scholarly journals Genome assembly of primitive cultivated potato Solanum stenotomum provides insights into potato evolution

Author(s):  
Lang Yan ◽  
Yizheng Zhang ◽  
Guangze Cai ◽  
Yuan Qing ◽  
Jiling Song ◽  
...  

Abstract Genetic diversity is the raw material for germplasm enhancement. Landraces and wild species relatives of potato, which contain a rich gene pool of valuable agronomic traits, can provide insights into the genetic diversity behind the adaptability of the common potato. The diploid plant, Solanum stenotomum (Sst), is believed to have an ancestral relationship with modern potato cultivars and be a potential source of resistance against disease. Sequencing of the Sst genome generated an assembly of 852.85 Mb (N50 scaffold size, 3.7 Mb). Pseudomolecule construction anchored 788.75 Mb of the assembly onto 12 pseudochromosomes, with an anchor rate of 92.4%. Genome annotation yielded 41,914 high-confidence protein-coding gene models and comparative analyses with closely related Solanaceae species identified 358 Sst-specific gene families, 885 gene families with expansion along the Sst lineage, and 149 genes experiencing accelerated rates of protein sequence evolution in Sst, the functions of which were mainly associated with defense responses, particularly against bacterial and fungal infection. Insights into the Sst genome and the genomic variation of cultivated potato taxa are valuable in elaborating the impact of potato evolution in early landrace diploid and facilitate modern potato breeding.

2017 ◽  
Author(s):  
Jacob Steenwyk ◽  
Antonis Rokas

AbstractDue to the importance ofSaccharomyces cerevisiaein wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences ofS. cerevisiaewine strains. We found an average of 97.8 CN variable regions (CNVRs) affecting ~4% of the genome per strain. Using two different measures of CN diversity, we found that gene families involved in fermentation-related processes such as copper resistance (CUP), flocculation (FLO), and glucose metabolism (HXT), as well as theSNOgene family whose members are expressed before or during the diauxic shift showed substantial CN diversity across the 132 strains examined. Importantly, these same gene families have been shown, through comparative transcriptomic and functional assays, to be associated with adaptation to the wine fermentation environment. Our results suggest that CN variation is a substantial contributor to the genomic diversity of wine yeast strains and identify several candidate loci whose levels of CN variation may affect the adaptation and performance of wine yeast strains during fermentation.


2018 ◽  
Vol 115 (4) ◽  
pp. 816-821 ◽  
Author(s):  
Benjamin Laenen ◽  
Andrew Tedder ◽  
Michael D. Nowak ◽  
Per Toräng ◽  
Jörg Wunder ◽  
...  

Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina. We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina. These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.


Author(s):  
Solveiga Luguza ◽  
Endijs Bāders ◽  
Pauls Zeltiņš ◽  
Roberts Čakšs ◽  
Dainis Edgars Ruņģis ◽  
...  

INTRODUCTION Norway spruce (Picea abies (L.) Karst.) is a high-yielding commercial tree species grown in the Baltic sea region. It not only ensures timber production, but also provides a notable amount of crown branch biomass and a substantial amount of technically accessible stump biomass for energy. Thus, it has a high potential as a source of renewable materials and energy in the bioeconomy. Recent studies in Latvia have shown no long-term negative consequences to forest ecosystems from whole-tree harvesting. Hence, this management method can be considered sustainable for Norway spruce stands in fertile mineral soils. Not only yield, but also risks need to be considered to ensure financial sustainability, mainly the impact of wind-storms, drought, and pests. A combination of silviculture and genetics (tree breeding) can be used to reduce the probability of damage to Norway spruce stands. The aim of our study was to assess the potential of simultaneously ensuring both genetic gain and diversity in Norway spruce plantations. MATERIALS AND METHODS Data characterizing/showing tree growth – current height, diameter at breast height, survival, as well as radial increment (increment cores) – were obtained from a 50-year-old Norway spruce plantation. Data characterizing genetic diversity were collected from a gene reserve stand (48 trees), Norway spruce seed orchard progenies consisting of 20 clones, as well as 12 pure Norway spruce stands. DNA was extracted and analysed with 6 to 14 nuclear SSR markers. RESULTS No significant differences were observed between the seed orchard progenies, the trees from the gene reserve stand and other Norway spruce stands using the assessed parameters – allelic richness, observed heterozygosity, genetic diversity and relatedness. This indicates that the use of a seed orchard containing a relatively low number of clones as a seed source for plant production and forest regeneration would not have a negative impact on genetic diversity. However, notable gains in productivity can be achieved using selected plant material. At the age of 50 years, phenotypically selected clones in the low-density (5×5m) plantation had a mean yield of 327±42 m3ha-1, significantly exceeding the mean yield (277±56 m3ha-1) observed in Norway spruce stands of the same age and the same site conditions (forest type), while no significant differences were observed compared to the average stand yield at the age of 80 years (347±47 m3ha-1). The target diameter of 31 cm was reached at the age of 42±0.9 years on average, but this varied significantly among clones. CONCLUSION The results demonstrate a notable potential to reduce the rotation period, thereby: a) increasing the availability of raw material for further processing and energy production, and b) reducing financial risks due to lowering the probability that the stand will sustain substantial damage (i.e. wind storm). This gain can be achieved without significantly compromising genetic diversity. Further studies shall address potential changes in genetic diversity at the landscape level over a longer period when using a very limited set of clones. Stands in nature reserves could serve as a basis for comparison in such studies.


2014 ◽  
Vol 281 (1779) ◽  
pp. 20133078 ◽  
Author(s):  
Mark de Bruyn ◽  
Malin L. Pinsky ◽  
Brenda Hall ◽  
Paul Koch ◽  
Carlo Baroni ◽  
...  

Genetic diversity provides the raw material for populations to respond to changing environmental conditions. The evolution of diversity within populations is based on the accumulation of mutations and their retention or loss through selection and genetic drift, while migration can also introduce new variation. However, the extent to which population growth and sustained large population size can lead to rapid and significant increases in diversity has not been widely investigated. Here, we assess this empirically by applying approximate Bayesian computation to a novel ancient DNA dataset that spans the life of a southern elephant seal ( Mirounga leonina ) population, from initial founding approximately 7000 years ago to eventual extinction within the past millennium. We find that rapid population growth and sustained large population size can explain substantial increases in population genetic diversity over a period of several hundred generations, subsequently lost when the population went to extinction. Results suggest that the impact of diversity introduced through migration was relatively minor. We thus demonstrate, by examining genetic diversity across the life of a population, that environmental change could generate the raw material for adaptive evolution over a very short evolutionary time scale through rapid establishment of a large, stable population.


2018 ◽  
Author(s):  
Peipei Wang ◽  
Bethany M. Moore ◽  
Nicholas L. Panchy ◽  
Fanrui Meng ◽  
Melissa D. Lehti-Shiu ◽  
...  

AbstractGene duplication and loss contribute to gene content differences as well as phenotypic divergence across species. However, the extent to which gene content varies among closely related plant species and the factors responsible for such variation remain unclear. Here, we used the Solanaceae family as a model to investigate differences in gene family size and the likely factors contributing to these differences. We found that genes in highly variable families have high turnover rate and tend to be involved in processes that have diverged between Solanaceae species, whereas genes in low-variability families tend to have housekeeping roles. In addition, genes in high-and low-variability gene families tend to be duplicated by tandem and whole genome duplication, respectively. This finding together with the observation that genes duplicated by different mechanisms experience different selection pressures suggests that duplication mechanism impacts gene family turnover. We explored using pseudogene number as a proxy for gene loss but discovered that a substantial number of pseudogenes are actually products of pseudogene duplication, contrary to the expectation that most plant pseudogenes are remnants of once-functional duplicates. Our findings reveal complex relationships between variation in gene family size, gene functions, duplication mechanism, and evolutionary rate. The patterns of lineage-specific gene family expansion within the Solanaceae provide the foundation for a better understanding of the genetic basis underlying phenotypic diversity in this economically important family.


2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Emmanuel A. Lozada-Soto ◽  
Christian Maltecca ◽  
Duc Lu ◽  
Stephen Miller ◽  
John B. Cole ◽  
...  

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.


2021 ◽  
Author(s):  
Nathalie D Lackus ◽  
Axel Schmidt ◽  
Jonathan Gershenzon ◽  
Tobias G Köllner

AbstractBenzenoids (C6–C1 aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C6–C3). The biosynthesis of C6–C1 aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C6–C1 aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal β-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.


Catalysts ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 62
Author(s):  
Won-Yong Jeon ◽  
Seyoung Mun ◽  
Wei Beng Ng ◽  
Keunsoo Kang ◽  
Kyudong Han ◽  
...  

Enzymatic biofuel cells (EBFCs) have excellent potential as components in bioelectronic devices, especially as active biointerfaces to regulate stem cell behavior for regenerative medicine applications. However, it remains unclear to what extent EBFC-generated electrical stimulation can regulate the functional behavior of human adipose-derived mesenchymal stem cells (hAD-MSCs) at the morphological and gene expression levels. Herein, we investigated the effect of EBFC-generated electrical stimulation on hAD-MSC cell morphology and gene expression using next-generation RNA sequencing. We tested three different electrical currents, 127 ± 9, 248 ± 15, and 598 ± 75 nA/cm2, in mesenchymal stem cells. We performed transcriptome profiling to analyze the impact of EBFC-derived electrical current on gene expression using next generation sequencing (NGS). We also observed changes in cytoskeleton arrangement and analyzed gene expression that depends on the electrical stimulation. The electrical stimulation of EBFC changes cell morphology through cytoskeleton re-arrangement. In particular, the results of whole transcriptome NGS showed that specific gene clusters were up- or down-regulated depending on the magnitude of applied electrical current of EBFC. In conclusion, this study demonstrates that EBFC-generated electrical stimulation can influence the morphological and gene expression properties of stem cells; such capabilities can be useful for regenerative medicine applications such as bioelectronic devices.


Foods ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 485
Author(s):  
Vera Schmid ◽  
Antje Trabert ◽  
Judith (Schäfer) Keller ◽  
Mirko Bunzel ◽  
Heike P. Karbstein ◽  
...  

Food by-products can be used as natural and sustainable food ingredients. However, a modification is needed to improve the technofunctional properties according to the specific needs of designated applications. A lab-scale twin-screw extruder was used to process enzymatically treated apple pomace from commercial fruit juice production. To vary the range of the thermomechanical treatment, various screw speeds (200, 600, 1000 min−1), and screw configurations were applied to the raw material. Detailed chemical and functional analyses were performed to develop a comprehensive understanding of the impact of the extrusion processing on apple pomace composition and technofunctional properties as well as structures of individual polymers. Extrusion at moderate thermomechanical conditions increased the water absorption, swelling, and viscosity of the material. An increase in thermomechanical stress resulted in a higher water solubility index, but negatively affected the water absorption index, viscosity, and swelling. Scanning electron microscopy showed an extrusion-processing-related disruption of the cell wall. Dietary fiber analysis revealed an increase of soluble dietary fiber from 12.6 to 17.2 g/100 g dry matter at maximum thermo-mechanical treatment. Dietary fiber polysaccharide analysis demonstrated compositional changes, mainly in the insoluble dietary fiber fraction. In short, pectin polysaccharides seem to be susceptible to thermo-mechanical stress, especially arabinans as neutral side chains of rhamnogalacturonan I.


Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 285
Author(s):  
Cynthia R. Adams ◽  
Vicki S. Blazer ◽  
Jim Sherry ◽  
Robert Scott Cornman ◽  
Luke R. Iwanowicz

Hepatitis B viruses belong to a family of circular, double-stranded DNA viruses that infect a range of organisms, with host responses that vary from mild infection to chronic infection and cancer. The white sucker hepatitis B virus (WSHBV) was first described in the white sucker (Catostomus commersonii), a freshwater teleost, and belongs to the genus Parahepadnavirus. At present, the host range of WSHBV and its impact on fish health are unknown, and neither genetic diversity nor association with fish health have been studied in any parahepadnavirus. Given the relevance of genomic diversity to disease outcome for the orthohepadnaviruses, we sought to characterize genomic variation in WSHBV and determine how it is structured among watersheds. We identified WSHBV-positive white sucker inhabiting tributaries of Lake Michigan, Lake Superior, Lake Erie (USA), and Lake Athabasca (Canada). Copy number in plasma and in liver tissue was estimated via qPCR. Templates from 27 virus-positive fish were amplified and sequenced using a primer-specific, circular long-range amplification method coupled with amplicon sequencing on the Illumina MiSeq. Phylogenetic analysis of the WSHBV genome identified phylogeographical clustering reminiscent of that observed with human hepatitis B virus genotypes. Notably, most non-synonymous substitutions were found to cluster in the pre-S/spacer overlap region, which is relevant for both viral entry and replication. The observed predominance of p1/s3 mutations in this region is indicative of adaptive change in the polymerase open reading frame (ORF), while, at the same time, the surface ORF is under purifying selection. Although the levels of variation we observed do not meet the criteria used to define sub/genotypes of human and avian hepadnaviruses, we identified geographically associated genome variation in the pre-S and spacer domain sufficient to define five WSHBV haplotypes. This study of WSHBV genetic diversity should facilitate the development of molecular markers for future identification of genotypes and provide evidence in future investigations of possible differential disease outcomes.


Sign in / Sign up

Export Citation Format

Share Document