Prevalent fast evolution of genes involved in heterochromatin functions DOI Creative Commons

Leila Lin,

Yuheng Huang, Jennifer McIntyre

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(9)

Published: Aug. 24, 2024

Heterochromatin is a gene-poor and repeat-rich genomic compartment universally found in eukaryotes. Despite its low transcriptional activity, heterochromatin plays important roles maintaining genome stability, organizing chromosomes, suppressing transposable elements. Given the importance of these functions, it expected that genes involved regulation would be highly conserved. Yet, handful were to evolve rapidly. To investigate whether previous findings are anecdotal or general modulating heterochromatin, we compile an exhaustive list 106 candidate functions their evolution over short long evolutionary time scales Drosophila. Our analyses find exhibit significantly more frequent changes, both forms amino acid substitutions gene copy number change, when compared Polycomb-based repressive chromatin. While positive selection drives changes within structured domains with diverse intrinsically disordered regions, purifying may have maintained proportions regions proteins. Together observed negative associations between rate abundance elements, propose model where fast inevitable outcome unique functional while rapid elements effect rather than cause. study provides global view this critical cellular domain insights into factors driving distinctive heterochromatin.

Language: Английский

Blessing or curse: how the epigenetic resolution of host-transposable element conflicts shapes their evolutionary dynamics DOI Creative Commons
Yuheng Huang, Yuh Chwen G. Lee

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 291(2020)

Published: April 9, 2024

Transposable elements (TEs) are selfish genetic whose antagonistic interactions with hosts represent a common conflict in eukaryotes. To resolve this conflict, have widely adopted epigenetic silencing that deposits repressive marks at TEs. However, mechanism is imperfect and fails to fully halt TE replication. Furthermore, can inadvertently spread adjacent functional sequences, phenomenon considered 'curse' of resolution. Here, we used forward simulations explore how its harmful side effects shape the evolutionary dynamics TEs their hosts. Our findings reveal allows stably coexist under wide range conditions, because underlying molecular mechanisms give rise copy-number dependency strength silencing. Interestingly, contrary intuitive expectations should evolve be as strong possible, found selective benefit for modifier alleles weaken biologically feasible conditions. These results dual nature silencing, both positive negative effects, complicates trajectory makes it challenging determine whether 'blessing' or 'curse'.

Language: Английский

Citations

7
Polymorphic transposable elements contribute to variation in recombination landscapes DOI Creative Commons
Yuheng Huang, Zita Y. Gao,

Kayla Ly

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(12)

Published: March 18, 2025

Meiotic recombination is a prominent force shaping genome evolution, and understanding why rates vary within between species has remained central, though challenging, question. Variation in widely thought to influence the efficacy of selection purging transposable elements (TEs), prevalent selfish genetic elements, leading observed negative correlations TE abundance across taxa. However, accumulating evidence suggests that TEs could instead be cause rather than consequence this relationship. To test prediction, we formally investigated polymorphic, putatively active on rates. We developed benchmarked an approach uses PacBio long-read sequencing efficiently, accurately, cost-effectively identify crossovers (COs), key product, among large numbers pooled recombinant individuals. By applying Drosophila strains with distinct insertion profiles, found polymorphic TEs, especially RNA-based local enrichment repressive marks, reduce occurrence COs. Such effect leads different CO frequencies homologous sequences without contributing varying maps The suppressive further supported by two orthogonal approaches–analyzing distributions COs panels inbred lines relation polymorphism marker-assisted estimations isogenic transgenically inserted TEs. Our investigations reveal how constantly changing landscape can actively modify recombination, evolution species.

Language: Английский

Citations

0
Sex chromosome evolution in haploid plants: Microchromosomes, disappearing chromosomes, and giant chromosomes DOI Creative Commons
Deborah Charlesworth

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(16)

Published: April 15, 2025

As in many diploid organisms with genetic sex determination, haploid-dominant have also evolved chromosomes or extensive genomic regions that lack recombination. An understanding of chromosome evolution should explain the causes and consequences such both diploids haploids. However, haploids been little studied, even though differences from carry implications concerning suppressed recombination organisms, make predictions about genome sex-linked can now be tested by approaches using sequences. I review these ideas, current empirical evidence them, more detail than recent reviews focusing on progress mechanisms involved determination. discuss one specific prediction, degeneration minor haploids, is not upheld. suggest this prediction does take account all processes leading to gene loss profound may evolve if genes become duplicated autosomes, a process appears occur diploids. emphasize types data are needed testing several ideas described.

Language: Английский

Citations

0
Construction of a comprehensive library of repeated sequences for the annotation of Citrus genomes DOI Creative Commons
Delphine Giraud, Nathalie Choisne, Marilyne Summo

et al.

BMC Genomic Data, Journal Year: 2025, Volume and Issue: 26(1)

Published: April 18, 2025

Language: Английский

Citations

0
The resolution of evolutionary conflicts within species DOI Creative Commons
J. Arvid Ågren, Göran Arnqvist,

Locke Rowe

et al.

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 291(2031)

Published: Sept. 1, 2024

Evolutionary conflicts of interest occur at all levels, scales and forms biological organization. They are a fundamental component the living world range from between genetic elements cells, to sexes competing individuals. Yet, existence admirably well functioning genomes, bodies, mating pairs societies suggests that processes must exist resolve or mitigate such conflicts. We organized this special feature ‘The resolution evolutionary within species’ encourage flow knowledge fields traditionally have often taken different approaches study Contributed papers discuss data bacteria, plants animals (including humans) present theory, molecular mechanisms population dynamics how resolved in nature. Together, they contribute synthetic theory conflict resolution.

Language: Английский

Citations

1
Prevalent fast evolution of genes involved in heterochromatin functions DOI Creative Commons

Leila Lin,

Yuheng Huang, Jennifer McIntyre

et al.

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

Published: March 6, 2024

Heterochromatin is a gene-poor and repeat-rich genomic compartment universally found in eukaryotes. Despite its low transcriptional activity, heterochromatin plays important roles maintaining genome stability, organizing chromosomes, suppressing transposable elements (TEs). Given the importance of these functions, it expected that genes involved regulation would be highly conserved. Yet, handful were to evolve rapidly. To investigate whether previous findings are anecdotal or general modulating heterochromatin, we compile an exhaustive list 106 candidate functions their evolution over short long evolutionary time scales

Language: Английский

Citations

0
Prevalent fast evolution of genes involved in heterochromatin functions DOI Creative Commons

Leila Lin,

Yuheng Huang, Jennifer McIntyre

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(9)

Published: Aug. 24, 2024

Heterochromatin is a gene-poor and repeat-rich genomic compartment universally found in eukaryotes. Despite its low transcriptional activity, heterochromatin plays important roles maintaining genome stability, organizing chromosomes, suppressing transposable elements. Given the importance of these functions, it expected that genes involved regulation would be highly conserved. Yet, handful were to evolve rapidly. To investigate whether previous findings are anecdotal or general modulating heterochromatin, we compile an exhaustive list 106 candidate functions their evolution over short long evolutionary time scales Drosophila. Our analyses find exhibit significantly more frequent changes, both forms amino acid substitutions gene copy number change, when compared Polycomb-based repressive chromatin. While positive selection drives changes within structured domains with diverse intrinsically disordered regions, purifying may have maintained proportions regions proteins. Together observed negative associations between rate abundance elements, propose model where fast inevitable outcome unique functional while rapid elements effect rather than cause. study provides global view this critical cellular domain insights into factors driving distinctive heterochromatin.

Language: Английский

Citations

0