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J F Wendel

Publications and source records attributed to J F Wendel.

At least 19 recordsLinked to original sources
PubMed2001

Polyploid formation in cotton is not accompanied by rapid genomic changes.

Recent work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes in the early generations following polyploid synthesis. To address the question of whether rapid genomic changes also occur in allopolyploid cotton (Gossypium) species, amplified fragment length polymorphism (AFLP) analysis was performed to evaluate nine sets of newly synthesized allotetraploid and allohexaploid plants, their parents, and the selfed progeny from colchicine-doubled synthetics. Using both methylation-sensitive and methylation-insensitive enzymes, the extent of fragment additivity in newly combined genomes was ascertained for a total of approximately 22,000 genomic loci. Fragment additivity was observed in nearly all cases, with the few exceptions most likely reflecting parental heterozygosity or experimental error. In addition, genomic Southern analysis on six sets of synthetic allopolyploids probed with five retrotransposons also revealed complete additivity. Because no alterations were observed using methylation-sensitive isoschizomers, epigenetic changes following polyploid synthesis were also minimal. These indications of genomic additivity and epigenetic stasis during allopolyploid formation provide a contrast to recent evidence from several model plant allopolyploids, most notably wheat and Brassica, where rapid and unexplained genomic changes have been reported. In addition, the data contrast with evidence from repetitive DNAs in Gossypium, some of which are subject to non-Mendelian molecular evolutionary phenomena in extant polyploids. These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phenomena, which will vary among both genomic constituents and taxa.

Alleles↗
PubMed2000

Phylogeny, duplication, and intraspecific variation of Adh sequences in New World diploid cottons (Gossypium l., malvaceae).

The 13 "D-genome"cotton species are a monophyletic assemblage of morphologically diverse diploids that inhabit arid to semiarid regions in Mexico, with 1 disjunct species each in Peru and the Galapagos Islands and 1 species whose range extends northward into Arizona. While these species lack commercially significant fiber (i. e., cotton), they are important in that they represent one of the parental genomes of the cultivated tetraploid cottons. To assess phylogenetic relationships among these species, we sequenced and analyzed a region of a nuclear-encoded alcohol dehydrogenase gene (AdhA). Phylogenetic analysis resulted in a topology that is generally consistent with current taxonomic alignment of the species, although the phylogeny based on AdhA sequences conflicts with those inferred from cpDNA and ITS data sets, most notably in the position of the anomalous species Gossypium gossypioides. In one lineage, we detected both gene duplication and sequence polymorphisms that transcend species boundaries; sequences in this lineage formed a monophyletic clade, yet no taxon within the clade contained a monophyletic collection of sequences. Potential explanations for this latter phenomenon, including gene duplication, gene flow, and lineage sorting, are discussed.

Alcohol Dehydrogenase↗
PubMed2000

Ty1-copia-retrotransposon behavior in a polyploid cotton.

Retrotransposons constitute a ubiquitous and dynamic component of plant genomes. Intragenomic and intergenomic comparisons of related genomes offer potential insights into retrotransposon behavior and genomic effects. Here, we have used fluorescent in-situ hybridization to determine the chromosomal distributions of a Ty1-copia-like retrotransposon in the cotton AD-genome tetraploid Gossypium hirsutum and closely related putative A- and D-genome diploid ancestors. Retrotransposon clone A108 hybridized to all G. hirsutum chromosomes, approximately equal in intensity in the A- and D-subgenomes. Similar results were obtained by hybridization of A108 to the A-genome diploid G. arboreum, whereas no signal was detected on chromosomes of the D-genome diploid G. raimondii. The significance and potential causes of these observations are discussed.

Gossypium↗
PubMed2000

Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium).

Nuclear-encoded genes exist in families of various sizes. To further our understanding of the evolutionary dynamics of nuclear gene families we present a characterization of the structure and evolution of the alcohol dehydrogenase (Adh) gene family in diploid and tetraploid members of the cotton genus (Gossypium, Malvaceae). A PCR-based approach was employed to isolate and sequence multiple Adh gene family members, and Southern hybridization analyses were used to document variation in gene copy number. Adh gene copy number varies among Gossypium species, with diploids containing at least seven Adh loci in two primary gene lineages. Allotetraploid Gossypium species are inferred to contain at least 14 loci. Intron lengths vary markedly between loci, and one locus has lost two introns usually found in other plant Adh genes. Multiple examples of apparent gene duplication events were observed and at least one case of pseudogenization and one case of gene elimination were also found. Thus, Adh gene family structure is dynamic within this single plant genus. Evolutionary rate estimates differ between loci and in some cases between organismal lineages at the same locus. We suggest that dynamic fluctuation in copy number will prove common for nuclear genes, and we discuss the implications of this perspective for inferences of orthology and functional evolution.

Alcohol Dehydrogenase↗
PubMed2000

Genome evolution in polyploids.

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

Evolution, Molecular↗
PubMed2000

Retrotransposon activation followed by rapid repression in introgressed rice plants.

Plant retrotransposons are largely inactive during normal development, but may be activated by stresses. Both copia-like and gypsy-like retrotransposons of rice were activated by introgression of DNA from the wild species Zizania latifolia Griseb. The copy number increase was associated with cytosine methylation changes of the elements. Activity of the elements was ephemeral, as evidenced by nearly identical genomic Southern hybridization patterns among randomly chosen individuals both within and between generations for a given line, and the absence of transcripts based on Northern analysis. DNA hypermethylation, internal sequence deletion, and possibly other mechanisms are likely responsible for the rapid element repression. Implications of the retroelement dynamics on plant genome evolution are discussed.

Cytosine↗
PubMed1999

Duplicated genes evolve independently after polyploid formation in cotton.

Of the many processes that generate gene duplications, polyploidy is unique in that entire genomes are duplicated. This process has been important in the evolution of many eukaryotic groups, and it occurs with high frequency in plants. Recent evidence suggests that polyploidization may be accompanied by rapid genomic changes, but the evolutionary fate of discrete loci recently doubled by polyploidy (homoeologues) has not been studied. Here we use locus-specific isolation techniques with comparative mapping to characterize the evolution of homoeologous loci in allopolyploid cotton (Gossypium hirsutum) and in species representing its diploid progenitors. We isolated and sequenced 16 loci from both genomes of the allopolyploid, from both progenitor diploid genomes and appropriate outgroups. Phylogenetic analysis of the resulting 73.5 kb of sequence data demonstrated that for all 16 loci (14.7 kb/genome), the topology expected from organismal history was recovered. In contrast to observations involving repetitive DNAs in cotton, there was no evidence of interaction among duplicated genes in the allopolyploid. Polyploidy was not accompanied by an obvious increase in mutations indicative of pseudogene formation. Additionally, differences in rates of divergence among homoeologues in polyploids and orthologues in diploids were indistinguishable across loci, with significant rate deviation restricted to two putative pseudogenes. Our results indicate that most duplicated genes in allopolyploid cotton evolve independently of each other and at the same rate as those of their diploid progenitors. These indications of genic stasis accompanying polyploidization provide a sharp contrast to recent examples of rapid genomic evolution in allopolyploids.

Biological Evolution↗
PubMed1999

Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.).

Levels of genetic diversity within and among populations and species are shaped by both external (population-level) and internal (genomic and genic) evolutionary forces. To address the effect of internal pressures, we estimated nucleotide diversity for a pair of homoeologous Adh loci in an allotetraploid species, Gossypium hirsutum. These data represent the first such estimates for a pair of homoeologous nuclear loci in plants. Estimates of nucleotide diversity for AdhA in Gossypium are lower than those for any plant nuclear gene yet described. This low diversity appears to reflect primarily a history of repeated, severe genetic bottlenecks associated with both speciation and recent domestication, supplemented by an unusually slow nucleotide substitution rate and an autogamous breeding system. While not statistically supportable, the sum of the observations also suggest differential evolutionary dynamics at each of the homoeologous loci.

Alcohol Dehydrogenase↗
PubMed1998

Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton.

Polyploid formation has played a major role in the evolution of many plant and animal genomes; however, surprisingly little is known regarding the subsequent evolution of DNA sequences that become newly united in a common nucleus. Of particular interest is the repetitive DNA fraction, which accounts for most nuclear DNA in higher plants and animals and which can be remarkably different, even in closely related taxa. In one recently formed polyploid, cotton (Gossypium barbadense L.; AD genome), 83 non-cross-hybridizing DNA clones contain dispersed repeats that are estimated to comprise about 24% of the nuclear DNA. Among these, 64 (77%) are largely restricted to diploid taxa containing the larger A genome and collectively account for about half of the difference in DNA content between Old World (A) and New World (D) diploid ancestors of cultivated AD tetraploid cotton. In tetraploid cotton, FISH analysis showed that some A-genome dispersed repeats appear to have spread to D-genome chromosomes. Such spread may also account for the finding that one, and only one, D-genome diploid cotton, Gossypium gossypioides, contains moderate levels of (otherwise) A-genome-specific repeats in addition to normal levels of D-genome repeats. The discovery of A-genome repeats in G. gossypioides adds genome-wide support to a suggestion previously based on evidence from only a single genetic locus that this species may be either the closest living descendant of the New World cotton ancestor, or an adulterated relic of polyploid formation. Spread of dispersed repeats in the early stages of polyploid formation may provide a tag to identify diploid progenitors of a polyploid. Although most repetitive clones do not correspond to known DNA sequences, 4 correspond to known transposons, most contain internal subrepeats, and at least 12 (including 2 of the possible transposons) hybridize to mRNAs expressed at readily discernible levels in cotton seedlings, implicating transposition as one possible mechanism of spread. Integration of molecular, phylogenetic, and cytogenetic analysis of dispersed repetitive DNA may shed new light on evolution of other polyploid genomes, as well as providing valuable landmarks for many aspects of genome analysis.

Amino Acid Sequence↗
PubMed1997

Bamboozled again! Inadvertent isolation of fungal rDNA sequences from bamboos (Poaceae: Bambusoideae).

Polymerase chain reaction (PCR) amplification of the nuclear internal transcribed spacer (ITS) and 5.8S regions of rDNA from woody bamboos (Bambuseae) led to the recovery of fungal instead of bamboo sequences under a variety of PCR conditions and irrespective of whether the plant DNA was extracted from fresh leaves or silica gel-dried material. Phylogenetic analyses based on the 5.8S sequences indicated that the fungi were most likely basidiomycetes and that none was an ascomycete. A diverse assemblage of nonascomycetous fungi was isolated from different bamboos, and various fungi coexisted in the same host plant. There was no evidence that closely related fungi consistently associate with closely related host bamboos. Phylogenetic analysis based on 5.8S sequences showed that some fungi were in lineages near Volvariella, Lentinula, Peniophora, and Rhizoctonia, but the insufficiency of basidiomycete and zygomycete ITS sequences in sequence data bases precluded more precise fungal identifications. Bamboo ITS regions were amplified only when fresh leaves were surface sterilized before DNA extraction, suggesting that the fungal associates are epiphyllous rather than endophytic. This study highlights the possibility of inadvertent PCR amplification of contaminating DNAs in molecular phylogenetic studies, particularly when using "universal" amplification primers.

Base Sequence↗
PubMed1997

Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae).

We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that are heterogeneity is correlated between loci at synonymous sites. At nonsynonymous sites, the pattern of rate heterogeneity is not correlated between loci, primarily due to an aberrant pattern of rate heterogeneity at nonsynonymous sites of rbcL. We compare patterns of synonymous rate heterogeneity to predictors based on the generation time effect and the speciation rate hypotheses. Although there is some evidence for generation time effects, neither generation time effects nor speciation rates appear to be sufficient to explain patterns of rate heterogeneity in the grass plastid sequences.

Bacterial Proteins↗
PubMed1996

Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons.

5S RNA genes and their nontranscribed spacers are tandemly repeated in plant genomes at one or more chromosomal loci. To facilitate an understanding of the forces that govern 5S rDNA evolution, copy-number estimation and DNA sequencing were conducted for a phylogenetically well-characterized set of 16 diploid species of cotton (Gossypium) and 4 species representing allopolyploid derivatives of the diploids. Copy number varies over twentyfold in the genus, from approximately 1,000 to 20,000 copies/2C genome. When superimposed on the organismal phylogeny, these data reveal examples of both array expansion and contraction. Across species, a mean of 12% of nucleotide positions are polymorphic within individual arrays, for both gene and spacer sequences. This shows, in conjunction with phylogenetic evidence for ancestral polymorphisms that survive speciation events, that intralocus concerted evolutionary forces are relatively weak and that the rate of interrepeat homogenization is approximately equal to the rate of speciation. Evidence presented also shows that duplicated 5S rDNA arrays in allopolyploids have retained their subgenomic identity since polyploid formation, thereby indicating that interlocus concerted evolution has not been an important factor in the evolution of these arrays. A descriptive model, one which incorporates the opposing forces of mutation and homogenization within a selective framework, is outlined to account for the empirical data presented. Weak homogenizing forces allow equivalent levels of sequence polymorphism to accumulate in the 5S gene and spacer sequences, but fixation of mutations is nearly prohibited in the 5S gene. As a consequence, fixed interspecific differences are statistically underrepresented for 5S genes. This result explains the apparent paradox that despite similar levels of gene and spacer diversity, phylogenetic analysis of spacer sequences yields highly resolved trees, whereas analyses based on 5S gene sequences do not.

Base Sequence↗
PubMed1996

Hairpins create minute inversions in non-coding regions of chloroplast DNA.

Minute inversions (4 bp in length), associated with probable hairpin secondary structures, were inferred from comparative analysis of rpl16 intron sequences from the chloroplast genomes of Chusquea species and related bamboos (Poaceae). The inverted sequences, which appear to have arisen independently on several occasions, comprise entire loops of the putative hairpins. The process of inversion seems dependent upon the stem length of the hairpin and its estimated free energy of formation. A similar inversion was uncovered for other plants in a previously published data set for a different non-coding region of the chloroplast genome, suggesting that the inversional process may be a common feature of non-coding DNA evolution. Several implications for phylogenetic analysis are noted.

Base Sequence↗
PubMed1995

Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium).

Polyploidy is a prominent process in plant evolution; yet few data address the question of whether homeologous sequences evolve independently subsequent to polyploidization. We report on ribosomal DNA (rDNA) evolution in five allopolyploid (AD genome) species of cotton (Gossypium) and species representing their diploid progenitors (A genome, D genome). Sequence data from the internal transcribed spacer regions (ITS1 and ITS2) and the 5.8S gene indicate that rDNA arrays are homogeneous, or nearly so, in all diploids and allopolyploids examined. Because these arrays occur at four chromosomal loci in allopolyploid cotton, two in each subgenome, repeats from different arrays must have become homogenized by interlocus concerted evolution. Southern hybridization analysis combined with copy-number estimation demonstrate that this process has gone to completion in the diploids and to completion or near-completion in all allopolyploid species and that it most likely involves the entire rDNA repeat. Phylogenetic analysis demonstrates that interlocus concerted evolution has been bidirectional in allopolyploid species--i.e., rDNA from four polyploid lineages has been homogenized to a D genome repeat type, whereas sequences from Gossypium mustelinum have concerted to an A genome repeat type. Although little is known regarding the functional significance of interlocus concerted evolution of homeologous sequences, this study demonstrates that the process occurs for tandemly repeated sequences in diploid and polyploid plants. That interlocus concerted evolution can occur bidirectionally subsequent to hybidization and polyploidization has significant implications for phylogeny reconstruction, especially when based on rDNA sequences.

Base Sequence↗
PubMed1995

An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression.

The New World allopolyploid (AD-genome) cottons (Gossypium) originated through hybridization of ancestral diploid species that presently have allopatric ranges in Africa-Asia (the A-genome) and the American tropics and subtropics (the D-genome). Phylogenetic analysis of sequence data from the ribosomal DNA internal transcribed spacer region (ITS1, 5.8S rRNA, ITS2) reveals two strongly supported clades, one corresponding to African species and the other containing all American D-genome species except Gossypium gossypioides, which occupies a basal position within the African clade. This placement conflicts with evidence from fertility relationships, morphology, cytogenetics allozymes, and cpDNA restriction site analysis, which specify a sister-species relationship for G. gossypioides and Gossypium raimondii, deeply embedded within the American D-genome clade. Several alternative explanations for this striking incongruence are considered. The most probable involves: (1) an ancient hybridization event, whereby G. gossypioides experienced contact with an A-genome, either at the diploid level or at the triploid level as a consequence of hybridization with a New World allopolyploid and (2) repeated backcrossing of the hybrid into the G. gossypioides lineage, thereby restoring a nearly pure D-genome, but in the process generating a recombinant ribosomal DNA. We suggest that this process may implicate G. gossypioides, rather than G. raimondii, as the closest living descendant of the ancestral D-genome parent of the allopolyploids. In addition, this example of cryptic, intergenomic introgression between species groups now occupying different hemispheres illustrates how ITS data may provide insights into genome composition and evolutionary history, especially when used in the context of a holistic view that encompasses information from a variety of sources.

Africa↗
PubMed1994

A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome.

We employ a detailed restriction fragment length polymorphism (RFLP) map to investigate chromosome organization and evolution in cotton, a disomic polyploid. About 46.2% of nuclear DNA probes detect RFLPs distinguishing Gossypium hirsutum and Gossypium barbadense; and 705 RFLP loci are assembled into 41 linkage groups and 4675 cM. The subgenomic origin (A vs. D) of most, and chromosomal identity of 14 (of 26), linkage groups is shown. The A and D subgenomes show similar recombinational length, suggesting that repetitive DNA in the physically larger A subgenome is recombinationally inert. RFLPs are somewhat more abundant in the D subgenome. Linkage among duplicated RFLPs reveals 11 pairs of homoelogous chromosomal regions-two appear homosequential, most differ by inversions, and at least one differs by a translocation. Most homoeologies involve chromosomes from different subgenomes, putatively reflecting the n = 13 to n = 26 polyploidization event of 1.1-1.9 million years ago. Several observations suggest that another, earlier, polyploidization event spawned n = 13 cottons, at least 25 million years ago. The cotton genome contains about 400-kb DNA per cM, hence map-based gene cloning is feasible. The cotton map affords new opportunities to study chromosome evolution, and to exploit Gossypium genetic resources for improvement of the world's leading natural fiber.

Biological Evolution↗