Fraction Of Genome Research Articles

On the diversity and origin of the barley complex agriocrithon inferred by iPBS transposon markers

The six-rowed barley with brittle rachis Hordeum agriocrithon A.E. Aberg is a diverse taxon connected with the evolution and domestication processes in the genus Hordeum. However, the origin and patterns of taxonomic divergence of this barley type is still hotly disputed. Here we utilized inter-primer binding site (iPBS) retrotransposon marker analysis to assess the genetic diversity of the complex taxonomic group H. agriocrithon in reference to the other two main barley taxa H. spontaneum K. Koch and H. vulgare L.. Based on selected iPBS primers, we demonstrated that the long-term process of natural evolution and human-driven domestication have influenced the dynamics of the TE fraction of the barley genome. iPBS markers reliably differentiated at molecular level the three main Hordeum taxa but also revealed genetic and phenotypic diversity patterns at within taxon level. Although H. agriocrithon can be considered as an autochthonous species due to its genetic divergence from H. spontaneum and H. vulgare, our results have shown that most of representatives of this taxon are of hybrid origin and hybridization events have shaped its highly heterogeneous genetic structure. Furthermore, our results strongly support the notion that H. spontaneum accessions are ancestors of the H. agriocrithon subgroup paradoxon and that the Caspian sea region is the likely place of initial cultivation and domestication of the six-rowed barley.

A hidden human proteome encoded by 'non-coding' genes.

It has been a long debate whether the 98% ‘non-coding’ fraction of human genome can encode functional proteins besides short peptides. With full-length translating mRNA sequencing and ribosome profiling, we found that up to 3330 long non-coding RNAs (lncRNAs) were bound to ribosomes with active translation elongation. With shotgun proteomics, 308 lncRNA-encoded new proteins were detected. A total of 207 unique peptides of these new proteins were verified by multiple reaction monitoring (MRM) and/or parallel reaction monitoring (PRM); and 10 new proteins were verified by immunoblotting. We found that these new proteins deviated from the canonical proteins with various physical and chemical properties, and emerged mostly in primates during evolution. We further deduced the protein functions by the assays of translation efficiency, RNA folding and intracellular localizations. As the new protein UBAP1-AST6 is localized in the nucleoli and is preferentially expressed by lung cancer cell lines, we biologically verified that it has a function associated with cell proliferation. In sum, we experimentally evidenced a hidden human functional proteome encoded by purported lncRNAs, suggesting a resource for annotating new human proteins.

The Landscape of Persistent Viral Genomes in ART-Treated SIV, SHIV, and HIV-2 Infections

Evaluation of HIV cure strategies is complicated by defective proviruses that persist in ART-treated patients but are irrelevant to cure. Non-human primates (NHP) are essential for testing cure strategies.However, the persisting proviral landscape in ART-treated NHPs is uncharacterized. Here, we describe viral genomes persisting in ART-treated, simian immunodeficiency virus (SIV)-infected NHPs, simian-human immunodeficiency virus (SHIV)-infected NHPs, and humans infected with HIV-2, an SIV-related virus. The landscapes of persisting SIV, SHIV, and HIV-2 genomes are also dominated by defective sequences. However, there was a significantly higher fraction of intact SIV proviral genomes compared to ART-treated HIV-1 or HIV-2 infected humans. Compared to humans with HIV-1, SIV-infected NHPs had more hypermutated genomes, a relative paucity of clonal SIV sequences, and a lower frequency of deleted genomes. Finally, we report an assay for measuring intact SIV genomes which may have value in cure research.

Abstract 2736: A molecular and histopathologic map of cancer metastasis

Abstract Metastatic disease is responsible for the vast majority of cancer-related deaths. Patterns of metastatic spread and colonization are, however, not random: routes of metastatic dissemination are cancer-type specific, and different cancer types exhibit varying levels of affinity for specific organs as metastatic target sites. We analyzed a cohort of more than 30,000 patients that were treated at Memorial Sloan Kettering Cancer Center (MSK) and had their tumors sequenced using the clinical MSK-IMPACT test, a targeted next-generation sequencing assay that identifies mutations, copy number changes and structural rearrangements in 468 genes. By querying the electronic medical record, we catalogued all metastatic events in the clinical history of these patients and mapped them to a set of 32 tissue sites. The primary diagnoses spanned 30 different cancer types, which were further stratified into >50 relevant molecular subtypes, based on a combination of molecular and histopathological features. Observed patterns of metastatic dissemination were cancer type specific and, in some cases, exhibited strong differences across molecular subtypes of the same cancer type. For example, HER2+ subtypes of breast cancer exhibited increased rates of brain (34% vs. 18%, p<0.0001) and lung (31% vs. 19%, p=0.006) metastasis when compared to HER2- subtypes. The median number of organs affected by metastatic disease per patient was 4 (range 1-14). The number of affected organs exhibited a strong positive correlation with the overall level of aneuploidy, as measured by the total fraction of genome altered by copy number changes (P<0.0001, Spearman correlation), but not with overall mutational burden. We identified genomic alterations that were significantly enriched in tumors from patients with metastasis to specific organs in a cancer-type dependent manner. For example, 244/556 (44%) of lung adenocarcinoma patients with EGFR amplification or activating mutations presented bone metastasis at some point of their clinical history, as opposed to only 400/1,124 (36%) of EGFR wild type patients (p=0.001, Fisher’s exact test). In the case of HR+/ER- breast adenocarcinoma patients, bone metastases were reported in 22/30 (73%) of patients with NF1 inactivated tumors, as opposed to only 330/745 (44%) of patients with NF1 wild-type (p=0.002, Fisher’s exact test). We present the first pan-cancer study that combines molecular and histopathological features to draw a comprehensive atlas of tumor metastasis. Our results provide novel insights into the biology of metastatic tumors and can have a direct impact on patient management and care by optimizing the use and frequency of specific imaging studies for metastasis surveillance. Citation Format: Francisco Sanchez-Vega, Christopher Fong, Walid Chatila, Philip Jonsson, Alexander V. Penson, Renzo G. DiNatale, Michael F. Berger, Ahmet Zehir, Ed Reznik, Jianjiong Gao, Karuna Ganesh, Barry S. Taylor, Nikolaus Schultz. A molecular and histopathologic map of cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2736.

Abstract 2534: A comparative analysis of fraction genome altered vs tumor mutational count in prostate cancer

Abstract Prostate cancer is the second leading cause of cancer related death among men in the United States. Although 5 new life-prolonging agents have been FDA-approved for castration resistant prostate cancer in the past 8 years, drug resistance limits the durability of responses to these agents for most patients. We hypothesized that biomarkers of genomic alterations, defined as fraction genome altered (% of copy number altered chromosome regions out of measured regions) and mutational count (number of mutational events per cases), were prognostic biomarkers which might provide insights into resistance mechanisms. We used The Cancer Genome Atlas (TCGA; n= 490 primary prostate cancer) dataset to analyze fraction of genome altered and tumor mutational count in prostate tumors. Patients whose primary prostate cancer harbored a high frequency of fraction genome altered exhibited significant disease progression in TCGA cohort . In contrast, we did not observe a significant association between high tumor mutational count and disease progression. Fraction genome altered was more significantly associated with Gleason grade compare to tumor mutation count. Interestingly, our preliminary observation showed that primary prostate cancer patients who harbor high fraction genome altered (>6%), but low tumor mutational count (<30/cases) exhibited shorter disease-free survival, indicating that those primary prostate cancer patients who harbor high fraction genome altered but low mutational count may have more aggressive prostate cancer. We have also developed a transcriptional signature which is associated with high fraction genome altered. . A detailed understanding of these molecular features will help us to design appropriate therapeutic approaches for different subsets of the disease. We hypothesize that cases with a high fraction of genome altered are associated with aggressive disease and those with lower mutational count may be associated with a diminished immunoresponsiveness. Tumor mutational count and fraction genome alteration in various stages TCGA prostate cancerDisease Status (Gleason unadjusted)p valueGleasonp value (trend)Disease FreeRecurred/ Progressed6 (n=45)7 (n=244)>=8 (n=198)Fraction Genome Altered (Mean + SEM)0.08248 ± 0.00490.1254 ± 0.01120.00030.02504 ±0.00370.05985 ± 0.00390.1425 ± 0.0087< 2.2e-16Mutational Count (Mean + SEM)35.05 ± 1.35439.88 ± 2.6550.394429.42 ± 1.749,34.69 ± 0.9089,38.58 ± 1.272,=9.971e-05 (7 vs >=8; p value 0.0445) Citation Format: Goutam Chakraborty, Mohammad Atiq, Subhiksha Nandakumar, Ying Z. Mazzu, Joshua Armenia, Yuki Yoshikawa, Nabeela Khan, Gwo-Shu M. Lee, Lorelei Mucci, Philip W. Kantoff. A comparative analysis of fraction genome altered vs tumor mutational count in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2534.

Isolation and characterisation of Ty1-copia retrotransposons from Pongamia pinnata

This manuscript mainly deals about the diversity and transcriptional activity of Ty1-copia in Pongamia genome. Pongamia pinnata, a leguminous tree, is popularly known for its biodiesel and medicinal application. However, the structure and the composition of Pongamia nuclear genome are largely unknown. Ty1-copia elements occupy a significant fraction of the plant genome and are responsible for sequence organisation. Here, we have isolated the reverse transcriptase (RT) and RNase H domain of Ty1-copia from Pongamia. In total, 28 Ty1-copia RT sequences were isolated with high levels of sequence heterogeneity. Besides this, the Ty1-copia like elements were also identified in the mitochondrial genome and in the transcriptome library. The analysis revealed that transcriptional activity of Ty1-copia element exists in leaf, root, and seed of salt-stressed and control plants. Dot blot hybridisation reveals that Ty1-copia like retrotransposons occupy around 8.5% of the haploid genome of Pongamia and the phylogenetic study categorised this class of retrotransposons into seven different lineages. These results are useful in understanding the diversity of Ty1-copia lineages and their transcriptional activity present in different tissues of Pongamia.

Overexpression of an evolutionarily conserved drought-responsive sugarcane gene enhances salinity and drought resilience

Background and AimsImproving drought adaptation is more pressing for crops such as sugarcane, rice, wheat and maize, given the high dependence of these crops on irrigation. One option for enhancing adaptation to water limitation in plants is by transgenic approaches. An increasing number of genes that are associated with mechanisms used by plants to cope with water scarcity have been discovered. Genes encoding proteins with unknown functions comprise a relevant fraction of the genes that are modulated by drought. We characterized a gene in response to environmental stresses to gain insight into the unknown fraction of the sugarcane genome. Scdr2 (Sugarcane drought-responsive 2) encodes a small protein and shares highly conserved sequences within monocots, dicots, algae and fungi.MethodsPlants overexpressing the Scdr2 sugarcane gene were examined in response to salinity and drought. Measurements of the gas exchange parameters, germination rate, water content, dry mass and oxidative damage were performed. Seeds as well as juvenile plants were used to explore the resilience level of the transgenic plants when compared with wild-type plants.Key ResultsOverexpression of Scdr2 enhanced germination rates in tobacco seeds under drought and salinity conditions. Juvenile transgenic plants overexpressing Scdr2 and subjected to drought and salinity stresses showed higher photosynthesis levels, internal CO2 concentration and stomatal conductance, reduced accumulation of hydrogen peroxide in the leaves, no penalty for photosystem II and faster recovery after submission to both stress conditions. Respiration was not strongly affected by both stresses in the Scdr2 transgenic plants, whereas wild-type plants exhibited increased respiration rates.Conclusions Scdr2 is involved in the response mechanism to abiotic stresses. Higher levels of Scdr2 enhanced resilience to salinity and drought, and this protection correlated with reduced oxidative damage. Scdr2 confers, at the physiological level, advantages to climate limitations. Therefore, Scdr2 is a potential target for improving sugarcane resilience to abiotic stress.

Molecular correlates of PD-L1 expression in patients with non-small cell lung cancer.

9018 Background: PD-L1 expression is the only FDA-approved predictive biomarker for patients with NSCLC treated with immune checkpoint inhibitors. The impact of tumor molecular profiling on tumor PD-L1 expression is not known. We hypothesized that somatic mutations and copy number alterations may be associated with distinct patterns of PD-L1 expression in patients with NSCLC. Methods: We examined patients with NSCLC in whom PD-L1 testing and targeted next-generation sequencing (MSK-IMPACT) were performed on the same tissue sample. PD-L1 expression was determined by IHC using the E1L3N antibody clone and categorized as PD-L1 high (≥ 50%), intermediate (1-49%), or negative ( < 1%) expression. The association of PD-L1 with individual genes, pathways, tumor mutation burden, whole genome duplication (WGD), and aneuploidy (fraction of genome altered (FGA)) were evaluated. P-values < 0.05 and q-values < 0.15 were considered significant for individual genes. Results: 1023 patients with NSCLC had PD-L1 testing and MSK-IMPACT performed on the same tissue sample, 18% (n = 180) had high, 21% (n = 218) had intermediate, and 61% (n = 625) had negative PD-L1 expression. High PD-L1 expression was significantly enriched in metastatic vs primary lesions (p < 0.001). There was a minor correlation between PD-L1 and TMB (spearman rho = 0.195) and PD-L1 and FGA (spearman rho = 0.11). Similar rates of WGD were found among patients with high, intermediate, and negative PD-L1 expression (p = 0.38). Mutations in KRAS and TERT were significantly enriched in PD-L1 high compared to other groups (p = 0.001, q = 0.14; p < 0.001, q = 0.003). By contrast, mutations in EGFR and STK11 were associated with PD-L1 negativity (p < 0.001, q = 0.001; p = 0.001, q = 0.14). Pathway analysis showed DNA repair (p < 0.001), TP53 (p < 0.001), and SWI/SNF (p = 0.04) pathways significantly associated with PD-L1 high compared to PD-L1 negative expression. Conclusions: The genetic features of NSCLC are associated with distinct patterns of PD-L1 expression. This data may provide insight to how the molecular phenotype can interact with the immunologic phenotype of tumors.

MiStImm: an agent-based simulation tool to study the self-nonself discrimination of the adaptive immune response

BackgroundThere is an increasing need for complex computational models to perform in silico experiments as an adjunct to in vitro and in vivo experiments in immunology. We introduce Microscopic Stochastic Immune System Simulator (MiStImm), an agent-based simulation tool, that is designed to study the self-nonself discrimination of the adaptive immune system. MiStImm can simulate some components of the humoral adaptive immune response, including T cells, B cells, antibodies, danger signals, interleukins, self cells, foreign antigens, and the interactions among them. The simulation starts after conception and progresses step by step (in time) driven by random simulation events. We also have provided tools to visualize and analyze the output of the simulation program.ResultsAs the first application of MiStImm, we simulated two different immune models, and then we compared performances of them in the mean of self-nonself discrimination. The first model is a so-called conventional immune model, and the second model is based on our earlier T-cell model, called “one-signal model”, which is developed to resolve three important paradoxes of immunology. Our new T-cell model postulates that a dynamic steady state coupled system is formed through low-affinity complementary TCR–MHC interactions between T cells and host cells. The new model implies that a significant fraction of the naive polyclonal T cells is recruited into the first line of defense against an infection. Simulation experiments using MiStImm have shown that the computational realization of the new model shows real patterns. For example, the new model develops immune memory and it does not develop autoimmune reaction despite the hypothesized, enhanced TCR–MHC interaction between T cells and self cells. Simulations also demonstrated that our new model gives better results to overcome a critical primary infection answering the paradox “how can a tiny fraction of human genome effectively compete with a vastly larger pool of mutating pathogen DNA?”ConclusionThe outcomes of our in silico experiments, presented here, are supported by numerous clinical trial observations from the field of immunotherapy. We hope that our results will encourage investigations to make in vitro and in vivo experiments clarifying questions about self-nonself discrimination of the adaptive immune system. We also hope that MiStImm or some concept in it will be useful to other researchers who want to implement or compare other immune models.

Inherited allelic variants and novel karyotype changes influence fertility and genome stability in Brassica allohexaploids.

Synthetic allohexaploid Brassica hybrids (2n=AABBCC) do not exist naturally, but can be synthesized by crosses between diploid and/or allotetraploid Brassica species. Using these hybrids, we aimed to identify how novel allohexaploids restore fertility and normal meiosis after formation. Chromosome inheritance, genome structure, fertility and meiotic behaviour were assessed in three segregating allohexaploid populations derived from the cross (B.napus×B.carinata)×B.juncea using a combination of molecular marker genotyping, phenotyping and cytogenetics. Plants with unbalanced A-C translocations in one direction (where a C-genome chromosome fragment replaces an A-genome fragment) but not the other (where an A-genome fragment replaces a C-genome fragment) showed significantly reduced fertility across all populations. Genomic regions associated with fertility contained several meiosis genes with putatively causal mutations inherited from the parents (copies of SCC2 in the A genome, PAIR1/PRD3, PRD1 and ATK1/KATA/KIN14a in the B genome, and MSH2 and SMC1/TITAN8 in the C genome). Reduced seed fertility associated with the loss of chromosome fragments from only one subgenome following homoeologous exchanges could comprise a mechanism for biased genome fractionation in allopolyploids. Pre-existing meiosis gene variants present in allotetraploid parents may help to stabilize meiosis in novel allohexaploids.

Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae).

Advances in high-throughput sequencing have promoted the collection of reference genomes and genome-wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single-nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e., presence/absence of TE insertions at specific loci). We identified 291,396 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic diversity and divergence across populations. Few SNPs were shared among populations and overall showed high population-specific variation, whereas most polymorphic TEs segregated among populations. The genomic context of these two classes of variants further highlighted candidate adaptive loci having a putative impact on functional genes. In particular, 4.96% of the SNPs were identified as nonsynonymous or affecting start/stop codons. In contrast, 43% of the polymorphic TEs were present next to Arabis genes enriched in functional categories related to the regulation of reproduction and responses to biotic as well as abiotic stresses. This unprecedented data set, mapping variation gained from SNPs and complementary polymorphic TEs within and among populations, will serve as a rich resource for addressing microevolutionary processes shaping genome variation.

Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.

In metagenomic studies of microbial communities, the short reads come from mixtures of genomes. Read assembly is usually an essential first step for the follow-up studies in metagenomic research. Understanding the power and limitations of various read assembly programs in practice is important for researchers to choose which programs to use in their investigations. Many studies evaluating different assembly programs used either simulated metagenomes or real metagenomes with unknown genome compositions. However, the simulated datasets may not reflect the real complexities of metagenomic samples and the estimated assembly accuracy could be misleading due to the unknown genomes in real metagenomes. Therefore, hybrid strategies are required to evaluate the various read assemblers for metagenomic studies. In this paper, we benchmark the metagenomic read assemblers by mixing reads from real metagenomic datasets with reads from known genomes and evaluating the integrity, contiguity and accuracy of the assembly using the reads from the known genomes. We selected four advanced metagenome assemblers, MEGAHIT, MetaSPAdes, IDBA-UD and Faucet, for evaluation. We showed the strengths and weaknesses of these assemblers in terms of integrity, contiguity and accuracy for different variables, including the genetic difference of the real genomes with the genome sequences in the real metagenomic datasets and the sequencing depth of the simulated datasets. Overall, MetaSPAdes performs best in terms of integrity and continuity at the species-level, followed by MEGAHIT. Faucet performs best in terms of accuracy at the cost of worst integrity and continuity, especially at low sequencing depth. MEGAHIT has the highest genome fractions at the strain-level and MetaSPAdes has the overall best performance at the strain-level. MEGAHIT is the most efficient in our experiments. Availability: The source code is available at https://github.com/ziyewang/MetaAssemblyEval.

Natural History of a Satellite DNA Family: From the Ancestral Genome Component to Species-Specific Sequences, Concerted and Non-Concerted Evolution.

Satellite DNA (satDNA) is the most variable fraction of the eukaryotic genome. Related species share a common ancestral satDNA library and changing of any library component in a particular lineage results in interspecific differences. Although the general developmental trend is clear, our knowledge of the origin and dynamics of satDNAs is still fragmentary. Here, we explore whole genome shotgun Illumina reads using the RepeatExplorer (RE) pipeline to infer satDNA family life stories in the genomes of Chenopodium species. The seven diploids studied represent separate lineages and provide an example of a species complex typical for angiosperms. Application of the RE pipeline allowed by similarity searches a determination of the satDNA family with a basic monomer of ~40 bp and to trace its transformation from the reconstructed ancestral to the species-specific sequences. As a result, three types of satDNA family evolutionary development were distinguished: (i) concerted evolution with mutation and recombination events; (ii) concerted evolution with a trend toward increased complexity and length of the satellite monomer; and (iii) non-concerted evolution, with low levels of homogenization and multidirectional trends. The third type is an example of entire repeatome transformation, thus producing a novel set of satDNA families, and genomes showing non-concerted evolution are proposed as a significant source for genomic diversity.

Unbiased subgenome evolution following a recent whole-genome duplication in pear (Pyrus bretschneideri Rehd.)

Genome fractionation (also known as diploidization) frequently occurs following paleopolyploidization events. Biased fractionation between subgenomes has been found in some paleo-allopolyploids, while this phenomenon is absent in paleo-autopolyploids. Pear (Pyrus bretschneideri Rehd.) experienced a recent whole-genome duplication (WGD, ~30 million years ago); however, the evolutionary fate of the two subgenomes derived from this WGD event is not clear. In this study, we identified the two paleo-subgenomes in pear using peach (Prunus persica) as an outgroup and investigated differences in the gene loss rate, evolutionary rate, gene expression level, and DNA methylation level between these two subgenomes. Fractionation bias was not found between the two pear subgenomes, which evolved at similar evolutionary rates. The DNA methylation level of the two subgenomes showed little bias, and we found no expression dominance between the subgenomes. However, we found that singleton genes and homeologous genes within each subgenome showed divergent evolutionary patterns of selective constraints, expression and epigenetic modification. These results provide insights into subgenome evolution following paleopolyploidization in pear.

Physical principles of retroviral integration in the human genome

Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integration as stochastic and quasi-equilibrium topological reconnections between polymers. We discover that physical effects, such as DNA accessibility and elasticity, play important and universal roles in this process. Our simulations predict that integration is favoured within nucleosomal and flexible DNA, in line with experiments, and that these biases arise due to competing energy barriers associated with DNA deformations. By considering a long chromosomal region in human T-cells during interphase, we discover that at these larger scales integration sites are predominantly determined by chromatin accessibility. Finally, we propose and solve a reaction-diffusion problem that recapitulates the distribution of HIV hot-spots within T-cells. With few generic assumptions, our model can rationalise experimental observations and identifies previously unappreciated physical contributions to retroviral integration site selection.

Characterization of repeated DNA sequences in genomes of blue-flowered flax

BackgroundMembers of different sections of the genus Linum are characterized by wide variability in size, morphology and number of chromosomes in karyotypes. Since such variability is determined mainly by the amount and composition of repeated sequences, we conducted a comparative study of the repeatomes of species from four sections forming a clade of blue-flowered flax. Based on the results of high-throughput genome sequencing performed in this study as well as available WGS data, bioinformatic analyses of repeated sequences from 12 flax samples were carried out using a graph-based clustering method.ResultsIt was found that the genomes of closely related species, which have a similar karyotype structure, are also similar in the repeatome composition. In contrast, the repeatomes of karyologically distinct species differed significantly, and no similar tandem-organized repeats have been identified in their genomes. At the same time, many common mobile element families have been identified in genomes of all species, among them, Athila Ty3/gypsy LTR retrotransposon was the most abundant. The 30-chromosome members of the sect. Linum (including the cultivated species L. usitatissimum) differed significantly from other studied species by a great number of satellite DNA families as well as their relative content in genomes.ConclusionsThe evolution of studied flax species was accompanied by waves of amplification of satellite DNAs and LTR retrotransposons. The observed inverse correlation between the total contents of dispersed repeats and satellite DNAs allowed to suggest a relationship between both classes of repeating sequences. Significant interspecific differences in satellite DNA sets indicated a high rate of evolution of this genomic fraction. The phylogenetic relationships between the investigated flax species, obtained by comparison of the repeatomes, agreed with the results of previous molecular phylogenetic studies.

The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)

BackgroundRepetitive sequences, including transposable elements (TEs) and satellite DNAs, occupy a considerable portion of plant genomes. Analysis of the repeat fraction benefits the understanding of genome structure and evolution. Spinach (Spinacia oleracea L.), an important vegetable crop, is also a model dioecious plant species for studying sex determination and sex chromosome evolution. However, the repetitive sequences of the spinach genome have not been fully investigated.ResultsWe extensively analyzed the repetitive components of draft spinach genome, especially TEs and satellites, by different strategies. A total of 16,002 full-length TEs were identified. Among the most abundant long terminal repeat (LTR) retrotransposons (REs), Copia elements were overrepresented compared with Gypsy ones. Angela was the most dominating Copia lineage; Ogre/Tat was the most abundant Gypsy lineage. The mean insertion age of LTR-REs was 1.42 million years; approximately 83.7% of these elements were retrotransposed during the last two million years. RepeatMasker totally masked about 64.05% of the spinach genome, with LTR-REs, non-LTR-REs, and DNA transposons occupying 49.2, 2.4, and 5.6%, respectively. Fluorescence in situ hybridization (FISH) analysis showed that most LTR-REs dispersed all over the chromosomes, by contrast, elements of CRM lineage were distributed at the centromeric region of all chromosomes. In addition, Ogre/Tat lineage mainly accumulated on sex chromosomes, and satellites Spsat2 and Spsat3 were exclusively located at the telomeric region of the short arm of sex chromosomes.ConclusionsWe reliably annotated the TE fraction of the draft genome of spinach. FISH analysis indicates that Ogre/Tat lineage and the sex chromosome-specific satellites DNAs might participate in sex chromosome formation and evolution. Based on FISH signals of microsatellites, together with 45S rDNA, a fine karyotype of spinach was established. This study improves our knowledge of repetitive sequence organization in spinach genome and aids in accurate spinach karyotype construction.

Genetic rescue and the maintenance of native ancestry

Genetic rescue (GR) is an important tool in conservation biology for the management of highly inbred populations. However, GR comes at a potential cost: the reduction in native genomic content. The degree to which adaptive evolution for new immigrant alleles lead to complete or partial replacement of the native genome, depends on recombination rates, genome size, effective population sizes, and distributions of fitness effects. As one of the most well-studied examples of an inbred species that exchanged genetic material with a less inbred species, we use Neanderthals and humans as an example. Using simulations, we show that for parameters realistic for these species, the increase in fitness caused by GR is mirrored by an almost proportional reduction in the fraction of the native genome preserved. The main reason is that the effect of selection will be strongest in the first few generations during which time there is only little break-up, by recombination, of the immigrant chromosomes. We also show that in the presence of a strong and short-lived bottleneck with recessive mutations, GR leads to a stronger increase in fitness than in the presence of additive effects or a more prolonged bottleneck.

X-ray irradiation induces subtle changes in the genome-wide distribution of DNA hydroxymethylation with opposing trends in genic and intergenic regions

ABSTRACTDNA hydroxymethylation has gained attention as an intermediate in the process of DNA demethylation. More recently, 5-hydroxymethylcytosine has been recognized as an independent epigenetic mark that can persist over time and that exerts influence on gene regulation and other biological processes. Deregulation of this DNA modification has been linked to tumorigenesis and a variety of other diseases. The impact of irradiation on DNA hydroxymethylation is poorly understood. In this study we exposed lung fibroblasts (IMR90) to 0.5 Gy and 2 Gy of X-rays, respectively. We characterized radiation induced changes of DNA hydroxymethylation 1 h, 6 h, 24 h and 120 h after exposure employing immunoprecipitation and subsequent deep sequencing of the genomic fraction enriched for hydroxymethylated DNA. Transcriptomic response to irradiation was analyzed for time points 6 h and 24 h post exposure by means of RNA sequencing. Irradiated and sham-irradiated samples shared the same overall distribution of 5-hydroxymethylcytosines with respect to genomic features such as promoters and exons. The frequency of 5-hydroxymethylcytosine peaks differentially detected in irradiated samples increased in genic regions over time, while the opposing trend was observed for intergenic regions. Onset and extent of this effect was dose dependent. Moreover, we demonstrated a biased distribution of 5-hmC alterations at CpG islands and sites occupied by the DNA binding protein CTCF. In summary, our study provides new insights into the epigenetic response to irradiation. Our data highlight genomic features more prone to irradiation induced changes of DNA hydroxymethylation, which might impact early and late onset effects of irradiation.

Genomic retained heterosis effects on fertility and lifetime productivity in beef heifers

This study evaluated the effects of three genomic indicators of heterosis on female fertility and lifetime productivity, and quantified changes over 11 production cycles in a crossbred cow herd. Pedigree-based breed composition (pBC) was determined and used to calculate retained heterozygosity for 412 replacement heifers born from 2004 to 2014 at the Lacombe Research and Development Centre (AB, Canada). Heifers were followed as cows over 1050 mating opportunities, 11 production cycles, and five parities. Heifers and their sires (51) were genotyped and these genotypes were used to predict each animal’s genomic breed composition (gBC) and three genomic indicators of heterosis: (1) retained heterozygosity (RHETg), (2) heterozygous proportion (H), and (3) retained heterosis (RHg). Correlations between pedigree and genomic breed fractions for Angus, Hereford, and Charolais were high (rp = 0.74–0.94; P < 0.001). Genomic indicators of heterosis were highly related (rp = 0.61 for RHETg vs. H; 0.71 for RHg vs. H; 0.96 for RHETg vs. RHg; P < 0.001). Each 10% change in RHETg resulted in 51 ± 20 d longer survival (P = 0.011) in the herd and 35.7 ± 15.2 kg more (P = 0.019) calf wean weight per cow exposed to breeding when summed over five parities. These differences resulted in an extra $161 per heifer in a year. Optimizing heterosis using genomic tools can be very beneficial for the cow herd if applied correctly.