polyploid species within the subfamily Schizothoracinae, holds economic value and ecological research significance. Currently, there are no related genomic studies. To obtain its genetic information lay foundation for subsequent whole-genome map construction, this study conducted genome survey analysis, preliminary assembly, microsatellite identification, repeat sequence annotation, mitochondrial characterization, phylogenetic relationship research. Methods: DNA was sequenced on DNBSEQ-T7 platform to paired-end data. The analyzed using GCE, draft assembled with SOAPdenovo. Microsatellites were identified MISA, NOVOPlasty. Genome features analyzed, trees constructed PhyloSuite MEGA. Results: size estimated at 2.53 Gb, heterozygosity of 6.55% 47.66% sequences. A 1.324 Gb obtained, sequences comprising 47.17%, majority being transposons (24.64%). Dinucleotide repeats most abundant (46.91%), followed by mononucleotide (38.31%), A/T AC/GT frequent. complete 16,589 bp assembled, 939 D-loop annotated. Phylogenetic relationships among genera in Schizothoracinae also clarified. Conclusions: This provides latest molecular data analysis S. curvilabiatus populations, first time offers resources adaptive evolution polyploidization high-altitude environments.

Language: Английский

Citations

0
Fitness consequences of structural variation inferred from a House Finch pangenome DOI Creative Commons
Bohao Fang, Scott V. Edwards

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(47)

Published: Nov. 12, 2024

Genomic structural variants (SVs) play a crucial role in adaptive evolution, yet their average fitness effects and characterization with pangenome tools are understudied wild animal populations. We constructed for House Finches ( Haemorhous mexicanus ), model studies of host-pathogen coevolution, using long-read sequence data on 16 individuals (32 de novo - assembled haplotypes) one outgroup. identified 887,118 SVs larger than 50 base pairs, mostly (60%) involving repetitive elements, reduced SV diversity the eastern US as result its introduction by humans. The distribution genome-wide was estimated maximum likelihood approaches revealed that both coding noncoding regions were more deleterious smaller indels or single nucleotide polymorphisms. reference-free facilitated identification > 10-My-old, 11-megabase-long pericentric inversion chromosome 1. found genotype frequencies inversion, from 135 birds widely sampled temporally geographically, increased steadily over 25 y since first exposed to bacterial pathogen Mycoplasma gallisepticum showed signatures balancing selection, capturing genes related immunity telomerase activity. also observed shorter telomeres populations greater number years exposure . Our study illustrates utility sequencing methods understanding populations, estimating SVs, advancing our evolution through variation.

Language: Английский

Citations

3
DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions DOI Creative Commons
Jie Wang, Guangpu Zhang, Cheng Sun

et al.

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: May 6, 2025

Language: Английский

Citations

0
Repetitive DNAs: The “invisible” regulators of insect adaptation and speciation DOI
Diogo Cavalcanti Cabral-de-Mello,

Octavio M. Palacios-Gimenez

Current Opinion in Insect Science, Journal Year: 2024, Volume and Issue: 67, P. 101295 - 101295

Published: Nov. 7, 2024

Language: Английский

Citations

1
From the genome's perspective: Bearing somatic retrotransposition to leverage the regulatory potential of L1 RNAs DOI Creative Commons
Damiano Mangoni,

Anna P. Mazzetti,

Federico Ansaloni

et al.

BioEssays, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 9, 2024

Transposable elements (TEs) are mobile genomic constituting a big fraction of eukaryotic genomes. They ignite an evolutionary arms race with host genomes, which in turn evolve strategies to restrict their activity. Despite being tightly repressed, TEs display precisely regulated expression patterns during specific stages mammalian development, suggesting potential benefits for the host. Among TEs, long interspersed nuclear element (LINE-1 or L1) has been found be active neurons. This activity prompted extensive research into its possible role cognition. So far, no cause-effect relationship between L1 retrotransposition and brain functions conclusively identified. Nevertheless, accumulating evidence suggests that interactions RNAs RNA/DNA binding proteins encode messages cells utilize activate repress entire transcriptional programs. We summarize recent findings highlighting at non-coding level early embryonic development. propose hypothesis mutualistic mRNAs cell. In this scenario, tolerate certain rate leverage regulatory effects L1s as on potentiating mitotic potential. turn, benefit from cell's proliferative state increase chance mobilize.

Language: Английский

Citations

1
Starships: a new frontier for fungal biology DOI
Andrew J. Urquhart, Aaron A. Vogan, Emile Gluck‐Thaler

et al.

Trends in Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

Citations

0
Size evolution of gigantic genomes suggests stochastic outcomes of transposable element/host silencing interactions DOI Creative Commons
Jie Wang, Guangpu Zhang, Cheng Sun

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 23, 2024

Abstract Size evolution among gigantic genomes involves gain and loss of many gigabases transposable elements (TEs), sequences that parasitize host genomes. Animals suppress TEs using piRNA KRAB-ZFP pathways. hosts coevolve in an arms race, where suppression strength reflects TE fitness costs. In enormous genomes, additional costs become miniscule. How, then, do invoke further addition massive DNA amounts? We analyzed proliferation histories, deletion rates, community diversities six salamander (21.3 - 49.9 Gb), alongside gonadal expression activity is higher testes than ovaries, attributable to lower suppression. Unexpectedly, genome size/expansion uncorrelated with rate, history, expression, Also, diversity increases size, contrasting theoretical predictions. TE/host antagonism likely produces stochastic accumulation, determined by noisy intermolecular interactions huge genomes/cells.

Language: Английский

Citations

0