Evolutionary history of LINE-1 in the major clades of placental mammals

BACKGROUND: LINE-1 constitutes an important component of mammalian genomes. It has a dynamic evolutionary history characterized by the rise, fall and replacement of subfamilies. Most data concerning LINE-1 biology and evolution are derived from the human and mouse genomes and are often assumed to hold for all placentals. METHODOLOGY: To examine LINE-1 relationships, sequences from the 3′ region of the reverse transcriptase from 21 species (representing 13 orders across Afrotheria, Xenarthra, Supraprimates and Laurasiatheria) were obtained from whole genome sequence assemblies, or by PCR with degenerate primers. These sequences were aligned and analysed. PRINCIPAL FINDINGS: Our analysis reflects accepted placental relationships suggesting mostly lineage-specific LINE-1 families. The data provide clear support for several clades including Glires, Supraprimates, Laurasiatheria, Boreoeutheria, Xenarthra and Afrotheria. Within the afrotherian LINE-1 (AfroLINE) clade, our tree supports Paenungulata, Afroinsectivora and Afroinsectiphillia. Xenarthran LINE-1 (XenaLINE) falls sister to AfroLINE, providing some support for the Atlantogenata (Xenarthra+Afrotheria) hypothesis. SIGNIFICANCE: LINEs and SINEs make up approximately half of all placental genomes, so understanding their dynamics is an essential aspect of comparative genomics. Importantly, a tree of LINE-1 offers a different view of the root, as long edges (branches) such as that to marsupials are shortened and/or broken up. Additionally, a robust phylogeny of diverse LINE-1 is essential in testing that site-specific LINE-1 insertions, often regarded as homoplasy-free phylogenetic markers, are indeed unique and not convergent

Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies

Background: Extant placental mammals are divided into four major clades (Laurasiatheria, Supraprimates, Xenarthra and Afrotheria). Given that Afrotheria is generally thought to root the eutherian tree in phylogenetic analysis of large nuclear gene data sets, the study of the organization of the genomes of afrotherian species provides new insights into the dynamics of mammalian chromosomal evolution. Here we test if there are chromosomal bands with a high tendency to break and reorganize in Afrotheria, and by analyzing the expression of aphidicolin-induced common fragile sites in three afrotherian species, whether these are coincidental with recognized evolutionary breakpoints. Results: We described 29 fragile sites in the aardvark (OAF) genome, 27 in the golden mole (CAS), and 35 in the elephant-shrew (EED) genome. We show that fragile sites are conserved among afrotherian species and these are correlated with evolutionary breakpoints when compared to the human (HSA) genome. Inddition, by computationally scanning the newly released opossum (Monodelphis domestica) and chicken sequence assemblies for use as outgroups to Placentalia, we validate the HSA 3/21/5 chromosomal synteny as a rare genomic change that defines the monophyly of this ancient African clade of mammals. On the other hand, support for HSA 1/19p, which is also thought to underpin Afrotheria, is currently ambiguous. Conclusion: We provide evidence that (i) the evolutionary breakpoints that characterise human syntenies detected in the basal Afrotheria correspond at the chromosomal band level with fragile sites, (ii) that HSA 3p/21 was in the amniote ancestor (i.e., common to turtles, lepidosaurs, crocodilians, birds and mammals) and was subsequently disrupted in the lineage leading to marsupials. Its expansion to include HSA 5 in Afrotheria is unique and (iii) that its fragmentation to HSA 3p/21 + HSA 5/21 in elephant and manatee was due to a fission within HSA 21 that is probably shared by all Paenungulata

Uniformity in the Wiener-Wintner theorem for nilsequences

We prove a uniform extension of the Wiener-Wintner theorem for nilsequences due to Host and Kra and a nilsequence extension of the topological Wiener-Wintner theorem due to Assani. Our argument is based on (vertical) Fourier analysis and a Sobolev embedding theorem.Comment: v3: 18 p., proof that the cube construction produces compact homogeneous spaces added, measurability issues in the proof of Theorem 1.5 addressed. We thank the anonymous referees for pointing out these gaps in v

Evaluation of Human Papilloma Virus Diagnostic Testing in Oropharyngeal Squamous Cell Carcinoma: Sensitivity, Specificity, and Prognostic Discrimination

Abstract Purpose: Human papillomavirus-16 (HPV16) is the causative agent in a biologically distinct subset of oropharyngeal squamous cell carcinoma (OPSCC) with highly favorable prognosis. In clinical trials, HPV16 status is an essential inclusion or stratification parameter, highlighting the importance of accurate testing. Experimental Design: Fixed and fresh-frozen tissue from 108 OPSCC cases were subject to eight possible assay/assay combinations: p16 immunohistochemistry (p16 IHC); in situ hybridization for high-risk HPV (HR HPV ISH); quantitative PCR (qPCR) for both viral E6 RNA (RNA qPCR) and DNA (DNA qPCR); and combinations of the above. Results: HPV16-positive OPSCC presented in younger patients (mean 7.5 years younger, P = 0.003) who smoked less than HPV-negative patients (P = 0.007). The proportion of HPV16-positive cases increased from 15% to 57% (P = 0.001) between 1988 and 2009. A combination of p16 IHC/DNA qPCR showed acceptable sensitivity (97%) and specificity (94%) compared with the RNA qPCR “gold standard”, as well as being the best discriminator of favorable outcome (overall survival P = 0.002). p16 IHC/HR HPV ISH also had acceptable specificity (90%) but the substantial reduction in its sensitivity (88%) impacted upon its prognostic value (P = 0.02). p16 IHC, HR HPV ISH, or DNA qPCR was not sufficiently specific to recommend in clinical trials when used in isolation. Conclusions: Caution must be exercised in applying HPV16 diagnostic tests because of significant disparities in accuracy and prognostic value in previously published techniques. Clin Cancer Res; 17(19); 6262–71. ©2011 AACR.</jats:p

Is mammalian chromosomal evolution driven by regions of genome fragility?

BACKGROUND: A fundamental question in comparative genomics concerns the identification of mechanisms that underpin chromosomal change. In an attempt to shed light on the dynamics of mammalian genome evolution, we analyzed the distribution of syntenic blocks, evolutionary breakpoint regions, and evolutionary breakpoints taken from public databases available for seven eutherian species (mouse, rat, cattle, dog, pig, cat, and horse) and the chicken, and examined these for correspondence with human fragile sites and tandem repeats. RESULTS: Our results confirm previous investigations that showed the presence of chromosomal regions in the human genome that have been repeatedly used as illustrated by a high breakpoint accumulation in certain chromosomes and chromosomal bands. We show, however, that there is a striking correspondence between fragile site location, the positions of evolutionary breakpoints, and the distribution of tandem repeats throughout the human genome, which similarly reflect a non-uniform pattern of occurrence. CONCLUSION: These observations provide further evidence that certain chromosomal regions in the human genome have been repeatedly used in the evolutionary process. As a consequence, the genome is a composite of fragile regions prone to reorganization that have been conserved in different lineages, and genomic tracts that do not exhibit the same levels of evolutionary plasticity

II. Horticultural performance of ‘Honeycrisp’ grown on a genetically diverse set of rootstocks under Western New York climatic conditions

A field experiment with 31 rootstocks representing a genetically diverse group of rootstocks featuring ‘Honeycrisp’ as the scion was planted in 2010 at Geneva, NY USA. Rootstocks included three from the Malling series (UK), nine from the Budagovsky series (Russia), 16 from the Cornell Geneva series (USA) and three from the Pillnitz series (Germany). Over the first 8 years (2010–2017) we measured final tree size (trunk cross-sectional area: TCA) and cumulative yield. In the last 4 years we measured fruit soluble solids, bitter pit incidence, biennial bearing, and leaf zonal chlorosis. Tree size varied dramatically with the largest trees on B.70-20-20 and smallest trees on B.71-7-22. Setting the most vigorous rootstock at 100% we categorized rootstocks into 5 size categories: sub-dwarfing class (10–25%), dwarfing class (25–35%), semi-dwarfing class (35–50%), semi-vigorous category (50–70%) and vigorous class (70–100%). Cumulative yield varied 8 fold between the highest yielding rootstock (CG.3001) and the lowest yielding rootstock (B.71-7-22). We calculated theoretical yield per ha by multiplying cumulative yield per tree by a theoretical optimal tree density (trees/ha) based on tree size (TCA). The dwarfing rootstocks G.814, G.41TC, G.11 and B.10 had the highest yields per hectare while the most vigorous rootstocks B.70.20.20 and B.71-7-22 were the least productive. Theoretical cumulative yields varied from a high of 400 t/ha to a low of 50 t/ha, an 8-fold difference. Rootstock also influenced the incidence of bitter pit with the lowest levels of bitter pit with the rootstocks B.10, CG.2034, B.71-7-22, G.41N, CG.4003, G.202N, G.214, and Supporter 3. Considering bitter pit, yield, and optimum tree density, the theoretical yield of bitter pit free fruit varied from a high of 340 t/ha to a low of 35 t/ha, almost a 10-fold difference. The dwarfing rootstocks B.10, G.11, G.41TC, G.214 and G.814 had the highest yields per hectare of bitter pit free fruit. Rootstocks B.9 and M.26 had significantly lower cumulative bitter pit free yield/ha. These data indicate that rootstock not only has a large influence on mature tree cumulative yield but also bitter pit incidence which combine to create a large economic impact of rootstock choice on the long-term economic result of an orchard. This leads to the need for “designer rootstocks” which combine the rootstock characteristics needed to maximize the economic potential of each scion cultivar.info:eu-repo/semantics/acceptedVersio

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Natural fruitlet abscission as related to apple tree carbon balance estimated with the MaluSim model

Apple trees produce many more flower clusters than needed for a full crop, but natural early season flower and fruitlet abscission drastically reduce the final fruit number. Natural fruit abscission varies significantly year to year. There have been attempts to try to model apple fruit abscission in the past. However, due to the great complexity of a perennial crop system in a dynamic environment with significant plant manipulations, regulatory processes and controlling environmental variables have been difficult to elucidate. In 1995, a field trial was planted at the New York State Agricultural Experiment Station in Geneva, New York with 3 apple cultivars (‘Delicious’, ‘Gala’, and ‘McIntosh’). Beginning in 2000 and for 18 years thereafter, we recorded the natural whole-season fruit abscission of untreated trees that received no chemical or hand thinning. We also estimated early season patterns of carbohydrate supply-to-demand each year with a carbon balance model. These data were used to correlate tree carbon balance status and other environmental variables with natural fruit abscission responses. In general terms, natural set, defined as final fruit/flower cluster, of ‘Gala’ averaged ˜1 fruit for each flower cluster (fruit set = 0.9), whereas fewer fruits were set on ‘Delicious’ and ‘McIntosh’ (fruit set = 0.7 and 0.6, respectively). Fruit set of ‘Gala’ was less variable than of ‘Delicious’ or ‘McIntosh’, and there was a clear pattern for decreasing fruit set when the number of initial flower clusters per tree increased. Fruit weight was less dependent on fruit number for ‘Delicious’ and ‘McIntosh’ than for ‘Gala’. Multiple regression models indicated that number of flower clusters per tree and average carbohydrate balance between 0–60 degree days (DD) after bloom and 300–360 DD after bloom were the main significant variables that explained 60–80% of the variability in natural fruit set or final fruit number. For ‘Delicious’, temperatures of the previous fall also explained a significant amount of variation in final fruit set and final fruit number. For ‘Gala’, carbon balance from bloom to shortly after petal fall and when fruits were about 18 mm were the two main periods, which were more sensible to carbohydrate deficiency triggering fruit abscission. A later susceptible period was also observed for ‘McIntosh’, suggesting a larger thinning window for this cultivar.info:eu-repo/semantics/acceptedVersio

Modelling physiological and environmental factors regulating relative fruit set and final fruit numbers in apple trees

Chemical thinning of apple (Malus domestica Borkh.) has been practised for 50 years but it remains an unpredictable part of apple production with large variations from year to year and within years. Carbohydrate availability to support young fruitlet growth may play a significant role in apple tree response to chemical thinners, especially when the carbohydrate supply is the limiting factor for fruit growth. To address the carbohydrate component, we have tested the MaluSim model that integrates many environmental and tree physiological factors as a tool to predict chemical thinner response. The model suggests that carbon supply-to-demand variations may explain some of the great variations in thinning spray response. Relative fruit set and final fruit number per tree were affected by the carbohydrate balance within 2 days before the spray and up to 5 days after. There was a period, 15–29 days after bloom that thinners showed higher action. The greater the carbohydrate supply relative to demand, the greater the relative set and the final fruit number. This suggested that carbohydrate supply-demand balance may be a baseline for thinner responses, and that integrative modelling of these balances can be useful in understanding variation in thinning responses. Apple relative fruit set and final fruit number per tree could be modelled relatively well with consideration of initial flower density, the carbohydrate balance model, and cumulative growing degree-days since bloom.info:eu-repo/semantics/acceptedVersio