Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa

Polyploidization, both ancient and recent, is frequent among plants. A “two-step theory" was proposed to explain the meso-triplication of the Brassica “A" genome: Brassica rapa. By accurately partitioning of this genome, we observed that genes in the less fractioned subgenome (LF) were dominantly expressed over the genes in more fractioned subgenomes (MFs: MF1 and MF2), while the genes in MF1 were slightly dominantly expressed over the genes in MF2. The results indicated that the dominantly expressed genes tended to be resistant against gene fractionation. By re-sequencing two B. rapa accessions: a vegetable turnip (VT117) and a Rapid Cycling line (L144), we found that genes in LF had less non-synonymous or frameshift mutations than genes in MFs; however mutation rates were not significantly different between MF1 and MF2. The differences in gene expression patterns and on-going gene death among the three subgenomes suggest that “two-step" genome triplication and differential subgenome methylation played important roles in the genome evolution of B. rapa

Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants

For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K–pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein–protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein–protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant

Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid "Brachypodium"

The “genomic shock” hypothesis posits that unusual challenges to genome integrity such as whole genome duplication may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and derepression of transposable elements in the immediate aftermath of whole genome duplication, others do not. Nonetheless, all polyploids show gradual diploidization over evolutionary time. To evaluate these hypotheses, we produced a chromosome-scale reference genome for the natural allotetraploid grass Brachypodium hybridum, accession “Bhyb26.” We compared 2 independently derived accessions of B. hybridum and their deeply diverged diploid progenitor species Brachypodium stacei and Brachypodium distachyon. The 2 B. hybridum lineages provide a natural timecourse in genome evolution because one formed 1.4 million years ago, and the other formed 140 thousand years ago. The genome of the older lineage reveals signs of gradual post-whole genome duplication genome evolution including minor gene loss and genome rearrangement that are missing from the younger lineage. In neither B. hybridum lineage do we find signs of homeologous recombination or pronounced transposable element activation, though we find evidence supporting steady post-whole genome duplication transposable element activity in the older lineage. Gene loss in the older lineage was slightly biased toward 1 subgenome, but genome dominance was not observed at the transcriptomic level. We propose that relaxed selection, rather than an abrupt genomic shock, drives evolutionary novelty in B. hybridum, and that the progenitor species’ similarity in transposable element load may account for the subtlety of the observed genome dominance

Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses

The grasses, Poaceae, are one of the largest and most successful angiosperm families. Like many radiations of flowering plants, the divergence of the major grass lineages was preceded by a whole-genome duplication (WGD), although these events are not rare for flowering plants. By combining identification of syntenic gene blocks with measures of gene pair divergence and different frequencies of ancient gene loss, we have separated the two subgenomes present in modern grasses. Reciprocal loss of duplicated genes or genomic regions has been hypothesized to reproductively isolate populations and, thus, speciation. However, in contrast to previous studies in yeast and teleost fishes, we found very little evidence of reciprocal loss of homeologous genes between the grasses, suggesting that post-WGD gene loss may not be the cause of the grass radiation. The sets of homeologous and orthologous genes and predicted locations of deleted genes identified in this study, as well as links to the CoGe comparative genomics web platform for analyzing pan-grass syntenic regions, are provided along with this paper as a resource for the grass genetics community

속간 잡종 배무채의 유전체 안정화 및 전사체 조절 네트워크 재정립

학위논문(박사)--서울대학교 대학원 :농업생명과학대학 식물생산과학부(원예과학전공),2020. 2. 허진회.Hybridization and polyploidization have facilitated the evolution of many plant species while resulting in speciation and production of novel characteristics to increase fitness in new environments. These phenomena have occurred in various organisms, especially in plants, and the evolution of complex and various sizes of plant genomes has been attributed to polyploidization events. Although increased genomic content and large changes of gene expression levels in polyploid genome provide various advantages for environmental adaptation, most early generated polyploid plants suffer from genomic instability that results in sterility and inviability. xBrassicoraphanus is an intergeneric allopolyploid between Chinese cabbage and radish, which is a rare case of genetic merging two different genus species. Unlike most neoallopolyploid plants, xBrassicoraphanus is fertile and genetically stable, but little is known about the stabilization of hybrid genome between extremely divergent species and the molecular mechanism of transcriptional and epigenetic changes. In this study, I investigated the genomic, transcriptomic and epigenomic changes in a new intergeneric allotetraploid species xBrassicoraphanus. For the genomic analysis, de novo assembly of xBrassicoraphanus genome was performed. Complete set of both parental chromosomes without apparent genome structure changes was observed and hypermethylation of transposable elements by small RNA in trans were proposed. In addition, genome-wide transcriptional changes relative to parental expression are dramatically observed, and the majority of the duplicated genes are adjusted to similar levels due to the high similarity of cis-elements and sharing common transcription factors. This study demonstrates that a certain level of parental genome divergence is helpful to suppress genomic shocks in the early generation of polyploidy and compatibility of regulatory elements would contribute to the massive reconstruction of transcription control network following after transcriptome shock.GENERAL INTRODUCTION 1 CHAPTER 1. Parental divergence allows hybrid genome stabilization in xBrassicoraphanus 28 ABSTRACT 29 INTRODUCTION 30 MATERIALS AND METHODS 34 Plant materials 34 Genome sequencing, assembly and genome size estimation 34 Chloroplast genome assembly 35 Assignment of scaffolds to A and R subgenomes 35 Gene and TE annotations and repeat analysis 36 Fluorescence in situ hybridization (FISH) analysis 37 Identification of orthologous and homoeologous gene pairs 38 RNA-seq analysis 38 BS-seq analysis 39 ChIP-seq analysis 40 Samll RNA-seq analysis 41 Northern blot analysis 42 Quantitative real-time polymerase chain reaction (qRT-PCR) analysis 42 RESULTS 49 Phenotypes of xBrassicoraphanus intermediate between B. rapa and R. sativus 49 Genomic feature of xBrassicoraphanus 51 Maintenance of TE compositions in xBrassicoraphanus 66 Epigenetic changes in xBrassicorpahanus 68 Correlation between epigenetic factors in xBrassicoraphanus 77 TE-specific hypermethylation in xBrassicoraphanus 80 DISCUSSION 89 Maintenance of chromosome stability in intergeneric allotetraploid 89 Hypermethylation and silencing of TEs in xBrassicoraphanus 93 Model of triangle of U expanded to the intergeneric level 97 REFERENCES 98 CHAPTER 2. Divergence of cis- and trans-regulatory elements drives reconstruction of transcriptome network in xBrassicoraphanus 109 ABSTRACT 110 INTRODUCTION 111 MATERIALS AND METHODS 114 Plant materials 114 Orthologous and homoeologous gene pairs 114 Transcription size estimation 115 RNA-seq analysis 115 Categorization of additive and non-additive expression patterns 116 Assignment of cis- and trans-regulatory divergence 117 Gene ontology analysis 118 RESULTS 119 Divergence of B. rapa and R. sativus genome 119 Maintenance of parental transcriptome size in xBrassicoraphanus 124 Expression similarity of homoeologous gene pairs in xBrassicoraphanus 128 Orthologous gene expression difference by divergence of trans-elements of parental species provokes transcriptional changes in xBrassicoraphanus 138 Simultaneous regulation of cellular response in xBrassicoraphanus subgenomes 143 DISCUSSION 148 Expression level dominance between species of Us triangle including R. sativus 148 Divergence of cis- and trans-elements between parental species determined the appearance of transcriptome shock in allopolyploids 151 REFERENCES 154 ABSTRACT IN KOREAN 161Docto

Gradual evolution of allopolyploidy in Arabidopsis suecica.

Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of 'genome shock', such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution

Transposable elements and polyploid evolution in animals

© The Author(s), 2018. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Current Opinion in Genetics & Development 49 (2018): 115-123, doi:10.1016/j.gde.2018.04.003.Polyploidy in animals is much less common than in plants, where it is thought to be pervasive in all higher plant lineages. Recent studies have highlighted the impact of polyploidization and the associated process of diploidy restoration on the evolution and speciation of selected taxonomic groups in the animal kingdom: from vertebrates represented by salmonid fishes and African clawed frogs to invertebrates represented by parasitic root-knot nematodes and bdelloid rotifers. In this review, we focus on the unique and diverse roles that transposable elements may play in these processes, from marking and diversifying subgenome-specific chromosome sets prior to hybridization, to influencing genome restructuring during rediploidization, to affecting subgenome-specific regulatory evolution, and occasionally providing opportunities for domestication and gene amplification to restore and improve functionality. There is still much to be learned from the future comparative genomic studies of chromosome-sized and haplotype-aware assemblies, and from post-genomic studies elucidating genetic and epigenetic regulatory phenomena across short and long evolutionary distances in the metazoan tree of life.Work in the laboratory is supported by R01GM111917 from the U.S. National Institutes of Health to I.A.2019-04-3

The genome of\u3ci\u3e Orychophragmus\u3c/i\u3e violaceus provides genomic insights into the evolution of Brassicaceaepolyploidizationandits distinct traits

Orychophragmus violaceus, referred to as ‘‘eryuelan’’ (February orchid) in China, is an early-flowering ornamental plant. The high oil content and abundance of unsaturated fatty acids in O. violaceus seeds make it a potential high-quality oilseed crop. Here, we generated a whole-genome assembly for O. violaceus using Nanopore and Hi-C sequencing technologies. The assembled genome of O. violaceus was ~1.3 Gb in size, with 12 pairs of chromosomes. Through investigation of ancestral genome evolution, we determined that the genome of O. violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype. Comparisons between the reconstructed subgenomes of O. violaceus identified indicators of subgenome dominance, indicating that subgenomes likely originated via allotetraploidy. O. violaceus was phylogenetically close to the Brassica genus, and tetraploidy in O. violaceus occurred approximately 8.57 million years ago, close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage. However, the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica, as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks. Moreover, identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O. violaceus. These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O. violaceus

Utilization of variation to understand Camelina sativa genome evolution

Camelina sativa is an oilseed crop gaining interest for its oil content, protein content, and potential as a new oilseed for human consumption. The main disadvantages of this crop are its smaller seed size and lower total yield compared to other commercial oilseed crops; however, breeding efforts has been progressing to improve yield traits. A low level of genetic diversity and limited breeding efforts have been identified as impediments in C. sativa crop improvement. This study was designed to improve access to genetic diversity in C. sativa by developing genetic tools and identifying genetic mechanisms to accelerate C. sativa breeding. The objectives of this study were: to explore the genetic diversity in available Camelina germplasm using Genotyping-by-Sequencing (GBS), with a focus on close relatives of C. sativa and a collection from Ukraine and Russia; to develop segregating generations through intra- and interspecific hybridization; and to complete whole genome transcriptome analysis to observe gene expression patterns across subgenomes in hexaploid species of Camelina. Genetic markers in this study were developed using GBS, whereas whole transcriptome analysis was performed for subgenome dominance analysis. The genetic diversity study with 193 genotypes identified two subpopulations in C. sativa, where C. microcarpa was found to be a close relative of this species. Winter C. sativa species, such as C. sativa ssp. pilosa and C. alyssum, formed a separate clade and were closely-associated with C. microcarpa. Principal coordinate and phylogenetic analysis differentiated the genotypes based on species and subpopulations. Mapping of reads to the reference genome identified C. neglecta as a progenitor species for the first subgenome of C. sativa. Likewise, a tetraploid was identified that encompassed the first and second subgenomes, and a novel C. microcarpa species differing from C. sativa in terms of genome structure was also identified. Flow cytometry analysis and chromosome count validated the read mapping and confirmed that the novel C. microcarpa possessed 19 chromosomes (n, haploid number) with a different third subgenome not present in C. sativa. The inter- and intraspecific hybridizations enabled genetic linkage maps to be developed, where a common C. sativa genotype was hybridized with other related species. A mapping study identified four quantitative trait loci (QTL) associated with winter behaviour in C. sativa. The winter trait mapped to one locus on chromosome 8 (subgenome 1) in C. sativa ssp. pilosa, to two loci in C. alyssum on chromosomes 13 (subgenome 2) and 20 (subgenome 3), and to one locus on chromosome 13 (subgenome 2) in C. microcarpa. All of the QTL represented homologous segments in the C. sativa reference genome and were proximate to a major flowering gene, Flowering Locus C (FLC). Differential gene expression analysis between the parents at the early seedling stage suggested FLC could be a candidate gene responsible for vernalization responses in winter C. sativa populations. In addition, interspecific hybridization identified a homoeologous recombination (HeR) event between subgenome 1 of C. sativa with subgenome 3 of C. microcarpa (n = 19), and a number of anueploids were identified, as expected. The nature of HeR could create challenges for the success of conventional breeding activities in Camelina species, as recombination could occur between any subgenomes due to the undifferentiated nature of the subgenomes. However, variation in morphology, such as leaf characteristics, days to flowering and fertility suggested a huge potential for increasing genetic variability in C. sativa by use of distantly-related Camelina species. Subgenome dominance has evolutionary significance and can play an important role in improving phenotypic diversity. Subgenome dominance analysis suggested the third subgenome was dominant in the case of Camelina species with n = 20, whereas the second subgenome was dominant for Camelina species with n = 19 and was correlated with the age of divergence of the subgenomes from C. neglecta. Overall, the results provided insight into the subgenome structure and a first step towards identifying the mechanism of a stepwise whole genome duplication process in polyploid C. sativa, which would be instrumental in developing genetic tools for Camelina breeding activities

Genome evolution in the allotetraploid frog Xenopus laevis

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of ???fossil??? transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.ope