Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of <i>Brassica</i> genomes

Liu, Beibei; Iwata‐Otsubo, Aiko; Yang, Diya; Baker, Robert L.; Liang, Chun; Jackson, Scott A.; S, Liu; Ma, Jianxin; Zhao, Meixia

doi:10.1111/tpj.15037

Cited by 6 publications

(2 citation statements)

References 94 publications

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“…Additional packages including Bismark methylation extractor, bismark2bedGraph, and coverage2cytosine under Bismark were used to extract the methylated cytosines, and to count methylated and unmethylated reads. The proportion of each type of methylation (CG, CHG, and CHH) was determined as weighted methylation levels in 50 bp windows without shifts of the 2 kb upstream and downstream regions of the duplicated genes ( Krueger and Andrews 2011 ; Liu et al 2021 ). Gene body methylation was measured on 40 equally sized bins, with bin size differing from gene to gene because of the different lengths.…”

Section: Methodsmentioning

confidence: 99%

The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments

Yin

Yang

et al. 2022

Molecular Biology and Evolution

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Subgenome dominance after whole genome duplication (WGD) has been observed in many plant species. However, the degree to which the chromatin environment affects this bias has not been explored. Here, we compared the dominant subgenome (maize1) and the recessive subgenome (maize2) with respect to patterns of sequence substitutions, genes expression, transposable element accumulation, small interfering RNAs, DNA methylation, histone modifications, and accessible chromatin regions (ACRs). Our data show that the degree of bias between subgenomes for all the measured variables does not vary significantly when both of the WGD genes are located in pericentromeric regions. Our data further indicate that the location of maize1 genes in chromosomal arms is pivotal for maize1 to maintain its dominance, but location has a less effect on maize2 homoeologs. In addition to homoeologous genes, we compared ACRs, which often harbor cis-regulatory elements, between the two subgenomes and demonstrate that maize1 ACRs have a higher level of chromatin accessibility, a lower level of sequence substitution, and are enriched in chromosomal arms. Furthermore, we find that a loss of maize1 ACRs near their nearby genes is associated with a reduction in purifying selection and expression of maize1 genes relative to their maize2 homoeologs. Taken together, our data suggest that chromatin environment and cis-regulatory elements are important determinants shaping the divergence and evolution of duplicated genes.

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Section: Methodsmentioning

confidence: 99%

The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments

Yin

Yang

et al. 2022

Molecular Biology and Evolution

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“…PCR duplicates were removed using Picardtools. Additional packages including Bismark methylation extractor, bismark2bedGraph and coverage2cytosine under Bismark were used to extract the methylated cytosines, and to count methylated and unmethylated reads (Liu et al 2021;Yin et al 2022).…”

Section: Analysis Of Wgbs Datamentioning

confidence: 99%

Heritable changes of epialleles in maize can be triggered in the absence of DNA methylation

Liu

Liang

et al. 2023

Preprint

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Trans-chromosomal interactions resulting in changes in DNA methylation during hybridization have been observed in several plant species. However, very little is known about the causes or consequences of these interactions, many of which result in changes in methylation of transposable elements. Here, we compared DNA methylomes of F1 hybrids that are mutant for two small RNA biogenesis genes,Mop1(mediator of paramutation1) andLbl1(leafbladeless1) with that of their parents, wild type siblings, and backcrossed progeny in maize. Our data show that hybridization triggers global changes in bothtrans-chromosomal methylation (TCM) andtrans-chromosomal demethylation (TCdM). Despite changes in CHH methylation in F1 hybrids, no significant changes in the quantity or distribution of small RNAs were observed. The methylation at the CHH TCM differentially methylated regions (DMRs) was largely removed in themop1mutant, although the effects of this mutant vary depending on the location of the CHH sites. Interestingly, an increase in CHH at TCM DMRs was associated with enhanced expression of a subset of highly expressed genes and suppressed expression of a small number of lowly expressed genes. Examination of the methylation levels in backcrossed plants demonstrates that the newly triggered methylation can be maintained to the subsequent generation, but that TCdM is maintained more stable than is TCM. Surprisingly, although increase CHH methylation in F1 plants did requireMop1, heritability of TCM or TCdMs did not require a functional copy of this gene, suggesting that initiation of these heritable changes in epigenetic state are not dependent on RdDM.

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Polyploidy and the evolution of phenotypic integration: Network analysis reveals relationships among anatomy, morphology, and physiology

Baker,

Brock,

Newsome

et al. 2024

Appl Plant Sci

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PremiseMost traits are polygenic and most genes are pleiotropic, resulting in complex, integrated phenotypes. Polyploidy presents an excellent opportunity to explore the evolution of phenotypic integration as entire genomes are duplicated, allowing for new associations among traits and potentially leading to enhanced or reduced phenotypic integration. Despite the multivariate nature of phenotypic evolution, studies often rely on simplistic bivariate correlations that cannot accurately represent complex phenotypes or data reduction techniques that can obscure specific trait relationships.MethodsWe apply network modeling, a common gene co‐expression analysis, to the study of phenotypic integration to identify multivariate patterns of phenotypic evolution, including anatomy and morphology (structural) and physiology (functional) traits in response to whole genome duplication in the genus Brassica.ResultsWe identify four key structural traits that are overrepresented in the evolution of phenotypic integration. Seeding networks with key traits allowed us to identify structure–function relationships not apparent from bivariate analyses. In general, allopolyploids exhibited larger, more robust networks indicative of increased phenotypic integration compared to diploids.DiscussionPhenotypic network analysis may provide important insights into the effects of selection on non‐target traits, even when they lack direct correlations with the target traits. Network analysis may allow for more nuanced predictions of both natural and artificial selection.

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Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes

Cited by 6 publications

References 94 publications

The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments

The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments

Heritable changes of epialleles in maize can be triggered in the absence of DNA methylation

Polyploidy and the evolution of phenotypic integration: Network analysis reveals relationships among anatomy, morphology, and physiology

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