Genome-Wide Epigenetic Landscape of Pig lincRNAs and their Evolution During Porcine Domestication

C, Li; Zou, Cheng; Cui, Yifan; Fu, Yongshui; Cui, Fang; Y, Li; Li, Jian; Wang, W; Xiang, Haitao

doi:10.2217/epi-2017-0117

Cited by 3 publications

(2 citation statements)

References 75 publications

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“…The second hypothesis implies that the functional regions implicated in domestication would be out of coding regions (promotors, enhancers, and others. (e.g., Li et al 2018, Rubin et al 2012, Anderson 2012). However, although being a promising hypothesis, we did not analyze those regions because it requires a very accurate analysis of homology and their associated functionality, which is very complicated at the genome level, especially for non-model species with a high proportion of missing data.…”

Section: Discussionmentioning

confidence: 99%

Pervasive selection pressure in wild and domestic pigs

Leno-Colorado

Guirao-Rico

Pérez‐Enciso

et al. 2020

Preprint

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Animal domestication typically affected numerous polygenic quantitative traits, such as behavior, development and reproduction. However, uncovering the genetic basis of quantitative trait variation is challenging, since they are caused by small allele-frequency changes. To date, only a few causative mutations related to domestication processes have been reported, strengthening the hypothesis that small effect variants have a prominent role. So far, approaches on domestication have been limited to the detection of the global effect of domestication on deleterious mutations and on strong beneficial variants, ignoring the importance of variants with small selective effects. To overcome these difficulties, here we propose to estimate the proportion of beneficial variants based on the asymptotic MacDonald Kreitman (MK) method, according to estimates of variability based on frequency spectrum. We applied this approach to the pig species, analyzing 46 complete genome sequences from 20 European wild boars, 6 Iberian and 20 Large White pigs at different molecular scales: gene, metabolic pathway and whole-genome. Descriptive variability analyses on pig populations indicate that domestic and wild pig populations do not differ in nonsynonymous fixed mutations. Instead, most variants are shared among them, despite that the phenotypes of wild and domestic individuals are clearly divergent. Additionally, asymptotic MK plots based on summary statistics show that small effects variants may affect the final calculation of α, the proportion of beneficial mutations. The distribution of fitness effects inferred with Approximate Bayesian Computation analysis indicates that both wild and domestic pigs display an important quantity of deleterious mutations at low frequency (~83% of total mutations) and a high number of nearly-neutral mutations (~17%) that may have a significant effect on the evolution of domestic and wild populations. Exclusive mutations show that recent demographic changes have severely affected the fitness of populations, especially of the local Iberian breed. Finally, the median proportion of the strong favorable mutations are very scarce in all cases (≤ 0.2%). The median estimated alpha values (weak and strong favorable) are 0.9% for wild and domestic pigs.

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Section: Discussionmentioning

confidence: 99%

Pervasive selection pressure in wild and domestic pigs

Leno-Colorado

Guirao-Rico

Pérez‐Enciso

et al. 2020

Preprint

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“…A mammal, the domestic pig Sus scrofa domesticus, and an insect, the domesticated silkworm Bombyx mori, were used as subjects to initially explore the relationship between the (G/C) 3 L 1-7 motif and DNA methylation. Data on DNA methylation profiling of the pig were provided by Li et al 49 (raw data were downloaded from NCBI with the accession no. GSM2429533) and those of the silkworm were downloaded from ftp://ftp.genomics.org.cn/pub/silkworm_methylation.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution

Niu

Cui

et al. 2021

Commun Biol

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G-quadruplex (G4) structures have been predicted in the genomes of many organisms and proven to play regulatory roles in diverse cellular activities. However, there is little information on the evolutionary history and distribution characteristics of G4s. Here, whole-genome characteristics of potential G4s were studied in 37 evolutionarily representative species. During evolution, the number, length, and density of G4s generally increased. Immunofluorescence in seven species confirmed G4s’ presence and evolutionary pattern. G4s tended to cluster in chromosomes and were enriched in genetic regions. Short-loop G4s were conserved in most species, while loop-length diversity also existed, especially in mammals. The proportion of G4-bearing genes and orthologue genes, which appeared to be increasingly enriched in transcription factors, gradually increased. The antagonistic relationship between G4s and DNA methylation sites was detected. These findings imply that organisms may have evolutionarily developed G4 into a novel reversible and elaborate transcriptional regulatory mechanism benefiting multiple physiological activities of higher organisms.

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Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle

Ren

et al. 2021

Journal of Integrative Agriculture

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Genome-Wide Epigenetic Landscape of Pig lincRNAs and their Evolution During Porcine Domestication

Cited by 3 publications

References 75 publications

Pervasive selection pressure in wild and domestic pigs

Pervasive selection pressure in wild and domestic pigs

Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution

Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle

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