Genome Fusion Research Articles

Why do hybrids turn down sex?

Asexual reproduction is ancestral in prokaryotes; the switch to sexuality in eukaryotes is one of the major transitions in the history of life. The study of the maintenance of sex in eukaryotes has raised considerable interest for decades and is still one of evolutionary biology's most prominent question. The observation that many asexual species are of hybrid origin has led some to propose that asexuality in hybrids results from sexual processes being disturbed because of incompatibilities between the two parental species' genomes. However, in some cases, failure to produce asexual F1s in the lab may indicate that this mechanism is not the only road to asexuality in hybrid species. Here, we present a mathematical model and propose an alternative, adaptive route for the evolution of asexuality from previously sexual hybrids. Under some reproductive alterations, we show that asexuality can evolve to rescue hybrids' reproduction. Importantly, we highlight that when incompatibilities only affect the fusion of sperm and egg's genomes, the two traits that characterize asexuality, namely unreduced meiosis and the initiation of embryogenesis without the incorporation of the sperm's pronucleus, can evolve separately, greatly facilitating the overall evolutionary route. Taken together, our results provide an alternative, potentially complementary explanation for the link between asexuality and hybridization.

The greening ashore.

More than half a billion years ago a streptophyte algal lineage began terraforming the terrestrial habitat and the Earth's atmosphere. This pioneering step enabled the subsequent evolution of all complex life on land, and the past decade has uncovered that many traits, both morphological and genetic, once thought to be unique to land plants, are conserved across some streptophyte algae. They provided the common ancestor of land plants with a repertoire of genes, of which many were adapted to overcome the new biotic and abiotic challenges. Exploring these molecular adaptations in non-tracheophyte species may help us to better prepare all green life, including our crops, for the challenges precipitated by the climate change of the Anthropocene because the challenges mostly differ by the speed with which they are now being met.

Optimization of Protoplast Formation, Regeneration, and Viability in <i>Sorangium cellulosum</i>

Sorangium cellulosum can product many secondary metabolites that is unique structural and makes these microorganisms highly attractive for drug development, especially epothilone, on cancer cells a cytotoxic macrolide which is naturally produced by Soxhlet cellulose that have the action of microtubule stabilization, is a promising anticancer drug. In this research, the factors affecting the regeneration and preparation of the protoplast of Sorangium cellulosum were discussed, those were regeneration media, enzymes and osmotic stabilizers. This study provide the distruction for improving the production of epothilone through genome shuffling, mutation, fusion and transformation.

Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple.

This study identified 57 basic leucine zipper (bZIP) genes from the pineapple genome, and the analysis of these bZIP genes was focused on the evolution and divergence after multiple duplication events in relation to the pineapple genome fusion. According to bioinformatics analysis of a phylogenetic tree, the bZIP gene family was divided into 11 subgroups in pineapple, Arabidopsis, and rice; gene structure and conserved motif analyses showed that bZIP genes within the same subgroup shared similar intron-exon organizations and motif composition. Further synteny analysis showed 17 segmental duplication events with 27 bZIP genes. The study also analyzed the pineapple gene expression of bZIP genes in different tissues, organs, and developmental stages, as well as in abiotic stress responses. The RNA-sequencing data showed that AcobZIP57 was upregulated in all tissues, including vegetative and reproductive tissues. AcobZIP28 and AcobZIP43 together with the other 25 bZIP genes did not show high expression levels in any tissue. Six bZIP genes were exposed to abiotic stress, and the relative expression levels were detected by quantitative real-time PCR. A significant response was observed for AcobZIP24 against all kinds of abiotic stresses at 24 and 48 h in pineapple root tissues. Our study provides a perspective for the evolutionary history and general biological involvement of the bZIP gene family of pineapple, which laid the foundation for future functional characterization of the bZIP genes in pineapple.

The Hybrid Genome of a New Goldfish-Like Fish Lineage Provides Insights Into the Origin of the Goldfish.

Distant hybridization leads to obvious changes in genotypes and phenotypes, giving rise to species with novel capabilities. However, the fusion of distinct genomes also polymerizes the DNA or gene variations that occur during the course of evolution. Knowledge of the early stages of post-hybridization evolution is particularly important. Here, we investigated the full-length (FL) transcriptomes and the sequences resulting from the genome resequencing of the red crucian carp-like homodiploid fish (RCC-L) and goldfish-like homodiploid fish (GF-L) derived from the interspecific hybridization of koi carp (KOC) and blunt snout bream (BSB) to provide molecular evidence for the hybrid origin of the goldfish (GF). We compared the orthologous genes in the transcriptomes of RCC-L and GF-L with those of KOC and BSB. We also mapped the orthologous genes to the common carp (CC) and BSB genomes and classified them into eight gene patterns in three categories (chimaera, mutant, and biparental origin genes). The results showed that 48.20% and 46.50% of the genes were chimaera and that 3.70% and 8.30% of the genes were mutations of orthologous genes in RCC-L and GF-L, respectively. In RCC-L and GF-L, 63.70% and 68.20% of the genetic materials were from KOC, and 12.30% and 11.90% of the genetic materials were from BSB. The sequences from the genome resequencing of RCC-L and GF-L were mapped to the genome sequences of CC and BSB, revealing that the similarities of both RCC-L and GF-L to the CC genome (92.52%, 90.18%) were obviously higher than to the BSB genome (50.33%, 49.18%), supporting the suggestion that the genomes of both RCC-L and GF-L were mainly inherited from KOC but had some DNA fragments from BSB. Overall, our results provide molecular biological evidence for the hybrid origin of red crucian carp (RCC) and GF.

Genome-wide identification and abiotic stress-responsive pattern of heat shock transcription factor family in Triticum aestivum L.

BackgroundEnhancement of crop productivity under various abiotic stresses is a major objective of agronomic research. Wheat (Triticum aestivum L.) as one of the world’s staple crops is highly sensitive to heat stress, which can adversely affect both yield and quality. Plant heat shock factors (Hsfs) play a crucial role in abiotic and biotic stress response and conferring stress tolerance. Thus, multifunctional Hsfs may be potentially targets in generating novel strains that have the ability to survive environments that feature a combination of stresses.ResultIn this study, using the released genome sequence of wheat and the novel Hsf protein HMM (Hidden Markov Model) model constructed with the Hsf protein sequence of model monocot (Oryza sativa) and dicot (Arabidopsis thaliana) plants, genome-wide TaHsfs identification was performed. Eighty-two non-redundant and full-length TaHsfs were randomly located on 21 chromosomes. The structural characteristics and phylogenetic analysis with Arabidopsis thaliana, Oryza sativa and Zea mays were used to classify these genes into three major classes and further into 13 subclasses. A novel subclass, TaHsfC3 was found which had not been documented in wheat or other plants, and did not show any orthologous genes in A. thaliana, O. sativa, or Z. mays Hsf families. The observation of a high proportion of homeologous TaHsf gene groups suggests that the allopolyploid process, which occurred after the fusion of genomes, contributed to the expansion of the TaHsf family. Furthermore, TaHsfs expression profiling by RNA-seq revealed that the TaHsfs could be responsive not only to abiotic stresses but also to phytohormones. Additionally, the TaHsf family genes exhibited class-, subclass- and organ-specific expression patterns in response to various treatments.ConclusionsA comprehensive analysis of Hsf genes was performed in wheat, which is useful for better understanding one of the most complex Hsf gene families. Variations in the expression patterns under different abiotic stress and phytohormone treatments provide clues for further analysis of the TaHsfs functions and corresponding signal transduction pathways in wheat.

High-Throughput Sequencing to Investigate Phytopathogenic Fungal Propagules Caught in Baited Insect Traps.

Studying the means of dispersal of plant pathogens is crucial to better understand the dynamic interactions involved in plant infections. On one hand, entomologists rely mostly on both traditional molecular methods and morphological characteristics, to identify pests. On the other hand, high-throughput sequencing (HTS) is becoming the go-to avenue for scientists studying phytopathogens. These organisms sometimes infect plants, together with insects. Considering the growing number of exotic insect introductions in Canada, forest pest-management efforts would benefit from the development of a high-throughput strategy to investigate the phytopathogenic fungal and oomycete species interacting with wood-boring insects. We recycled formerly discarded preservative fluids from the Canadian Food Inspection Agency annual survey using insect traps and analysed more than one hundred samples originating from across Canada. Using the Ion Torrent Personal Genome Machine (PGM) HTS technology and fusion primers, we performed metabarcoding to screen unwanted fungi and oomycetes species, including Phytophthora spp. Community profiling was conducted on the four different wood-boring, insect-attracting semiochemicals; although the preservative (contained ethanol) also attracted other insects. Phytopathogenic fungi (e.g., Leptographium spp. and Meria laricis in the pine sawyer semiochemical) and oomycetes (mainly Peronospora spp. and Pythium aff. hypogynum in the General Longhorn semiochemical), solely associated with one of the four types of semiochemicals, were detected. This project demonstrated that the insect traps’ semiochemical microbiome represents a new and powerful matrix for screening phytopathogens. Compared to traditional diagnostic techniques, the fluids allowed for a faster and higher throughput assessment of the biodiversity contained within. Additionally, minimal modifications to this approach would allow it to be used in other phytopathology fields.

The Landscape and Implications of Chimeric RNAs in Cervical Cancer.

BackgroundGene fusions and fusion products have been proven to be ideal biomarkers and drug targets for cancer. Even though a comprehensive study of cervical cancer has been conducted as part of the Cancer Genome Atlas (TCGA) project, few recurrent gene fusions have been found, and none above 3% of frequency.MethodsWe believe that chimeric fusion RNAs generated by intergenic splicing represent a new repertoire of biomarkers and/or therapeutic targets. However, they would be missed when only genome sequences and fusions at DNA level are considered. We performed extensive data mining for chimeric RNAs using both our and TCGA cervical cancer RNA-Seq datasets. Multiple criteria were applied. We analyzed the landscape of chimeric RNAs at various levels, and from different angles.FindingsThe chimeric RNA landscape changed as different filters were applied. 15 highly frequent (>10%) chimeric RNAs were identified. LHX6-NDUFA8 was detected exclusively in cervical cancer tissues and Pap smears, but not in normal controls. Mechanistically, it is not due to interstitial deletion, but a product of cis-splicing between adjacent genes. Silencing of another recurrent chimera, SLC2A11-MIF, resulted in cell cycle arrest and reduced cellular proliferation. This effect is unique to the chimera, and not shared by the two parental genes.InterpretationHighly frequent chimeric RNAs are present in cervical cancers. They can be formed by intergenic splicing. Some have clear implications as potential biomarkers, or for shedding new light on the biology of the disease.FundStand Up To Cancer and the National Science Foundation of China.

A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value

Chenopodium quinoa is a halophytic pseudocereal crop that is being cultivated in an ever-growing number of countries. Because quinoa is highly resistant to multiple abiotic stresses and its seed has a better nutritional value than any other major cereals, it is regarded as a future crop to ensure global food security. We generated a high-quality genome draft using an inbred line of the quinoa cultivar Real. The quinoa genome experienced one recent genome duplication about 4.3 million years ago, likely reflecting the genome fusion of two Chenopodium parents, in addition to the γ paleohexaploidization reported for most eudicots. The genome is highly repetitive (64.5% repeat content) and contains 54 438 protein-coding genes and 192 microRNA genes, with more than 99.3% having orthologous genes from glycophylic species. Stress tolerance in quinoa is associated with the expansion of genes involved in ion and nutrient transport, ABA homeostasis and signaling, and enhanced basal-level ABA responses. Epidermal salt bladder cells exhibit similar characteristics as trichomes, with a significantly higher expression of genes related to energy import and ABA biosynthesis compared with the leaf lamina. The quinoa genome sequence provides insights into its exceptional nutritional value and the evolution of halophytes, enabling the identification of genes involved in salinity tolerance, and providing the basis for molecular breeding in quinoa.

Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage

Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described. In a previous study, we detected a trpB gene of gammaproteobacterial origin in 'Ca. Tremblaya phenacola' from two Phenacoccus species, apparently indicating an unusual case of horizontal gene transfer (HGT) in a bacterial endosymbiont. What we found by sequencing the genome of 'Ca. Tremblaya phenacola' PPER, single endosymbiont of Phenacoccus peruvianus, goes beyond a HGT phenomenon. It rather represents a genome fusion between a beta and a gammaproteobacterium, followed by massive rearrangements and loss of redundant genes, leading to an unprecedented evolutionary collage. Mediated by the presence of several repeated sequences, there are many possible genome arrangements, and different subgenomic sequences might coexist within the same population.

Intraspecific chromosome polymorphisms can lead to reproductive isolation and speciation: an example in red brocket deer (Mazama americana).

The red brocket (Mazama americana) is a South American deer with a wide geographical distribution that presents different chromosomal variants depending on their location. At least six different cytotypes belonging to two distinct evolutionary lineages have been described. This study aimed to verify the existence of postzygotic reproductive isolation between cytotypes of M. americana by comparative evaluation of pure and hybrid males. Seven 18-month-old bucks were submitted to seminal collection and evaluation and testicle histological evaluations. The pure males showed normal parameters for sperm quality and testicular histology. Hybrids from the same evolutionary lineage (≤3 chromosomes different from the progenitors) showed similar results to pure males, except for the reduced ratio of round spermatids to pachytene spermatocytes. Hybrids between cytotypes of different evolutionary lineages (≥10 chromosomes different from progenitors) presented azoospermia and evidence of testicular degeneration. Despite the striking morphological similarities, we can conclude that populations with more distinct karyotypes possess an effective reproductive barrier; moreover, there is evidence that reproductive isolation mechanisms exist between some closer karyotypes, corroborating the hypothesis that M. americana is best characterized as a superspecies. Thus, the future description of several new species for this taxon is expected, since the tendency is to establish efficient mechanisms of postzygotic reproductive isolation, preventing the introgression and fusion of genomes from different populations through chromosome variation.

Applying Topological Principles to Genomic Analysis

In On the Origin of the Species in 1859, Charles Darwin proposed phylogenetic trees to depict evolutionary relationships on the basis of phenotypic attributes. Since then, biologists have shifted to using molecular traits to characterize evolutionary relationships between and among species. These approaches typically assume that traits are inherited vertically, and that evolution is strictly clonal. However, several other modes of genetic exchange add complexity to this process, including lateral gene transfers in bacteria, recombination and reassortment in viruses, viral integration in eukaryotes, and fusion of genomes of symbiotic species.

Abstract LB-161: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

Abstract Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm and the mitochondrial double membrane. Despite these physical barriers we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements and the features of the fusion fragments indicate that non-homologous end joining and/or replication-dependent DNA double strand break repair are the dominant mechanism involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells. Citation Format: Young Seok Ju, Jose Tubio, William Mifsud, Beiyuan Fu, ICGC Prostate Cancer, Bone Cancer, Breast Cancer Working Groups, Fengtang Yang, Peter Campbell, Michael Stratton. Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-161. doi:10.1158/1538-7445.AM2015-LB-161

Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells.

Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm, and the mitochondrial double membrane. Despite these physical barriers, we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements, and the features of the fusion fragments indicate that nonhomologous end joining and/or replication-dependent DNA double-strand break repair are the dominant mechanisms involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells.

The fusion of genomes leads to more options: A comparative investigation on the desulfo-glucosinolate sulfotransferases of Brassica napus and homologous proteins of Arabidopsis thaliana

Sulfotransferases (SOTs) (EC 2.8.2.-) play a crucial role in the glucosinolate (Gl) biosynthesis, by catalyzing the final step of the core glucosinolate formation. In Arabidopsis thaliana the three desulfo (ds)-Gl SOTs AtSOT16, AtSOT17 and AtSOT18 were previously characterized, showing different affinities to ds-Gls. But can the knowledge about these SOTs be generally transferred to other Gl-synthesizing plants? It was investigated how many SOTs are present in the economically relevant crop plant Brassica napus L., and if it is possible to predict their characteristics by sequence analysis. The recently sequenced B. napus is a hybrid of Brassica rapa and Brassica oleracea. By database research, 71 putative functional BnSOT family members were identified and at least eleven of those are putative ds-Gl SOTs. Besides the homologs of AtSOT16 – 18, phylogenetic analyses revealed new subfamilies of ds-Gl SOTs, which are not present in A. thaliana. Three of the B. napus ds-Gl SOT proteins were expressed and purified, and characterized by determining the substrate affinities to different ds-Gls. Two of them, BnSOT16-a and BnSOT16-b, showed a significantly higher affinity to an indolic ds-Gl, similarly to AtSOT16. Additionally, BnSOT17-a was characterized and showed a higher affinity to long chained aliphatic Gls, similarly to AtSOT17. Identification of homologs to AtSOT18 was less reliable, because putative SOT18 sequences are more heterogeneous and confirmation of similar characteristics was not possible.

Toward breeding new land-sea plant hybrid species irrigable with seawater for dry regions

A plant species growing in sea or coastal saltmarsh is greatly tolerant to high concentrations of salts, and a plant species growing in desert or dry regions is highly tolerant to drought. Breeding a new plant hybrid species from both species by means of cellular grafting, genome fusion or nuclear transfer would generate, at least in theory, a hybrid plant species that should be strongly tolerant to harsh aridity and salinity and would be potentially irrigable with seawater. Such prospective species can be used for example as a fodder, biofuel crop or stabilizer species to protect soil from wind erosion and sandy storms in dry regions. Breeding such species would change the surface of the world and help to solve major challenges of starvation, malnutrition and poverty. Here, I propose potential approaches that would be worthy of investigation toward this purpose.

Genome-wide analysis and expression profile of the bZIP transcription factor gene family in grapevine (Vitis vinifera).

BackgroundBasic leucine zipper (bZIP) transcription factor gene family is one of the largest and most diverse families in plants. Current studies have shown that the bZIP proteins regulate numerous growth and developmental processes and biotic and abiotic stress responses. Nonetheless, knowledge concerning the specific expression patterns and evolutionary history of plant bZIP family members remains very limited.ResultsWe identified 55 bZIP transcription factor-encoding genes in the grapevine (Vitis vinifera) genome, and divided them into 10 groups according to the phylogenetic relationship with those in Arabidopsis. The chromosome distribution and the collinearity analyses suggest that expansion of the grapevine bZIP (VvbZIP) transcription factor family was greatly contributed by the segment/chromosomal duplications, which may be associated with the grapevine genome fusion events. Nine intron/exon structural patterns within the bZIP domain and the additional conserved motifs were identified among all VvbZIP proteins, and showed a high group-specificity. The predicted specificities on DNA-binding domains indicated that some highly conserved amino acid residues exist across each major group in the tree of land plant life. The expression patterns of VvbZIP genes across the grapevine gene expression atlas, based on microarray technology, suggest that VvbZIP genes are involved in grapevine organ development, especially seed development. Expression analysis based on qRT-PCR indicated that VvbZIP genes are extensively involved in drought- and heat-responses, with possibly different mechanisms.ConclusionsThe genome-wide identification, chromosome organization, gene structures, evolutionary and expression analyses of grapevine bZIP genes provide an overall insight of this gene family and their potential involvement in growth, development and stress responses. This will facilitate further research on the bZIP gene family regarding their evolutionary history and biological functions.

Genome Fusion Detection: a novel method to detect fusion genes from SNP-array data

Motivation: Fusion genes result from genomic rearrangements, such as deletions, amplifications and translocations. Such rearrangements can also frequently be observed in cancer and have been postulated as driving event in cancer development. to detect them, one needs to analyze the transition region of two segments with different copy number, the location where fusions are known to occur. Finding fusion genes is essential to understanding cancer development and may lead to new therapeutic approaches.Results: Here we present a novel method, the Genomic Fusion Detection algorithm, to predict fusion genes on a genomic level based on SNP-array data. This algorithm detects genes at the transition region of segments with copy number variation. With the application of defined constraints, certain properties of the detected genes are evaluated to predict whether they may be fused. We evaluated our prediction by calculating the observed frequency of known fusions in both primary cancers and cell lines. We tested a set of cell lines positive for the BCR-ABL1 fusion and prostate cancers positive for the TMPRSS2-ERG fusion. We could detect the fusions in all positive cell lines, but not in the negative controls.Availability: The algorithm is available from the supplement.Contact: philip.groth@bayer.comSupplementary information: Supplementary data are available at Bioinformatics online.

Improvement of a Candida antarctica lipase B-displaying yeast whole-cell biocatalyst and its application to the polyester synthesis reaction

A Candida antarctica lipase B (CALB)-displaying yeast whole-cell biocatalyst was constructed with the integration of the CALB cell-surface display expression cassette in the yeast genome and cell fusion by mating. Lipase hydrolytic activity of the yeast whole-cell biocatalyst subsequently increased, in both a- and alpha-type yeast cells, with the number of copies of the CALB cell-surface display expression cassette introduced, and reached 43.6 and 32.2 U/g-dry cell at 168 h cultivation, respectively. The lipase hydrolytic activity of whole cells in diploid yeast cells containing eight copies of the CALB cell-surface expression cassette reached 117 U/g-dry cell, and this value is approximately ninefold higher than that of the previously reported haploid CALB cell-surface displaying yeast using a multi-copy plasmid (Tanino et al. Appl. Microbial Biotechnol 75:1319-1325, 2007). This improved novel CALB-displaying yeast whole-cell biocatalyst could repeatedly catalyze the polyester, polybutylene adipate, synthesis reaction, using adipic acid and 1, 4-butandiol as the monomer molecules, four times in succession. This is the first report of the polymer synthesis using enzyme displaying yeast as the catalyst. The ratios of cyclic compounds in the polybutylene adipates synthesized with the CALB-displaying yeast whole-cells were lower than that in the polybutylene adipate synthesized with conventional metal catalysis. From these results, it appears that the use of CALB-displaying yeast cells could be useful for the polyester synthesis reaction, with reduced by-product production.

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

Large-scale (segmental or whole) genome duplication has been recurring in angiosperm evolution. Subsequent gene loss and rearrangements further affect gene copy numbers and fractionate ancestral gene linkages across multiple chromosomes. The fragmented "multiple-to-multiple" correspondences resulting from this distinguishing feature of angiosperm evolution complicates comparative genomic studies. Using a robust computational framework that combines information from multiple orthologous and duplicated regions to construct local syntenic networks, we show that a shared ancient hexaploidy event (or perhaps two roughly concurrent genome fusions) can be inferred based on the sequences from several divergent plant genomes. This "paleo-hexaploidy" clearly preceded the rosid-asterid split, but it remains equivocal whether it also affected monocots. The model resulting from our multi-alignments lays the foundation for approximating the number and arrangement of genes in the last universal common ancestor of angiosperms. Comparative analysis of inferred homologous genes derived from this model shows patterns of preferential gene retention or loss after polyploidy and reveals large variability of nucleotide substitution rates among plant nuclear genomes.