Phylogenetic analysis and molecular evolution of the dormancy associated MADS-box genes from peach

BACKGROUND: Dormancy associated MADS-box (DAM) genes are candidates for the regulation of growth cessation and terminal bud formation in peach. These genes are not expressed in the peach mutant evergrowing, which fails to cease growth and enter dormancy under dormancy-inducing conditions. We analyzed the phylogenetic relationships among and the rates and patterns of molecular evolution within DAM genes in the phylogenetic context of the MADS-box gene family. RESULTS: The peach DAM genes grouped with the SVP/StMADS11 lineage of type II MIKC(C )MADS-box genes. Phylogenetic analyses suggest that the peach SVP/StMADS11-like gene family, which contains significantly more members than annual model plants, expanded through serial tandem gene duplication. We found evidence of strong purifying selection acting to constrain functional divergence among the peach DAM genes and only a single codon, located in the C-terminal region, under significant positive selection. CONCLUSION: Because all DAM genes are expressed in peach and are subjected to strong purifying selection we suggest that the duplicated genes have been maintained by subfunctionalization and/or neofunctionalization. In addition, this pattern of selection suggests that the DAM genes are important for peach growth and development

Building a feral future: Open questions in crop ferality.

The phenomenon of feral crops, that is, free-living populations that have established outside cultivation, is understudied. Some researchers focus on the negative consequences of domestication, whereas others assert that feral populations may serve as useful pools of genetic diversity for future crop improvement. Although research on feral crops and the process of feralization has advanced rapidly in the last two decades, generalizable insights have been limited by a lack of comparative research across crop species and other factors. To improve international coordination of research on this topic, we summarize the current state of feralization research and chart a course for future study by consolidating outstanding questions in the field. These questions, which emerged from the colloquium “Darwins' reversals: What we now know about Feralization and Crop Wild Relatives” at the BOTANY 2021 conference, fall into seven categories that span both basic and applied research: (1) definitions and drivers of ferality, (2) genetic architecture and pathway, (3) evolutionary history and biogeography, (4) agronomy and breeding, (5) fundamental and applied ecology, (6) collecting and conservation, and (7) taxonomy and best practices. These questions serve as a basis for ferality researchers to coordinate research in these areas, potentially resulting in major contributions to food security in the face of climate change

The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: a repetitive path to resistance

Abstract Background The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase ( EPSPS ) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment. To understand the genomic unit and mechanism of EPSPS gene copy number proliferation, we developed and used a bacterial artificial chromosome (BAC) library from a highly resistant biotype to sequence the local genomic landscape flanking the EPSPS gene. Results By sequencing overlapping BACs, a 297\ua0kb sequence was generated, hereafter referred to as the \u201c EPSPS cassette .\u201d This region included several putative genes, dense clusters of tandem and inverted repeats, putative helitron and autonomous replication sequences, and regulatory elements. Whole genome shotgun sequencing (WGS) of two biotypes exhibiting high and no resistance to glyphosate was performed to compare genomic representation across the EPSPS cassette . Mapping of sequences for both biotypes to the reference EPSPS cassette revealed significant differences in upstream and downstream sequences relative to EPSPS with regard to both repetitive units and coding content between these biotypes. The differences in sequence may have resulted from a compounded-building mechanism such as repetitive transpositional events. The association of putative helitron sequences with the cassette suggests a possible amplification and distribution mechanism. Flow cytometry revealed that the EPSPS cassette added measurable genomic content. Conclusions The adoption of glyphosate resistant cropping systems in major crops such as corn, soybean, cotton and canola coupled with excessive use of glyphosate herbicide has led to evolved glyphosate resistance in several important weeds. In Amaranthus palmeri , the amplification of the EPSPS cassette , characterized by a complex array of repetitive elements and putative helitron sequences, suggests an adaptive structural genomic mechanism that drives amplification and distribution around the genome. The added genomic content not found in glyphosate sensitive plants may be driving evolution through genome expansion

Signatures of Demography and Recombination at Coding Genes in Naturally-Distributed Populations of <em>Arabidopsis Lyrata</em> Subsp. <em>Petraea</em>

<div><p>Demography impacts the observed standing level of genetic diversity present in populations. Distinguishing the relative impacts of demography from selection requires a baseline of expressed gene variation in naturally occurring populations. Six nuclear genes were sequenced to estimate the patterns and levels of genetic diversity in natural <i>Arabidopsis lyrata</i> subsp. <i>petraea</i> populations that differ in demographic histories since the Pleistocene. As expected, northern European populations have genetic signatures of a strong population bottleneck likely due to glaciation during the Pleistocene. Levels of diversity in the northern populations are about half of that in central European populations. Bayesian estimates of historical population size changes indicate that central European populations also have signatures of population size change since the last glacial maxima, suggesting that these populations are not as stable as previously thought. Time since divergence amongst northern European populations is higher than amongst central European populations, suggesting that the northern European populations were established before the Pleistocene and survived glaciation in small separated refugia. Estimates of demography based on expressed genes are complementary to estimates based on microsatellites and transposable elements, elucidating temporal shifts in population dynamics and confirming the importance of marker selection for tests of demography.</p> </div

Map of <i>Arabidopsis lyrata</i> subsp. <i>petraea</i> sampling in Europe.

<p>The number of sampled individuals from each population is in parentheses. Exact locations for each of the samples are as follows: Skutustasir (65°34′N, 17°08′W), Sjonaripa (64°02′N, 16°56′W), Spiterstulen (61°38′N, 8°24′E), Stolberg (51°30 N, 10°56′E), Plech (49°38′N, 11°31′E), Neutras (49°32′N, 11°33′E), Haselbrunn (49°47′N, 11°25′E), and Schaerftal (47°55′N, 15°59′E).</p

Population structure as inferred from the best fit number of groupings in STRUCTURE.

<p>Best fit model had K = 6 populations. Each color represents population assignment inferred from best fit STRUCTURE output. Individuals are shown as a separate line in the box of the population in which they were collected as labeled on top.</p

Pairwise inferred population histories from IMa and Arlequin.

*<p>Point estimates from IMa are reported from data compiled from three separate runs. HPD-90 s are given in parentheses.</p>‡<p>Average of the estimates across all 6 loci from Arlequin.</p><p>The numbers of sites that were significant for Ф_ST (first) and for the exact tests of differentiation (second) are given in parentheses.</p

Recombination rate by population.

<p>Recombination events/10 bp is the number of recombination events counted for each gene (from the 4 gamete test) divided by the length of the gene in basepairs and multiplied by 10. These are averaged across all 6 loci. Average 4 N<i>_C</i>/bp across 6 loci is shown by the bar. The dots indicate estimates for each locus.</p

IMa results for inferred population histories.

<p>The current estimated effective population sizes are relative to the width of the box for each population. Times since divergence (in millions of years before present) are indicated by lines connecting boxes. The full black lines indicate the most recent divergence time for each population, while the dotted grey lines indicated less recent divergence times. Insert: Relative migration rates are indicated by the size of arrows. For simplicity only migration rates for the most recent divergence times for each population were included.</p

Estimates of current effective population sizes (N_ef) inferred from the best fit model in IMa.

<p>Point estimates are averages across all pairwise comparisons. The highest and lowest values for 90% of the highest probability densities are given in parentheses.</p