Homoeologous recombination, aneuploidy, and other genetic changes are common in resynthesized all... 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...
Genome sizes of plants have long piqued the interest of researchers due to the vast differences a... 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...
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally ... 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...
The complex manner in which organisms respond to changes in their gene dosage has long fascinated... 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...
By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ec... more By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level. Using a new network bipartition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure.
Most plants convert sunlight into chemical energy using C3 photosynthesis. However, a modified pa... 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 pa... 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 ... 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...
Polyploidy has long been recognized as a prominent force shaping the evolution of eukaryotes, esp... more Polyploidy has long been recognized as a prominent force shaping the evolution of eukaryotes, especially flowering plants. New phenotypes often arise with polyploid formation and can contribute to the success of polyploids in nature or their selection for use in agriculture. Although the causes of novel variation in polyploids are not well understood, they could involve changes in gene expression through increased variation in dosage-regulated gene expression, altered regulatory interactions, and rapid genetic and epigenetic changes. New research approaches are being used to study these mechanisms and the results should provide a more complete understanding of polyploidy.
Homoeologous regions of Brassica genomes were analyzed at the sequence level. These represent seg... 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...
In the historical context of plant systematics over the last 50 years, systematics is examined in... more In the historical context of plant systematics over the last 50 years, systematics is examined in terms of where it is now, where it is headed, where it should be, and how it should get there. Issues and concerns of the past decades are still with us today. Molecular systematics has become the over-arching field in systematics, but each of eight other areas (genome, chromosomes, morphology and anatomy, development, population biology, speciation, floristics and monography, nomenclature and classification) are evaluated. A revolution in systematics is not necessary for the next 50 years in plant systematics. What is needed is a re-mapping of our discipline that involves four elements for the future growth and health of botanical systematics: plant systematics and its utility, dialogue with other disciplines, multidisciplinary training, and a pluralistic viewpoint.
Allopolyploid formation requires the adaptation of two nuclear genomes within a single cytoplasm,... 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...
Phylogenetic relationships of the five families of the order Commelinales remain an area of deep ... more Phylogenetic relationships of the five families of the order Commelinales remain an area of deep uncertainty in higher-level monocot systematics, despite intensive morphological and anatomical study. To test the monophyly of the Commelinales and the subclass Commelinidae, evaluate their relationships, and analyze evolutionary trends in their morphology, ecology, and biogeography, we conducted parsimony analyses on 95 rbcL sequences representing 17 taxa of Commelinales, 16 taxa of other Commelinidae, and 63 taxa from Arecidae, Liliidae, and Zingiberidae. Commelinales is polyphyletic and Commelinidae paraphyletic, with Eriocaulaceae and Xyridaceae sister to Poaceae and its relatives, Rapateaceae sister to Bromeliaceae and Mayacaceae, and Commelinaceae sister to Philydrales and allies. Thurnia is sister to Prionium at the base of Cyperaceae-Juncaceae; only 1 of Cronquist's multifamily commelinoid orders is diagnosed as monophyletic. We propose a revised Commelinidae, incorporating 4 revised superorders (Bromelianae, Commelinanae, Dasypogonanae, Arecanae) and 10 orders ((Poales, Eriocaulales, Cyperales, Typhales, Bromeliales), (Commelinales, Philydrales, Zingiberales), (Dasypogonales), (Arecales)). Morphological and anatomical characters used to define the original Commelinales and Commelinidae appear to be plesiomorphic or to reflect convergence or recurrent mutation; several characters supporting our revised classification are anatomical traits that seem relatively insulated from environmental selection pressures. The Commelinidae distal to the Arecales arose in South America, with amphiatlantic Bromeliaceae-Mayacaceae-Rapateaceae originating in the Guayana Shield. Ecological diversification involved the repeated invasion of shady, infertile, or arid microsites. The numbers of species in families of the revised Commelinidae are related partly to the extent of adaptive radiation in those families, but seem more strongly related to nonadaptive features promoting speciation, such as restricted seed dispersal (especially in forest interior groups with fleshy fruits), polyploidy, aneuploidy, and apomixis. Species diversity is unrelated to the rate/amount of rbcL sequence evolution. 1999 Academic Press
Naupactus (Curculionidae: Entiminae) is the most speciose weevil genus of the tribe Naupactini. T... more Naupactus (Curculionidae: Entiminae) is the most speciose weevil genus of the tribe Naupactini. The main objective of this work is to recognize species groups within Naupactus and to analyze the relationships between this and other Neotropical genera. For this purpose, we compiled a combined data matrix of 60 terminal units corresponding to 40 species for which we recorded 812 molecular and morphological characters (763 and 49 respectively), which were analyzed by Maximum Parsimony and Bayesian analyses. The single tree obtained from each analysis was rooted with Cyrtomon inhalatus. The species of Naupactus were recovered as different monophyletic groups, some of them closer to other genera of Naupactini (Lanterius, Teratopactus, Pantomorus and Parapantomorus) than to species of the same genus. We conclude that Naupactus is non-monophyletic, even though most species can be recognized based on a particular combination of morphological characters, which are probably symplesiomorphic. To be consistent with the cladistic principles, some genera diversified in marginal areas of the Pantomorus-Naupactus complex should be synonymized with Naupactus; however, these nomenclatural changes may not ensure a generic definition based on synapomorphies. We prefer to be conservative about the current classification until more evidence is available. The only nomenclatural amendments proposed herein are the transference of Naupactus inermis Hustache to Lanterius and of N. setarius to Symmathetes.
Investigating recombination of homoeologous chromosomes in allopolyploid species is central to un... 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...
Background: Evolution of the Brassica species has been recursively affected by polyploidy events,... more Background: Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity. Results: A genome-wide physical map of a rapid-cycling strain of B. oleracea was constructed by integrating highinformation-content fingerprinting (HICF) of Bacterial Artificial Chromosome (BAC) clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences) to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of B. oleracea and Arabidopsis thaliana, a relatively high level of genomic change since their divergence. Comparison of the B. oleracea physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity. Conclusions: A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes. All the physical mapping data is freely shared at a WebFPC site (http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/ WebFPC/; Temporarily password-protected: account: pgml; password: 123qwe123.
Background The Brassica species, related to Arabidopsis thaliana, include an important group of c... 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...
Novel phenotypes often arise in generations immediately following polyploidization. Previous stud... more Novel phenotypes often arise in generations immediately following polyploidization. Previous studies have shown that separate lineages derived from a resynthesized Brassica napus allopolyploid rapidly evolved heritable differences in flowering time. These early-flowering and late-flowering polyploid lines were expected to be genetically identical because they were derived from a single, chromosome-doubled amphihaploid plant. In this study, we investigated the molecular genetic basis for these flowering time differences. We assessed the diploid B. rapa and B. oleracea parents and the early-and late-flowering B. napus lineages for changes in genome structure, and for changes in transcript levels of four sets of FLOWERING LOCUS C (FLC) genes. No such changes were observed for BnFLC1 , but we detected chromosomal rearrangements (e.g. de novo non-reciprocal transpositions) and changes in transcript level for BnFLC2 and BnFLC3 between the early-and late-flowering B. napus. A chromosomal rearrangement of a genomic segment containing BnFLC3 was responsible for 29% of the phenotypic variation among the B. napus lines. Expression of BnFLC5 was silenced in all polyploids, although no changes in genome structure were detected. An ongoing investigation of 50 identical B. napus allopolyploids may further reveal the dynamics of changes in phenotype, genome and transcriptome at the early stages in polyploid evolution.
The crop species within the genus Brassica have highly replicated genomes. Three base 'diploid' s... more The crop species within the genus Brassica have highly replicated genomes. Three base 'diploid' species, Brassica oleracea , B. nigra and B. rapa , are likely ancient polyploids, and three derived allopolyploid species, B. carinata , B. juncea and B. napus , are created from the interspecific hybridization of these base genomes. The base Brassica genome is thought to have hexaploid ancestry, and both recent and ancient polyploidization events have been proposed to generate a large number of genome rearrangements and novel genetic variation for important traits. Here, we revisit and refine these hypotheses. We have examined the B. oleracea linkage map using the Arabidopsis thaliana genome sequence as a template and suggest that there is strong evidence for genome replication and rearrangement within the base Brassicas, but less evidence for genome triplication. We show that novel phenotypic variation within the base Brassicas can be achieved by replication of a single gene, BrFLC , that acts additively to influence flowering time. Within the derived allopolyploids, intergenomic heterozygosity is associated with higher seed yields. Some studies have reported that de novo genomic variation occurs within derived polyploid genomes, whereas other studies have not detected these changes. We discuss reasons for these different findings. Large translocations and tetrasomic inheritance can explain some but not all genomic changes within the polyploids. Transpositions and other small-scale sequence changes probably also have contributed to genomic novelty. Our results have shown that the Brassica genomes are remarkably plastic, and that polyploidy generates novel genetic variation through gene duplication, intergenomic heterozygosity and perhaps epigenetic change.
Phylogenetic analyses of plastid DNA sequences of ndhF, trnL-F intron and spacer regions, and rpl... more Phylogenetic analyses of plastid DNA sequences of ndhF, trnL-F intron and spacer regions, and rpl16 are presented separately and combined for 41 taxa from all 12 genera of the Themidaceae and for 20 taxa from nine related families in the higher Asparagales. The results from the combined analysis are the most resolved and provide a high level of support for the monophyly of Themidaceae. Within Themidaceae, the Milla complex of Mexico is supported as monophyletic within a paraphyletic Brodiaea complex of western North America. Four major clades are identified in each of the individual and combined analyses: (1) the Milla complex; (2) Brodiaea, Dichelostemma, and Triteleiopsis; (3) Triteleia, Bloomeria, and Muilla clevelandii; and (4) Androstephium and the other species of Muilla. These well-defined clades suggest that morphological characters (e.g., an extended perianth tube) that have been traditionally used to circumscribe the genera within the Brodiaea complex have evolved independently at least twice. In addition, common biogeographic distribution patterns (e.g., Brodiaea and Triteleia having centers of diversity in northern California and the Pacific Northwest) appear to be the result of separate evolutionary radiations.
Homoeologous recombination, aneuploidy, and other genetic changes are common in resynthesized all... 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...
Genome sizes of plants have long piqued the interest of researchers due to the vast differences a... 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...
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally ... 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...
The complex manner in which organisms respond to changes in their gene dosage has long fascinated... 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...
By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ec... more By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level. Using a new network bipartition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure.
Most plants convert sunlight into chemical energy using C3 photosynthesis. However, a modified pa... 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 pa... 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 ... 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...
Polyploidy has long been recognized as a prominent force shaping the evolution of eukaryotes, esp... more Polyploidy has long been recognized as a prominent force shaping the evolution of eukaryotes, especially flowering plants. New phenotypes often arise with polyploid formation and can contribute to the success of polyploids in nature or their selection for use in agriculture. Although the causes of novel variation in polyploids are not well understood, they could involve changes in gene expression through increased variation in dosage-regulated gene expression, altered regulatory interactions, and rapid genetic and epigenetic changes. New research approaches are being used to study these mechanisms and the results should provide a more complete understanding of polyploidy.
Homoeologous regions of Brassica genomes were analyzed at the sequence level. These represent seg... 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...
In the historical context of plant systematics over the last 50 years, systematics is examined in... more In the historical context of plant systematics over the last 50 years, systematics is examined in terms of where it is now, where it is headed, where it should be, and how it should get there. Issues and concerns of the past decades are still with us today. Molecular systematics has become the over-arching field in systematics, but each of eight other areas (genome, chromosomes, morphology and anatomy, development, population biology, speciation, floristics and monography, nomenclature and classification) are evaluated. A revolution in systematics is not necessary for the next 50 years in plant systematics. What is needed is a re-mapping of our discipline that involves four elements for the future growth and health of botanical systematics: plant systematics and its utility, dialogue with other disciplines, multidisciplinary training, and a pluralistic viewpoint.
Allopolyploid formation requires the adaptation of two nuclear genomes within a single cytoplasm,... 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...
Phylogenetic relationships of the five families of the order Commelinales remain an area of deep ... more Phylogenetic relationships of the five families of the order Commelinales remain an area of deep uncertainty in higher-level monocot systematics, despite intensive morphological and anatomical study. To test the monophyly of the Commelinales and the subclass Commelinidae, evaluate their relationships, and analyze evolutionary trends in their morphology, ecology, and biogeography, we conducted parsimony analyses on 95 rbcL sequences representing 17 taxa of Commelinales, 16 taxa of other Commelinidae, and 63 taxa from Arecidae, Liliidae, and Zingiberidae. Commelinales is polyphyletic and Commelinidae paraphyletic, with Eriocaulaceae and Xyridaceae sister to Poaceae and its relatives, Rapateaceae sister to Bromeliaceae and Mayacaceae, and Commelinaceae sister to Philydrales and allies. Thurnia is sister to Prionium at the base of Cyperaceae-Juncaceae; only 1 of Cronquist's multifamily commelinoid orders is diagnosed as monophyletic. We propose a revised Commelinidae, incorporating 4 revised superorders (Bromelianae, Commelinanae, Dasypogonanae, Arecanae) and 10 orders ((Poales, Eriocaulales, Cyperales, Typhales, Bromeliales), (Commelinales, Philydrales, Zingiberales), (Dasypogonales), (Arecales)). Morphological and anatomical characters used to define the original Commelinales and Commelinidae appear to be plesiomorphic or to reflect convergence or recurrent mutation; several characters supporting our revised classification are anatomical traits that seem relatively insulated from environmental selection pressures. The Commelinidae distal to the Arecales arose in South America, with amphiatlantic Bromeliaceae-Mayacaceae-Rapateaceae originating in the Guayana Shield. Ecological diversification involved the repeated invasion of shady, infertile, or arid microsites. The numbers of species in families of the revised Commelinidae are related partly to the extent of adaptive radiation in those families, but seem more strongly related to nonadaptive features promoting speciation, such as restricted seed dispersal (especially in forest interior groups with fleshy fruits), polyploidy, aneuploidy, and apomixis. Species diversity is unrelated to the rate/amount of rbcL sequence evolution. 1999 Academic Press
Naupactus (Curculionidae: Entiminae) is the most speciose weevil genus of the tribe Naupactini. T... more Naupactus (Curculionidae: Entiminae) is the most speciose weevil genus of the tribe Naupactini. The main objective of this work is to recognize species groups within Naupactus and to analyze the relationships between this and other Neotropical genera. For this purpose, we compiled a combined data matrix of 60 terminal units corresponding to 40 species for which we recorded 812 molecular and morphological characters (763 and 49 respectively), which were analyzed by Maximum Parsimony and Bayesian analyses. The single tree obtained from each analysis was rooted with Cyrtomon inhalatus. The species of Naupactus were recovered as different monophyletic groups, some of them closer to other genera of Naupactini (Lanterius, Teratopactus, Pantomorus and Parapantomorus) than to species of the same genus. We conclude that Naupactus is non-monophyletic, even though most species can be recognized based on a particular combination of morphological characters, which are probably symplesiomorphic. To be consistent with the cladistic principles, some genera diversified in marginal areas of the Pantomorus-Naupactus complex should be synonymized with Naupactus; however, these nomenclatural changes may not ensure a generic definition based on synapomorphies. We prefer to be conservative about the current classification until more evidence is available. The only nomenclatural amendments proposed herein are the transference of Naupactus inermis Hustache to Lanterius and of N. setarius to Symmathetes.
Investigating recombination of homoeologous chromosomes in allopolyploid species is central to un... 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...
Background: Evolution of the Brassica species has been recursively affected by polyploidy events,... more Background: Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity. Results: A genome-wide physical map of a rapid-cycling strain of B. oleracea was constructed by integrating highinformation-content fingerprinting (HICF) of Bacterial Artificial Chromosome (BAC) clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences) to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of B. oleracea and Arabidopsis thaliana, a relatively high level of genomic change since their divergence. Comparison of the B. oleracea physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity. Conclusions: A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes. All the physical mapping data is freely shared at a WebFPC site (http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/ WebFPC/; Temporarily password-protected: account: pgml; password: 123qwe123.
Background The Brassica species, related to Arabidopsis thaliana, include an important group of c... 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...
Novel phenotypes often arise in generations immediately following polyploidization. Previous stud... more Novel phenotypes often arise in generations immediately following polyploidization. Previous studies have shown that separate lineages derived from a resynthesized Brassica napus allopolyploid rapidly evolved heritable differences in flowering time. These early-flowering and late-flowering polyploid lines were expected to be genetically identical because they were derived from a single, chromosome-doubled amphihaploid plant. In this study, we investigated the molecular genetic basis for these flowering time differences. We assessed the diploid B. rapa and B. oleracea parents and the early-and late-flowering B. napus lineages for changes in genome structure, and for changes in transcript levels of four sets of FLOWERING LOCUS C (FLC) genes. No such changes were observed for BnFLC1 , but we detected chromosomal rearrangements (e.g. de novo non-reciprocal transpositions) and changes in transcript level for BnFLC2 and BnFLC3 between the early-and late-flowering B. napus. A chromosomal rearrangement of a genomic segment containing BnFLC3 was responsible for 29% of the phenotypic variation among the B. napus lines. Expression of BnFLC5 was silenced in all polyploids, although no changes in genome structure were detected. An ongoing investigation of 50 identical B. napus allopolyploids may further reveal the dynamics of changes in phenotype, genome and transcriptome at the early stages in polyploid evolution.
The crop species within the genus Brassica have highly replicated genomes. Three base 'diploid' s... more The crop species within the genus Brassica have highly replicated genomes. Three base 'diploid' species, Brassica oleracea , B. nigra and B. rapa , are likely ancient polyploids, and three derived allopolyploid species, B. carinata , B. juncea and B. napus , are created from the interspecific hybridization of these base genomes. The base Brassica genome is thought to have hexaploid ancestry, and both recent and ancient polyploidization events have been proposed to generate a large number of genome rearrangements and novel genetic variation for important traits. Here, we revisit and refine these hypotheses. We have examined the B. oleracea linkage map using the Arabidopsis thaliana genome sequence as a template and suggest that there is strong evidence for genome replication and rearrangement within the base Brassicas, but less evidence for genome triplication. We show that novel phenotypic variation within the base Brassicas can be achieved by replication of a single gene, BrFLC , that acts additively to influence flowering time. Within the derived allopolyploids, intergenomic heterozygosity is associated with higher seed yields. Some studies have reported that de novo genomic variation occurs within derived polyploid genomes, whereas other studies have not detected these changes. We discuss reasons for these different findings. Large translocations and tetrasomic inheritance can explain some but not all genomic changes within the polyploids. Transpositions and other small-scale sequence changes probably also have contributed to genomic novelty. Our results have shown that the Brassica genomes are remarkably plastic, and that polyploidy generates novel genetic variation through gene duplication, intergenomic heterozygosity and perhaps epigenetic change.
Phylogenetic analyses of plastid DNA sequences of ndhF, trnL-F intron and spacer regions, and rpl... more Phylogenetic analyses of plastid DNA sequences of ndhF, trnL-F intron and spacer regions, and rpl16 are presented separately and combined for 41 taxa from all 12 genera of the Themidaceae and for 20 taxa from nine related families in the higher Asparagales. The results from the combined analysis are the most resolved and provide a high level of support for the monophyly of Themidaceae. Within Themidaceae, the Milla complex of Mexico is supported as monophyletic within a paraphyletic Brodiaea complex of western North America. Four major clades are identified in each of the individual and combined analyses: (1) the Milla complex; (2) Brodiaea, Dichelostemma, and Triteleiopsis; (3) Triteleia, Bloomeria, and Muilla clevelandii; and (4) Androstephium and the other species of Muilla. These well-defined clades suggest that morphological characters (e.g., an extended perianth tube) that have been traditionally used to circumscribe the genera within the Brodiaea complex have evolved independently at least twice. In addition, common biogeographic distribution patterns (e.g., Brodiaea and Triteleia having centers of diversity in northern California and the Pacific Northwest) appear to be the result of separate evolutionary radiations.
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Papers by J. Chris Pires