Molecular evolution at homoeologous loci in allotetraploid cotton (Malvaceae: Gossypium hirsutum L)

Duplicated genes created during polyploid formation (\u27homoeologues\u27) may experience a variety of fates depending upon the evolutionary forces operating on these loci. Homoeologue divergence may be limited if selection operates to maintain duplicate gene function, or divergence may be permitted if selective pressure on a functionally redundant locus is relaxed. In an attempt to determine the fate of duplicate loci in a polyploid genome, I have isolated and described sequence evolution at 15 sets of homoeologous loci from allotetraploid cotton (Gossypium L.) and the corresponding orthologues from its progenitor diploid genomes. Homoeology and orthology relationships of these loci have been demonstrated by in-situ hybridization for the 5S rDNA array, and by comparative linkage mapping for 12 low-copy anonymous loci and two known cellulose synthase genes, CelA1 and CelA2. In combination, these results demonstrate that relaxation of selective pressure (as indicated by an increase in the substitution rate) at duplicate loci subsequent to polyploidization may be minimal across the majority of loci in this duplicated genome. Ten of these loci (which correspond to mapped anonymous PstI-genomic probes) show rate equivalency between polyploid subgenomes and between subgenomes and their progenitor diploid genomes, indicating that selection continues to limit divergence at these loci. In contrast, the remaining five loci (5SrDNA, A1550, A1713, CelA1 and CelA2) show significant rate differences among the genomes tested. Two of these loci (CelA1 and CelA2) are known to be preferentially expressed in developing cotton fiber, and they show significantly elevated substitution rates in the D- and A-subgenome lineages, respectively. In addition, CelA2 from the A-subgenome of G. hirsutum has experienced a marked rate acceleration since polyploidization, and has accumulated a greater than expected number of non-synonymous substitutions without exhibiting the hallmarks of pseudogenization. These results indicate that cellulose synthase A2 may be responding to directional or diversifying selection, perhaps as a consequence of human-mediated selection upon fiber quality attributes

Cryptic Trysts, Genomic Mergers, and Plant Speciation

It has long been recognized that interspecific hybridization is common in plants, enhancing processes of diversification and speciation. With the widespread utilization of molecular tools, interspecific hybridization – as revealed through incongruence among two or more phylogenetic data sets – is now inferred to be even more prevalent than indicated by morphological and cytogenetic evidence. UsingGossypium as an example, we show how multiple molecular markers have implicated a high frequency of historical hybridization between lineages whose modern descendants are strongly isolated by geography and intrinsic genetic barriers. For example, transoceanic dispersal of propagules from Africa to the New World led to the creation of a novel allotetraploid lineage, as well as the introgression of African repetitive elements into a Mexican diploid species. By mechanisms that remain obscure, fully one-quarter of modern Gossypiumspecies appear to have experienced historical interspecific cytoplasmic and possibly nuclear introgression. These remarkable observations of interspecific genetic exchange emerge from a genus for which such contact would appear improbable, implying that historical hybridization is a more creative force than suspected in angiosperm evolution

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

<p>Abstract</p> <p>Background</p> <p>Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels?</p> <p>Results</p> <p>We reconstruct the infrageneric phylogeny of <it>Pinus </it>from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with ≥ 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve <it>Pinus</it>, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (<it>ycf</it>1, <it>ycf</it>2), highlighting their unusual evolutionary properties.</p> <p>Conclusion</p> <p>Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling, such as phylogeographic analyses and species-level DNA barcoding.</p

Use of Nuclear Genes for Phylogeny Reconstruction in Plants

Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic of low-copy nuclear genes, however, often compensates for the experimental effort required to obtain them. In this review, we briefly discuss the strengths and limitations of chloroplast and rDNA sequences, and then focus our attention on the use of low-copy nuclear sequences. Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Challenges intrinsic to the use of low-copy nuclear sequences include distinguishing orthologous loci from divergent paralogous loci in the same gene family, being mindful of the complications arising from concerted evolution or recombination among paralogous sequences, and the presence of intraspecific, intrapopulational and intraindividual polymorphism. Finally, we provide a detailed protocol for the isolation, characterisation and use of low-copy nuclear sequences for phylogenetic studies

Cryptic Repeated Genomic Recombination During Speciation in Gossypium gossypioides

The Mexican cotton Gossypium gossypioides is a perplexing entity, with conflicting morphological, cytogenetic, and molecular evidence of its phylogenetic affinity to other American cottons. We reevaluated the evolutionary history of this enigmatic species using 16.4 kb of DNA sequence. Phylogenetic analyses show that chloroplast DNA (7.3 kb), nuclear ribosomal internal transcribed spacers (ITS; 0.69 kb), and unique nuclear genes (8.4 kb) yield conflicting resolutions for G. gossypioides. Eight low-copy nuclear genes provide a nearly unanimous resolution of G. gossypioides as the basalmost American diploid cotton, whereas cpDNA sequences resolve G. gossypioides deeply nested within the American diploid clade sister to Peruvian G. raimondii, and ITS places G. gossypioides in an African (rather than an American) clade. These data, in conjunction with previous evidence from the repetitive fraction of the genome, implicate a complex history for G. gossypioides possibly involving temporally separated introgression events from genetically divergent cottons that are presently restricted to different hemispheres. Based on repetitive nuclear DNA, it appears that G. gossypioides experienced nuclear introgression from an African species shortly after divergence from the remainder of the American assemblage. More recently, hybridization with a Mexican species may have resulted in cpDNA introgression, and possibly a second round of cryptic nuclear introgression. Gossypium gossypioides provides a striking example of the previously unsuspected chimeric nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events

Genes Duplicated by Polyploidy Show Unequal Contributions to the Transcriptome and Organ-Specific Reciprocal Silencing

Most eukaryotes have genomes that exhibit high levels of gene redundancy, much of which seems to have arisen from one or more cycles of genome doubling. Polyploidy has been particularly prominent during flowering plant evolution, yielding duplicated genes (homoeologs) whose expression may be retained or lost either as an immediate consequence of polyploidization or on an evolutionary timescale. Expression of 40 homoeologous gene pairs was assayed by cDNA-single-stranded conformation polymorphism in natural (1- to 2-million-yr-old) and synthetic tetraploid cotton (Gossypium) to determine whether homoeologous gene pairs are expressed at equal levels after polyploid formation. Silencing or unequal expression of one homoeolog was documented for 10 of 40 genes examined in ovules of Gossypium hirsutum. Assays of homoeolog expression in 10 organs revealed variable expression levels and silencing, depending on the gene and organ examined. Remarkably, silencing and biased expression of some gene pairs are reciprocal and developmentally regulated, with one homoeolog showing silencing in some organs and the other being silenced in other organs, suggesting rapid subfunctionalization. Duplicate gene expression was examined in additional natural polyploids to characterize the pace at which expression alteration evolves. Analysis of a synthetic tetraploid revealed homoeolog expression and silencing patterns that sometimes mirrored those of the natural tetraploid. Both long-term and immediate responses to polyploidization were implicated. Data suggest that some silencing events are epigenetically induced during the allopolyploidization process

Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

<p>Abstract</p> <p>Background</p> <p>Science-based wildlife management relies on genetic information to infer population connectivity and identify conservation units. The most commonly used genetic marker for characterizing animal biodiversity and identifying maternal lineages is the mitochondrial genome. Mitochondrial genotyping figures prominently in conservation and management plans, with much of the attention focused on the non-coding displacement ("D") loop. We used massively parallel multiplexed sequencing to sequence complete mitochondrial genomes from 40 fishers, a threatened carnivore that possesses low mitogenomic diversity. This allowed us to test a key assumption of conservation genetics, specifically, that the D-loop accurately reflects genealogical relationships and variation of the larger mitochondrial genome.</p> <p>Results</p> <p>Overall mitogenomic divergence in fishers is exceedingly low, with 66 segregating sites and an average pairwise distance between genomes of 0.00088 across their aligned length (16,290 bp). Estimates of variation and genealogical relationships from the displacement (<it>D</it>) loop region (299 bp) are contradicted by the complete mitochondrial genome, as well as the protein coding fraction of the mitochondrial genome. The sources of this contradiction trace primarily to the near-absence of mutations marking the D-loop region of one of the most divergent lineages, and secondarily to independent (recurrent) mutations at two nucleotide position in the D-loop amplicon.</p> <p>Conclusions</p> <p>Our study has two important implications. First, inferred genealogical reconstructions based on the fisher D-loop region contradict inferences based on the entire mitogenome to the point that the populations of greatest conservation concern cannot be accurately resolved. Whole-genome analysis identifies Californian haplotypes from the northern-most populations as highly distinctive, with a significant excess of amino acid changes that may be indicative of molecular adaptation; D-loop sequences fail to identify this unique mitochondrial lineage. Second, the impact of recurrent mutation appears most acute in closely related haplotypes, due to the low level of evolutionary signal (unique mutations that mark lineages) relative to evolutionary noise (recurrent, shared mutation in unrelated haplotypes). For wildlife managers, this means that the populations of greatest conservation concern may be at the highest risk of being misidentified by D-loop haplotyping. This message is timely because it highlights the new opportunities for basing conservation decisions on more accurate genetic information.</p

Allozyme Variation in Domesticated Annual Sunflower and Its Wild Relatives

The annual sunflower (Helianthus annuus L.) is a morphologically and genetically variable species composed of wild, weedy, and domesticated forms that are used for ornament, oilseed, and edible seeds. In this study, we evaluated genetic variation in 146 germplasm accessions of wild and domesticated sunflowers using allozyme analysis. Results from this survey showed that wild sunflower exhibits geographically structured genetic variation, as samples from the Great Plains region of the central United States were genetically divergent from accessions from California and the southwestern United States. Sunflower populations from the Great Plains harbored greater allelic diversity than did wild sunflower from the western United States. Comparison of genetic variability in wild and domesticated sunflower by principal coordinate analysis showed these groups to be genetically divergent, in large part due to differences in the frequency of common alleles. Neighbor-Joining analyses of domesticated H. annuus, wild H. annuus and two closely related wild species (H. argophyllus T. & G. and H. petiolaris Nutt.) showed that domesticated sunflowers form a genetically coherent group and that wild sunflowers from the Great Plains may include the most likely progenitor of domesticated sunflowers