J. Chris Pires
University of Missouri Columbia, Biological Sciences, Faculty Member
- Plant Evolution, Phylogenomics, Polyploidy, Systems/Network Biologyedit
Homoeologous recombination, aneuploidy, and other genetic changes are common in resynthesized allopolyploid Brassica napus. In contrast, the chromosomes of cultivars have long been considered to be meiotically stable. To gain a better... more
Homoeologous recombination, aneuploidy, and other genetic changes are common in resynthesized allopolyploid Brassica napus. In contrast, the chromosomes of cultivars have long been considered to be meiotically stable. To gain a better understanding of the underlying mechanisms leading to stabilization in the allopolyploid, the behavior of chromosomes during meiosis can be compared by unambiguous chromosome identification between resynthesized and natural B. napus. Compared with natural B. napus, resynthesized lines show high rates of nonhomologous centromere association, homoeologous recombination leading to translocation, homoeologous chromosome replacement, and association and breakage of 45S rDNA loci. In both natural and resynthesized B. napus, we observed low rates of univalents, A–C bivalents, and early sister chromatid separations. Reciprocal homoeologous chromosome exchanges and double reductions were photographed for the first time in meiotic telophase I. Meiotic errors wer...
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Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to... more
Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana—chosen as the model plant system for this reason—as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa acro...
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Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. The genomic features... more
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of emergence of subgenome dominance, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural, less than 140 year old allopolyploid (Mimulus peregrinus), a resynthesized inter-species triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and progenitor species (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of divergent genomes and significantly increases over generations. Additionally, CHH methylation levels are reduced in regions near genes and within TEs in the first-generat...
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The complex manner in which organisms respond to changes in their gene dosage has long fascinated geneticists. Oddly, although the existence of dominance implies that dosage reductions often have mild phenotypes, extra copies of whole... more
The complex manner in which organisms respond to changes in their gene dosage has long fascinated geneticists. Oddly, although the existence of dominance implies that dosage reductions often have mild phenotypes, extra copies of whole chromosomes (aneuploidy) are generally strongly deleterious. Even more paradoxically, an extra copy of the genome is better tolerated than is aneuploidy. We review the resolution of this paradox, highlighting the roles of biochemistry, protein aggregation, and disruption of cellular microstructure in that explanation. Returning to life's curious combination of robustness and sensitivity to dosage changes, we argue that understanding how biological robustness evolved makes these observations less inexplicable. We propose that noise in gene expression and evolutionary strategies for its suppression play a role in generating dosage phenotypes. Finally, we outline an unappreciated mechanism for the preservation of duplicate genes, namely preservation t...
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Most plants convert sunlight into chemical energy using C3 photosynthesis. However, a modified pathway, C4 photosynthesis, allows some plants to be more drought tolerant and fertilizer-use efficient. Strikingly, C4 photosynthesis has... more
Most plants convert sunlight into chemical energy using C3 photosynthesis. However, a modified pathway, C4 photosynthesis, allows some plants to be more drought tolerant and fertilizer-use efficient. Strikingly, C4 photosynthesis has evolved independently in dozens of different plant lineages, a testament to its diversity and advantages in many common terrestrial environments. Currently, massive international efforts are focused on breeding and bioengineering C4 photosynthesis into C3 rice and other food and sustainable energy crops. What these efforts often overlook is that there is no “one” C4 photosynthesis. In fact, with its 60-plus distinct evolutionary origins, 20-plus anatomies, and 3 basic enzymatic sub-types, C4 is more of a diverse syndrome than it is one generalized photosynthesis type. Because the various C4 sub-types have evolved in diverse environments, different sub-types may be more efficient for different agricultural applications. Our study uses the grass tribe Pan...
Most plants convert sunlight into chemical energy using C3 photosynthesis. However, a modified pathway, C4 photosynthesis, allows some plants to be more drought tolerant and fertilizer-use efficient. Strikingly, C4 photosynthesis has... more
Most plants convert sunlight into chemical energy using C3 photosynthesis. However, a modified pathway, C4 photosynthesis, allows some plants to be more drought tolerant and fertilizer-use efficient. Strikingly, C4 photosynthesis has evolved independently in dozens of different plant lineages, a testament to its diversity and advantages in many common terrestrial environments. Currently, massive international efforts are focused on breeding and bioengineering C4 photosynthesis into C3 rice and other food and sustainable energy crops. What these efforts often overlook is that there is no “one” C4 photosynthesis. In fact, with its 60-plus distinct evolutionary origins, 20-plus anatomies, and 3 basic enzymatic sub-types, C4 is more of a diverse syndrome than it is one generalized photosynthesis type. Because the various C4 sub-types have evolved in diverse environments, different sub-types may be more efficient for different agricultural applications. Our study uses the grass tribe Pan...
Requirements to maintain dosage balance shape many genome-scale patterns in organisms, including the resolution of whole genome duplications (WGD), as well as the varied effects of aneuploidy, segmental duplications, tandem duplications,... more
Requirements to maintain dosage balance shape many genome-scale patterns in organisms, including the resolution of whole genome duplications (WGD), as well as the varied effects of aneuploidy, segmental duplications, tandem duplications, gene copy number variations (CNV), and epigenetic marks. Like neofunctionalization and subfunctionalization, the impact of absolute and relative dosage varies over time. These variations are of particular importance in understanding the role of dosage in the evolution of polyploid organisms. Numerous investigations have found the consequences of polyploidy remain distinct from small-scale duplications (SSD). This observation is significant as all flowering plants have experienced at least two ancient polyploid events, and many angiosperm lineages have undergone additional rounds of polyploidy. Intriguingly, recent studies indicate a link between how epigenetic marks in recent allopolyploids may induce immediate changes in gene expression and the lon...
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Research Interests: Genetics, Biology, Evolution, Epigenetics, Medicine, and 15 moreGene expression, Polyploidy, Biological Sciences, Plant Genome Project, Genome evolution, Regulation of Gene Expression, Plant, Plants, Gene, Biological evolution, Gene Dosage, Phenotype, Genetic variation, Gene Expression Regulation, and Medical and Health Sciences
Homoeologous regions of Brassica genomes were analyzed at the sequence level. These represent segments of the Brassica A genome as found in Brassica rapa and Brassica napus and the corresponding segments of the Brassica C genome as found... more
Homoeologous regions of Brassica genomes were analyzed at the sequence level. These represent segments of the Brassica A genome as found in Brassica rapa and Brassica napus and the corresponding segments of the Brassica C genome as found in Brassica oleracea and B. napus. Analysis of synonymous base substitution rates within modeled genes revealed a relatively broad range of times (0.12 to 1.37 million years ago) since the divergence of orthologous genome segments as represented in B. napus and the diploid species. Similar, and consistent, ranges were also identified for single nucleotide polymorphism and insertion-deletion variation. Genes conserved across the Brassica genomes and the homoeologous segments of the genome of Arabidopsis thaliana showed almost perfect collinearity. Numerous examples of apparent transduplication of gene fragments, as previously reported in B. oleracea, were observed in B. rapa and B. napus, indicating that this phenomenon is widespread in Brassica spec...
Research Interests: Genetics, Molecular Evolution, Comparative Genomics, Plant Biology, Biology, and 15 moreMedicine, Arabidopsis thaliana, Brassicaceae, Comparative Analysis, Genome, Gene, Research Articles, Brassica oleracea, Brassica, Brassica Napus, Brassica rapa, Plant cell, Ploidy, Biochemistry and cell biology, and Molecular Sequence Data
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Allopolyploid formation requires the adaptation of two nuclear genomes within a single cytoplasm, which may involve programmed genetic and epigenetic changes during the initial generations following genome fusion. To study the dynamics of... more
Allopolyploid formation requires the adaptation of two nuclear genomes within a single cytoplasm, which may involve programmed genetic and epigenetic changes during the initial generations following genome fusion. To study the dynamics of genome change, we synthesized 49 isogenic Brassica napus allopolyploids and surveyed them with 76 restriction fragment length polymorphism (RFLP) probes and 30 simple sequence repeat (SSR) primer pairs. Here, we report on the types and distribution of genetic and epigenetic changes within the S1 genotypes. We found that insertion/deletion (indel) events were rare, but not random. Of the 57,710 (54,383 RFLP and 3,327 SSR) parental fragments expected among the amphidiploids, we observed 56,676 or 99.9%. Three loci derived from Brassica rapa had indels, and one indel occurred repeatedly across 29% (14/49) of the lines. Loss of one parental fragment was due to the 400-bp reduction of a guanine-adenine dinucleotide repeat-rich sequence. In contrast to t...
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Research Interests: Evolutionary Biology, Genetics, Morphological evolution, Molecular Evolution, Biology, and 15 moreSeed Dispersal, Medicine, Phylogeny, Adaptive Radiation, Sequence alignment, Plants, Paraphyly, Molecular Phylogenetics and Evolution, Species Diversity, South America, Molecular phylogenetics, Monophyly, Genetic variation, PLANT PROTEINS, and Molecular Sequence Data
Research Interests: Evolutionary Biology, Genetics, Diversity, Systematic Biology, Molecular Systematics, and 14 moreMolecular Evolution, Plant Biology, Biology, Polynesia, Biometry, DNA, Sequence alignment, Simuliidae, Animals, Phylogenetic analysis, Ecosystem, Phylogenetic Tree, Base Sequence, and Molecular Sequence Data
Investigating recombination of homoeologous chromosomes in allopolyploid species is central to understanding plant breeding and evolution. However, examining chromosome pairing in the allotetraploid Brassica napus has been hampered by the... more
Investigating recombination of homoeologous chromosomes in allopolyploid species is central to understanding plant breeding and evolution. However, examining chromosome pairing in the allotetraploid Brassica napus has been hampered by the lack of chromosome-specific molecular probes. In this study, we establish the identification of all homoeologous chromosomes of allopolyploid B. napus by using robust molecular cytogenetic karyotypes developed for the progenitor species Brassica rapa (A genome) and Brassica oleracea (C genome). The identification of every chromosome among these three Brassica species utilized genetically mapped bacterial artificial chromosomes (BACs) from B. rapa as probes for fluorescent in situ hybridization (FISH). With this BAC-FISH data, a second karyotype was developed using two BACs that contained repetitive DNA sequences and the ubiquitous ribosomal and pericentromere repeats. Using this diagnostic probe mix and a BAC that contained a C-genome repeat in two...
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Research Interests: Genetics, Molecular Evolution, Biology, Medicine, Biological Sciences, and 13 morePlant Genome Project, Euchromatin, Molecular Phylogenetics and Evolution, Genome, Arabidopsis, Brassica, Genomic Library, Comparative Genomic Hybridization, Heterochromatin, Contig, Synteny, BMC, and Medical and Health Sciences
Background The Brassica species, related to Arabidopsis thaliana, include an important group of crops and represent an excellent system for studying the evolutionary consequences of polyploidy. Previous studies have led to a proposed... more
Background The Brassica species, related to Arabidopsis thaliana, include an important group of crops and represent an excellent system for studying the evolutionary consequences of polyploidy. Previous studies have led to a proposed structure for an ancestral karyotype and models for the evolution of the B. rapa genome by triplication and segmental rearrangement, but these have not been validated at the sequence level. Results We developed computational tools to analyse the public collection of B. rapa BAC end sequence, in order to identify candidates for representing collinearity discontinuities between the genomes of B. rapa and A. thaliana. For each putative discontinuity, one of the BACs was sequenced and analysed for collinearity with the genome of A. thaliana. Additional BAC clones were identified and sequenced as part of ongoing efforts to sequence four chromosomes of B. rapa. Strikingly few of the 19 inter-chromosomal rearrangements corresponded to the set of collinearity d...
Research Interests: Genetics, Genomics, Molecular Evolution, Biology, Medicine, and 15 moreArabidopsis thaliana, Biological Sciences, Plant Genome Project, Genome evolution, Karyotyping, Molecular Phylogenetics and Evolution, Genome, Arabidopsis, Molecular cloning, Brassica rapa, Linkage Group, Reproducibility of Results, BMC, Medical and Health Sciences, and Gene Rearrangement
Research Interests: Botany, Genetics, Biology, Evolution, Molecular Genetics, and 15 moreEpigenetics, Translocations, Gene Silencing, Polyploidy, Biological Sciences, Chromosome Evolution, Brassicaceae, Biological, Phenotypic evolution, Divergence, Copy Number Variation (CNV), Brassica, Brassica Napus, Phenotypic variation, and Genome Rearrangement
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Research Interests: Evolutionary Biology, Molecular Systematics, Plant Biology, Biology, Ecology, and 14 morePlant Systematics, Medicine, Western North America, Paraphyly, Asparagaceae, Morphological Characters, Geographic distribution, Monophyly, Asparagales, Phylogenetic Tree, Monocot, DNA sequence, Brodiaea, and Themidaceae
Research Interests: Botany, Evolutionary Biology, Plant Biology, Biology, Ecology, and 4 moreMedicine, Onagraceae, Monophyly, and Taxon
Research Interests: Botany, Evolutionary Biology, Plant Biology, Biology, Ecology, and 4 moreMedicine, Urticaceae, Monophyly, and Moraceae
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To obtain better insight into the mechanisms of selenium hyperaccumulation in Stanleya pinnata, transcriptome-wide differences in root and shoot gene expression levels were investigated in S. pinnata and related nonaccumulator Stanleya... more
To obtain better insight into the mechanisms of selenium hyperaccumulation in Stanleya pinnata, transcriptome-wide differences in root and shoot gene expression levels were investigated in S. pinnata and related nonaccumulator Stanleya elata grown with or without 20 μm selenate. Genes predicted to be involved in sulphate/selenate transport and assimilation or in oxidative stress resistance (glutathione-related genes and peroxidases) were among the most differentially expressed between species; many showed constitutively elevated expression in S. pinnata. A number of defence-related genes predicted to mediate synthesis and signalling of defence hormones jasmonic acid (JA, reported to induce sulphur assimilatory and glutathione biosynthesis genes), salicylic acid (SA) and ethylene were also more expressed in S. pinnata than S. elata. Several upstream signalling genes that up-regulate defence hormone synthesis showed higher expression in S. pinnata than S. elata and might trigger these...
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The carbohydrate-rich cell walls of land plants and algae have been the focus of much interest given the value of cell wall based products to our current and future economies. Hydroxyproline-rich glycoproteins (HRGPs), a major group of... more
The carbohydrate-rich cell walls of land plants and algae have been the focus of much interest given the value of cell wall based products to our current and future economies. Hydroxyproline-rich glycoproteins (HRGPs), a major group of wall glycoproteins, play important roles in plant growth and development, yet little is known about how they have evolved in parallel with the polysaccharide components of walls. We investigate the origins and evolution of the HRGP superfamily, which is commonly divided into three major multigene families: the arabinogalactan-proteins (AGPs), extensins (EXTs) and proline-rich proteins (PRPs). Using MAAB, a newly developed bioinformatics pipeline, we identified HRGPs in sequences from the 1000 plants (1KP) transcriptome project (www.onekp.com). Our analyses provide new insights into the evolution of HRGPs across major evolutionary milestones, including the transition to land and early radiation of angiosperms. Significantly, data mining reveals the ori...
Research Interests: Botany, Molecular Evolution, Biology, Medicine, Transcriptome, and 13 moreBiological Sciences, Phylogeny, Plant Physiology, P-glycoprotein, Plants, Molecular Phylogenetics and Evolution, Glycoproteins, Time Factors, Hydroxyproline, Amino Acid Sequence, Cell Wall, PLANT PROTEINS, and Likelihood Functions
Research Interests: Genetics, Chemistry, Plant Biology, Biology, Medicine, and 15 moreMultidisciplinary, Polyploidy, Phylogeny, Plant Genome Project, Genome evolution, Brassicaceae, Pangenome, General Chemistry, Gene, Brassica oleracea, Brassica, Genetic variation, Physics and Astronomy, PLANT PROTEINS, and Nature Communications
Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once or possibly twice in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number... more
Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once or possibly twice in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n=2x=20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion or retrotransposon proliferation in dioecious species. We first estimate genome sizes or use published values for four hermaphrodites and four dioecious species distributed across the phylogeny and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient who...
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The grass tribe Paniceae includes important food, forage, and bioenergy crops such as switchgrass, napiergrass, various millet species, and economically important weeds. Paniceae are also valuable for answering scientific and evolutionary... more
The grass tribe Paniceae includes important food, forage, and bioenergy crops such as switchgrass, napiergrass, various millet species, and economically important weeds. Paniceae are also valuable for answering scientific and evolutionary questions about C4 photosynthetic evolution, drought tolerance, and spikelet variation. However, the phylogeny of the tribe remains incompletely resolved. Forty-five taxa were selected from across the tribe Paniceae and outgroups for genome survey sequencing (GSS). These data were used to build a phylogenetic tree of the Paniceae based on 102 markers (78 chloroplast, 22 mitochondrial, 2 nrDNA). Ancestral state reconstruction analyses were also performed within the Paniceae using both the traditional and two subtype classification systems to test hypotheses of C4 subtype evolution. The phylogenetic tree resolves many areas of the Paniceae with high support and provides insight into the origin and number of C4 evolution events within the tribe. The r...
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Unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of true orthologs in... more
Unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of true orthologs in divergent taxa. Here, we employed an integrated syntenic and phylogenomic analyses to reveal an ancient WGD that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas (Musa acuminata), ginger, palms, and other plants of fundamental, agricultural, and/or horticultural interest. First, comprehensive phylogenomic analyses revealed 1421 putative gene families that retained ancient duplication shared by Musa (Zingiberales) and grass (Poales) genomes, indicating an ancient WGD in monocots. Intergenomic synteny blocks of Musa and Oryza were investigated, and 30 blocks were shown to be duplicated before Musa-Oryza divergence an estimated 120 to 150 million years ago. Synteny comparisons of four monocot (rice [Oryza sativa], sorghum [...
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The domestication of plants and animals marks one of the most significant transitions in human, and indeed global, history. Traditionally, study of the domestication process was the exclusive domain of archaeologists and agricultural... more
The domestication of plants and animals marks one of the most significant transitions in human, and indeed global, history. Traditionally, study of the domestication process was the exclusive domain of archaeologists and agricultural scientists; today it is an increasingly multidisciplinary enterprise that has come to involve the skills of evolutionary biologists and geneticists. Although the application of new information sources and methodologies has dramatically transformed our ability to study and understand domestication, it has also generated increasingly large and complex datasets, the interpretation of which is not straightforward. In particular, challenges of equifinality, evolutionary variance, and emergence of unexpected or counter-intuitive patterns all face researchers attempting to infer past processes directly from patterns in data. We argue that explicit modeling approaches, drawing upon emerging methodologies in statistics and population genetics, provide a powerful...
Research Interests: Bioinformatics, Genetics, Archaeology, Computer Science, Genomics, and 15 moreComputational Biology, Modeling, Biology, Agriculture, Evolution, Archaeogenetics, Ancient DNA Research, Medicine, Multidisciplinary, Animal domestication, Humans, Data Science, Animals, Domestication, and Crop domestication
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Significance Ancient plant polyploids contain dissimilar subgenomes. Subgenomes that have lost fewer genes are subgenomes that tend to express their genes to higher mRNA levels: “genome dominance.” Genome dominance is heritable through... more
Significance Ancient plant polyploids contain dissimilar subgenomes. Subgenomes that have lost fewer genes are subgenomes that tend to express their genes to higher mRNA levels: “genome dominance.” Genome dominance is heritable through multiple rounds of polyploidy and over tens of millions of years. Twenty-four–nucleotide RNA coverage of noncoding, transposon DNA upstream of genes marks the recessive subgenomes of Brassica rapa and Arabidopsis with only a small effect of gene expression. We hypothesize that the “diploid” parent of a tetraploidy with the lowest transposon load was to become the dominant subgenome. The balance of transposon position effects on genes is important for the regulation of quantity (and perhaps to solve the heterosis and C-value paradoxes).
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Research Interests: Evolutionary Biology, Genetics, Molecular Evolution, Biology, Medicine, and 15 moreMultidisciplinary, Polyploidy, Mitosis, Plant Genome Project, Chromosome Evolution, Meiosis, Research article, Karyotyping, Asteraceae, Molecular Cytogenetics, PLoS one, Concerted Evolution, Ribosomal DNA, Diploidy, and Tragapogon
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ABSTRACT: BACKGROUND: Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. RESULTS: To determine when this polyploidization occurred relative to... more
ABSTRACT: BACKGROUND: Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. RESULTS: To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the d...
Research Interests: Bioinformatics, Evolutionary Biology, Molecular Evolution, Biology, Medicine, and 15 morePolyploidy, Biological Sciences, Phylogeny, Plant Genome Project, Environmental Sciences, Genomics and Proteomics, Plant Genome Evolution, Molecular Phylogenetics and Evolution, Genome, Gene Duplication, Phylogenetics and Phylogenomics, Angiosperms, Phylogenetic Tree, PLANT PROTEINS, and Gene expression profiling
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Research Interests: Botany, Evolutionary Biology, Phylogenetics, Computational Biology, Molecular Evolution, and 15 morePlant Biology, Biology, Ecology, Mitochondria, Genome Size, Medicine, Phylogeny, Molecular Phylogenetics and Evolution, Genome, Mitochondrial Genome, Molecular phylogenetics, Cell nucleus, Massive Parallel Sequencing, Phylogenetic Tree, and Liliaceae
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Research Interests: Evolutionary Biology, Genetics, Microbiology, Genomics, Computational Biology, and 15 moreCoevolution, Molecular Evolution, Biotechnology, Comparative Genomics, Biology, Medicine, Biological Sciences, Genome evolution, Genome, Arabidopsis, Gene Regulatory Networks, Associations, Convergent Evolution, Organisms, and Mycorrhizae
Genes that are inherently subject to strong selective constraints tend to be overretained in duplicate after polyploidy. They also continue to experience similar, but somewhat relaxed, constraints after that polyploidy event. We sought to... more
Genes that are inherently subject to strong selective constraints tend to be overretained in duplicate after polyploidy. They also continue to experience similar, but somewhat relaxed, constraints after that polyploidy event. We sought to assess for how long the influence of polyploidy is felt on these genes' selective pressures. We analyzed two nested polyploidy events in Brassicaceae: the At-α genome duplication that is the most recent polyploidy in the model plant Arabidopsis thaliana and a more recent hexaploidy shared by the genus Brassica and its relatives. By comparing the strength and direction of the natural selection acting at the population and at the species level, we find evidence for continued intensified purifying selection acting on retained duplicates from both polyploidies even down to the present. The constraint observed in preferentially retained genes is not a result of the polyploidy event: the orthologs of such genes experience even stronger constraint in ...
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In eukaryotes, protein deacetylation is carried out by two well-conserved histone deacetylase (HDAC) families: RPD3/HDA1 and SIR2. Intriguingly, model plants such as Arabidopsis express an additional plant-specific HDAC family, termed... more
In eukaryotes, protein deacetylation is carried out by two well-conserved histone deacetylase (HDAC) families: RPD3/HDA1 and SIR2. Intriguingly, model plants such as Arabidopsis express an additional plant-specific HDAC family, termed type-2 HDACs (HD2s). Transcriptomic analyses from more than 1300 green plants generated by the 1000 plants (1KP) consortium showed that HD2s appeared early in green plant evolution, the first members being detected in several streptophyte green alga. The HD2 family has expanded via several rounds of successive duplication; members are expressed in all major green plant clades. Interestingly, angiosperm species express new HD2 genes devoid of a zinc-finger domain, one of the main structural features of HD2s. These variants may have been associated with the origin and/or the biology of the ovule/seed.
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Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust... more
Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage. 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage. The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidenc...