Biology subjects
Publications and source records attributed to Civan, P..
AGR, for Ancestral Genome Reconstruction, is an automatic publicly available and open-source pipeline to infer paleogenomes from modern species genome comparisons exploiting the concept of inter-species chromosomal synteny relationships hierarchical clustering that can be used to unveil how ancestral genomes, genes, sequences and functions have been shaped during million years of present-day plant evolution.
Epigenetic mechanisms including DNA methylation are assumed to play crucial roles in the maintenance of genome integrity, regulation of gene expression and development, and their increasing exploitation in breeding applications is anticipated. However, the relationship between DNA methylation and gene expression remains ambiguous and difficult to generalize. Here we explored the hypothesized causality between the level of transcription and cytosine methylation at the 5 end of genes (around transcription start sites and start codons) in relation to whole-genome duplication in natural and synthetic allohexaploid wheat (Triticum/Aegilops complex). Using transcriptomes and a sequence capture protocol coupled with bisulfite sequencing, we observed sometimes significant, but overall very weak associations between gene expression and 5 end methylation on a genome-wide scale. In synthetic wheat allohexaploids, global methylation differences between subgenomes are not triggered by the polyploidization, as the subgenome patterns are rather faithfully inherited from parents. A small number of genes differentially methylated between the parents and synthetics was consistently recovered in reciprocal synthetics and subsequent generations. Differences in transcription between homeologs are not clearly associated with 5 end methylation in either natural or synthetic wheat. Overall, allopolyploidization triggers only minor methylation changes around transcription start sites and start codons of nascent wheat allopolyploids, and these are not statistically associated with differential expression. Although there is a measurable methylation difference between expressed and non-expressed genes, our results do not support the hypothesis that 5 end DNA methylation is engaged in the regulation of gene expression in natural and synthetic wheat. SIGNIFICANCE STATEMENTWhile agenome shock hypothesis predicts extensive transcriptomic and epigenetic reorganization after polyploidization, DNA methylation patterns around transcription start sites are generally undisturbed in nascent wheat allohexaploids. Although this stability might indicate importance for gene regulation, a clear relationship between DNA methylation and transcription was not observed either on a genome-wide scale, or among triads of homeologous genes.
Bread wheat is a recent allohexaploid (genomic constitution AABBDD) that emerged through a hybridization between tetraploid Triticum turgidum (AABB) and diploid Aegilops tauschii (DD) <10,000 years ago. The hexaploidization can be re-created artificially, producing synthetic wheat that has been used to study immediate genomic responses to polyploidization. Here we produced several synthetic wheats from alternative parental genotypes and reciprocal crosses, and examined transcriptomes from two different tissues and successive generations. We did not detect a massive reprogramming in gene expression, with only [~]1% of expressed genes showing significant differences compared to their lower-ploidy parents. Most of the differential expression is located on the D subgenome, without consistency in the direction of the expression change. Leaves and developing endosperm show distinct patterns of homoeologous expression bias, and almost non-overlapping sets of differentially expressed genes, implying that the polyploidization-triggered reprogramming is not effectuated through permanent (epi)genetic changes. While 0-3 families of transposable elements (TEs) became upregulated in wheat synthetics, we did not detect any significant association between TEs and the expression of nearby genes. We conclude that the modest tissue-specific and partially genotype-specific transcriptomic response to polyploidization is likely caused by rare incompatibilities of parental regulomes, and we discuss the pitfalls of transcriptomic comparisons across ploidy levels that can inflate the de-regulation signal.
In 2015, we published an analysis of rice genomic data and showed that the japonica, indica and aus groups of cultivated rice were independently domesticated. Our conclusions were controversial as they contradicted a previous, high-profile analysis of the same dataset, which had suggested that all of cultivated rice derives from a single origin. Although there have been attempts since 2015 to bolster the single-origin hypothesis, until recently there has been no direct rebuttal of the methodology that we used to infer multiple origins. Such a rebuttal has now been published (Choi J.Y., Purugganan M.D., 2018 Multiple origin but single domestication led to Oryza sativa. G3 8:797-803), but the reanalysis that is presented only supports the single origin hypothesis if phylogenetic trees that are clearly paraphyletic are interpreted as monophyletic, and furthermore addresses only one component of the evidence that we presented for multiple domestications. We caution against accepting these analyses uncritically.
Cultivated Asian rice (O. sativa L.) comprises several groups with distinct ecological requirements and culinary uses. While the two subspecies of O. sativa - indica and japonica - have been subjected to a multitude of genetic and genomic analyses, less is known about the origins and diversity of the agronomically marginal groups - aus and aromatic rice. Here we reconstructed complete chloroplast genomes of over 1,800 accessions of wild and cultivated rice, including 240 aus and 73 aromatic varieties, and analysed the haplotype diversity of the taxonomic groups. We confirm the deep phylogenetic divergence between the main chloroplast haplotypes of japonica and indica, and reveal unique profiles of chloroplast diversity in aus and aromatic rice. Our results indicate that the latter two groups are not simple derivatives of indica and japonica, respectively, but originated from independent and/or reticulate domestication processes. Absence of phylogeographic patterns in the wild distribution of chloroplast haplogroups did not allow firm conclusions about geographic origins and the role of inter-group gene flow. Nonetheless, our results suggest that the domestication of indica, japonica, aus and aromatic rice operated on genetically different gene pools and followed different dynamics.