Genome-Wide Identification and Quantification of cis- and trans-Regulated Genes Responding to Marek’s Disease Virus Infection via Analysis of Allele-Specific Expression

Speciation occurs when reproductive barriers prevent the exchange of genetic information between individuals. A common form of reproductive barrier between species capable of interbreeding is hybrid sterility. Genomic incompatibilities between the divergent genomes of different species contribute to a reduction in hybrid fitness. These incompatibilities continue to accumulate after speciation, therefore, young divergent taxa with incomplete reproductive isolation are important in understating the genetics leading to speciation. Here, I use two Drosophila subspecies pairs. The first is D. willistoni consisting of D. w. willistoni and D. w. winge. The second subspecies pair is D. pseudoobscura, which is composed of D. p. pseudoobscura and D. p. bogotana. Both subspecies pairs are at the early stages of speciation and show incomplete reproductive isolation through unidirectional hybrid male sterility. In this thesis, I performed an exploratory survey of genome-wide expression analysis using RNA-sequencing on D. willistoni and determined the extent of regulatory divergence between the subspecies using allele-specific expression analysis. I found that misexpressed genes showed a degree of tissue specificity and that the sterile male hybrids had a higher proportion of misexpressed genes in the testes relative to the fertile hybrids. The analysis of regulatory divergence between this subspecies pair found a large (66-70%) proportion of genes with conserved regulatory elements. Of the genes showing evidence or regulatory divergence between subspecies, cis-regulatory divergence was more common than other types. In the D. pseudoobscura subspecies pair, I compared sequence and expression divergence and found no support for directional selection driving gene misexpression in their hybrids. Allele-specific expression analysis revealed that compensatory cis-trans mutations partly explained gene misexpression in the hybrids. The remaining hybrid misexpression occurs due to interacting gene networks or possible co-option of cis-regulatory elements by divergent transacting factors. Overall, the results of this thesis highlight the role of regulatory interactions in a hybrid genome and how these interactions could lead to hybrid breakdown by disrupting gene interaction networks.

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Landscape and evolution of cis- and trans-regulatory divergence in chicken genome between two contrasted breeds analyzed in three tissues at one day age

10.21203/rs.2.10726/v2 ◽

2019 ◽

Author(s):

Qiong Wang ◽

Yaxiong Jia ◽

Yuan Wang ◽

Zhihua Jiang ◽

Xiang Zhou ◽

...

Keyword(s):

Chicken Genome ◽

Reproductive Traits ◽

Purifying Selection ◽

Population Divergence ◽

Specific Reference ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific ◽

Trans Regulation ◽

Cis And Trans

Abstract Background: Gene expression variation is an important mechanism underlying phenotypic variation, and can occur via cis- and trans-regulation. In order to understand the role of cis- and trans-regulatory variation on population divergence of chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, with major differences in body size and reproductive traits, and used them to identify the degree of cis versus trans variation in brain, liver and muscle of both male and female samples at 1 day age. Results: We provided a landscape about how the transcriptomes are regulated in the hybrid progenies of two contrasted breeds by allele specific expression analysis. Our results showed that compared with the cis-regulatory divergence, trans-acted genes existed more extensively in the chicken genome. Furthermore, a widespread tendency of compensatory regulation exists in chicken genome. Most importantly, we found the evidence of stronger purifying selection on genes regulated by trans variations than the cis elements. Conclusions: We demonstrated a pipeline to explore the allele-specific expression in the hybrid progenies of inbred lines without specific reference genome. Our research performed the first study to describe the regulatory divergence between two contrasted breeds. The results suggested that artificial selection associated with domestication in chicken may have more often acted on trans-regulatory divergence than cis.

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Expression profiles of genes within a subregion of chicken major histocompatibility complex B in spleen after Marek’s disease virus infection

Poultry Science ◽

10.3382/ps.2010-00919 ◽

2010 ◽

Vol 89 (10) ◽

pp. 2123-2129 ◽

Cited By ~ 19

Author(s):

L. Lian ◽

L.J. Qu ◽

J.X. Zheng ◽

C.J. Liu ◽

Y.P. Zhang ◽

...

Keyword(s):

Major Histocompatibility Complex ◽

Virus Infection ◽

Disease Virus ◽

Expression Profiles ◽

Marek's Disease Virus ◽

Marek's Disease ◽

Marek’S Disease Virus ◽

Major Histocompatibility ◽

Histocompatibility Complex ◽

Chicken Major Histocompatibility Complex

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Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1820513116 ◽

2019 ◽

Vol 116 (12) ◽

pp. 5653-5658 ◽

Cited By ~ 15

Author(s):

Lin Shao ◽

Feng Xing ◽

Conghao Xu ◽

Qinghua Zhang ◽

Jian Che ◽

...

Keyword(s):

Genetic Basis ◽

Molecular Mechanisms ◽

Sequencing Data ◽

Specific Expression ◽

Allele Specific Expression ◽

Parental Allele ◽

Genetic Components ◽

Genome Wide ◽

A Genome ◽

Allele Specific

Utilization of heterosis has greatly increased the productivity of many crops worldwide. Although tremendous progress has been made in characterizing the genetic basis of heterosis using genomic technologies, molecular mechanisms underlying the genetic components are much less understood. Allele-specific expression (ASE), or imbalance between the expression levels of two parental alleles in the hybrid, has been suggested as a mechanism of heterosis. Here, we performed a genome-wide analysis of ASE by comparing the read ratios of the parental alleles in RNA-sequencing data of an elite rice hybrid and its parents using three tissues from plants grown under four conditions. The analysis identified a total of 3,270 genes showing ASE (ASEGs) in various ways, which can be classified into two patterns: consistent ASEGs such that the ASE was biased toward one parental allele in all tissues/conditions, and inconsistent ASEGs such that ASE was found in some but not all tissues/conditions, including direction-shifting ASEGs in which the ASE was biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The results suggested that these patterns may have distinct implications in the genetic basis of heterosis: The consistent ASEGs may cause partial to full dominance effects on the traits that they regulate, and direction-shifting ASEGs may cause overdominance. We also showed that ASEGs were significantly enriched in genomic regions that were differentially selected during rice breeding. These ASEGs provide an index of the genes for future pursuit of the genetic and molecular mechanism of heterosis.

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