scholarly journals Genome-wide transcription during early wheat meiosis is independent of synapsis, ploidy level and the Ph1 locus

2018 ◽  
Author(s):  
A.C. Martín ◽  
P. Borrill ◽  
J. Higgins ◽  
A.K. Alabdullah ◽  
R.H. RamÍrez-González ◽  
...  
Keyword(s):  
Structural Changes ◽  
Classical Model ◽  
Diploid Species ◽  
Plant Evolution ◽  
Early Prophase ◽  
Post Translational Modifications ◽  
Genome Wide ◽  
Chromatin Structural ◽  
Ph1 Locus ◽  
Large Genome Size

ABSTRACTPolyploidization is a fundamental process in plant evolution. One of the biggest challenges faced by a new polyploid is meiosis, particularly discriminating between multiple related chromosomes so that only homologous chromosomes synapse and recombine to ensure regular chromosome segregation and balanced gametes. Despite its large genome size, high DNA repetitive content and similarity between homoeologous chromosomes, hexaploid wheat completes meiosis in a shorter period than diploid species with a much smaller genome. Therefore, during wheat meiosis, mechanisms additional to the classical model based on DNA sequence homology, must facilitate more efficient homologous recognition. One such mechanism could involve exploitation of differences in chromosome structure between homologues and homoeologues at the onset of meiosis. In turn, these chromatin changes, can be expected to be linked to transcriptional gene activity. In this study, we present an extensive analysis of a large RNA-Seq data derived from six different genotypes: wheat, wheat-rye hybrids and newly synthesized octoploid triticale, both in the presence and absence of the Ph1 locus. Plant material was collected at early prophase, at the transition leptotene-zygotene, when the telomere bouquet is forming and synapsis between homologues is beginning. The six genotypes exhibit different levels of synapsis and chromatin structure at this stage; therefore, recombination and consequently segregation, are also different. Unexpectedly, our study reveals that neither synapsis, whole genome duplication nor the absence of the Ph1 locus are associated with major changes in gene expression levels during early meiotic prophase. Overall wheat transcription at this meiotic stage is therefore highly resilient to such alterations, even in the presence of major chromatin structural changes. This suggests that post-transcriptional and post-translational processes are likely to be more important. Thus, further studies will be required to reveal whether these observations are specific to wheat meiosis, and whether there are significant changes in post-transcriptional and post-translational modifications in wheat and other polyploid species associated with their polyploidisation.

SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 948-956 ◽  
Author(s):  
G. Durstewitz ◽  
A. Polley ◽  
J. Plieske ◽  
H. Luerssen ◽  
E. M. Graner ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Oilseed Rape ◽  
Expressed Sequence Tag ◽  
Diploid Species ◽  
Amplicon Sequencing ◽  
Snp Markers ◽  
Snp Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Illumina Goldengate

Oilseed rape ( Brassica napus ) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

scholarly journals Epigenomics of Plant’s Responses to Environmental Stress

2017 ◽  
Author(s):  
Suresh Kumar
Keyword(s):  
Gene Expression ◽  
Nuclear Dna ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Epigenetic Changes ◽  
Post Translational Modifications ◽  
Genome Wide ◽  
A Cell ◽  
Non Coding Rnas ◽  
Function Activity

Genome-wide epigenetic changes in plants are being reported during the development and environmental stresses, which are often correlated with gene expression at the transcriptional level. Sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of non-coding RNAs in a cell is known as epigenome. These changes are often responsible for variation in expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting into the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli which affect phenotypic plasticity of the organism. Both, the epigenetic changes and variation in gene expression might return to the pre-stress state soon after withdrawal of the stress. However, a part of the epigenetic changes may be retained which is reported to play role in acclimatization, adaptation as well as in the evolutionary processes. Understanding epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic factors. This review delineates the importance of epigenomics towards possible improvement of plant’s responses to environmental stresses for climate resilient agriculture.

scholarly journals Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data

2019 ◽  
Author(s):  
Hyeon-Jin Kim ◽  
Galip Gürkan Yardımcı ◽  
Giancarlo Bonora ◽  
Vijay Ramani ◽  
Jie Liu ◽  
...  
Keyword(s):  
Single Cell ◽  
Topic Modeling ◽  
Biological Information ◽  
Chromatin Interaction ◽  
Cell Type ◽  
3D Genome ◽  
Genome Wide ◽  
Significant Barrier ◽  
Chromatin Structural ◽  
Cell Type Specific

AbstractSingle-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate twelve different single-cell combinatorial indexed Hi-C (sciHi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 25,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sciHi-C data in the form of “chromatin topics.” We further show enrichment of particular compartment structures associated with locus pairs in these topics.

Abstract P252: Loss of HMGB2 Induces Chromatin Remodeling and Hypertrophic Growth in Cardiomyocytes

2011 ◽  
Vol 109 (suppl_1) ◽  
Author(s):  
Sarah Franklin ◽  
Haodong Chen ◽  
Scherise Mitchell-Jordan ◽  
Shuxun Ren ◽  
Peipei Ping ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mass Spectrometry ◽  
Chromatin Remodeling ◽  
Nuclear Dna ◽  
Specific Pattern ◽  
Altered Expression ◽  
Hypertrophic Growth ◽  
Knock Down ◽  
Genome Wide ◽  
Chromatin Structural

Nuclear DNA is packaged around the octameric nucleosome core particle, constituting the basic building block of chromatin. Non-nucleosome chromatin structural molecules have been shown to induce higher order packaging of DNA into structurally compact and inactive heterochromatin, or loosely packed and active euchromatin. These chromatin remodeling events are thought to establish a cell type specific pattern of gene expression. During the development of cardiac hypertrophy and failure, genes normally only expressed during development are re-activated. While a number of transcription factors involved in these changes in fetal gene expression have been identified, the means for genome-wide structural remodeling of DNA are unknown. To identify factors controlling genomic plasticity in cardiomyocytes, we used mass spectrometry to quantify chromatin-associated proteins from cardiac nuclei during stages of hypertrophy and failure in the mouse. Adult mice were subjected to cardiac pressure overload by transverse aortic constriction. Chromatin was fractionated from cardiac nuclei and DNA-bound proteins were acid extracted and analyzed by mass spectrometry. We measured chromatin occupancy patterns for >300 proteins during distinct stages of heart failure. To explore the isoform specific roles of individual chromatin structural proteins, we used siRNA to knock-down expression of two high mobility group proteins (HMGB1 and 2) exhibiting altered expression in the hypertrophic heart. Loss of HMGB2 (but not HMGB1) induced robust hypertrophic growth in cardiomyocytes. qRT-PCR analyses demonstrated that HMGB2 is responsible for some but not all changes in the fetal gene program (ANF increased 150% and SERCA decreased 20%, whereas α- and β-MHC were unchanged). To further explore the endogenous regions of the genome under control of HMGB2 packing, we performed microarrays following HMGB2 knockdown. Hypertrophy or HMGB2 knock-down induced global chromatin remodeling conducive to gene expression, as measured by histone post-translational modifications and the ratio of core to linker histones. These studies reveal a novel role of HMGB2 to inhibit hypertrophic growth and provide insights into general principles for genome-wide chromatin remodeling.

scholarly journals Detection and application of genome-wide variations in peach for association and genetic relationship analysis

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Liping Guan ◽  
Ke Cao ◽  
Yong Li ◽  
Jian Guo ◽  
Qiang Xu ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Dna Markers ◽  
High Throughput Sequencing ◽  
Prunus Persica ◽  
Genetic Research ◽  
Diploid Species ◽  
Sequencing Data ◽  
Relationship Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. Results In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. Conclusions The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

scholarly journals Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Kai-Hua Jia ◽  
Hui Liu ◽  
Ren-Gang Zhang ◽  
Jie Xu ◽  
Shan-Shan Zhou ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Whole Genome Duplication ◽  
Sequence Variation ◽  
Genome Duplication ◽  
Ornamental Plants ◽  
Plant Evolution ◽  
Genomic Rearrangements ◽  
Genome Wide Analysis ◽  
Salvia Splendens ◽  
Genome Wide

AbstractPolyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.

scholarly journals Comparative Genome-wide Analysis and Expression Profiling of Histone Acetyltransferase (HAT) Gene Family in Response to Hormonal Applications, Metal and Abiotic Stresses in Cotton

2019 ◽  
Vol 20 (21) ◽  
pp. 5311 ◽  
Author(s):  
Muhammad Imran ◽  
Sarfraz Shafiq ◽  
Muhammad Ansar Farooq ◽  
Muhammad Kashif Naeem ◽  
Emilie Widemann ◽  
...  
Keyword(s):  
Fiber Quality ◽  
Purifying Selection ◽  
Fiber Development ◽  
Amino Acid Sequences ◽  
Environmental Cues ◽  
Post Translational Modifications ◽  
Cellular Processes ◽  
Genome Wide ◽  
Selection Gene ◽  
Almost All

Post-translational modifications are involved in regulating diverse developmental processes. Histone acetyltransferases (HATs) play vital roles in the regulation of chromation structure and activate the gene transcription implicated in various cellular processes. However, HATs in cotton, as well as their regulation in response to developmental and environmental cues, remain unidentified. In this study, 9 HATs were identified from Gossypium raimondi and Gossypium arboretum, while 18 HATs were identified from Gossypium hirsutum. Based on their amino acid sequences, Gossypium HATs were divided into three groups: CPB, GNAT, and TAFII250. Almost all the HATs within each subgroup share similar gene structure and conserved motifs. Gossypium HATs are unevenly distributed on the chromosomes, and duplication analysis suggests that Gossypium HATs are under strong purifying selection. Gene expression analysis showed that Gossypium HATs were differentially expressed in various vegetative tissues and at different stages of fiber development. Furthermore, all the HATs were differentially regulated in response to various stresses (salt, drought, cold, heavy metal and DNA damage) and hormones (abscisic acid (ABA) and auxin (NAA)). Finally, co-localization of HAT genes with reported quantitative trait loci (QTL) of fiber development were reported. Altogether, these results highlight the functional diversification of HATs in cotton growth and fiber development, as well as in response to different environmental cues. This study enhances our understanding of function of histone acetylation in cotton growth, fiber development, and stress adaptation, which will eventually lead to the long-term improvement of stress tolerance and fiber quality in cotton.

Genome Wide Profiling Of Chromosomal Abnormalities In 37 Patients With Monoclonal Gammopathy Of Undetermined Significance (MGUS)

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1874-1874
Author(s):  
Aneta Mikulasova ◽  
Vladimira Vallova ◽  
Jan Smetana ◽  
Henrieta Greslikova ◽  
Renata Kupska ◽  
...  
Keyword(s):  
Structural Changes ◽  
Plasma Cells ◽  
Array Cgh ◽  
Chromosomal Abnormalities ◽  
Conflicts Of Interest ◽  
Multiple Displacement Amplification ◽  
Chromosome 8 ◽  
Genome Wide ◽  
Technique Optimization ◽  
Chromosomal Changes

Abstract Introduction The incidence of clonal DNA copy number alterations (CNAs) in plasma cells (PCs) is considered as one of the most important and independent prognostic factors in patients with multiple myeloma (MM). Also in the premalignancy MGUS, there are specific chromosomal changes in PCs such as del(13)(q14), IGHtranslocation, gain(1)(q21) and hyperdiploidy. However, not much is known about their significance in relation to malignant transformation. Also, MGUS research is further complicated by small number of malignant cells that could be obtained from patients. Aim Array-CGH technique optimization and DNA CNAs analysis in relation to prognosis at genome-wide level in MGUS patients. Material and methods We have analysed 37 MGUS patients (22M/15F; median age 62) using array-CGH, Agilent platforms “Human Genome CGH, 4×44K” (n=10) and “SurePrint G3 CGH+SNP, 4×180K” (n=27). DNA was isolated from separated PCs (using CD138, CD19 and CD56 markers) and amplified by multiple displacement amplification (MDA). Results CNAs were observed in 57% (21/37) MGUS patients. Numerical and structural CNAs were found in 46% (17/37) and 41% (15/37) MGUS patients, respectively. We distinguished two genetic subgroups similar to MM patients: hyperdiploid and non-hyperdiploid. Hyperdiploidy was present in 32% (12/37) MGUS patients. The most frequent whole-chromosome gains were: 9 (83%, 10/12), 19 (83%, 10/12), 3 (75%, 9/12), 11 (67%, 8/12) and 15 (58%, 7/12). Non-hyperdiploidy was detected in 68% (25/37) MGUS patients. In both, hyperdiploid and non-hyperdiploid subgroups we have found loss of chromosomes 13 (25% vs. 20%) and Y (17% vs. 4%). Loss of chromosome 8 was detected only in hyperdiploid subgroup (8%) and losses of chromosomes 21, 22 and X only in non-hyperdiploid subgroup (8%, 4% and 8%, respectively). Structural changes were significantly more often present in hyperdiploid than in non-hyperdiploid patients (67% vs. 28%, p<0.05). We have identified whole-arm chromosome changes 1q gain and 16q loss in both hyperdiploid and non-hyperdiploid patients (17% vs. 12%, 8% vs. 8%, respectively), but 16p gain was seen only in hyperdiploid patients (8%). Segmental chromosome changes were also present in both hyperdiploid and non-hyperdiploid patients (58% vs. 24%). Interestingly, we have detected more segmental losses (15 vs. 8) and gains (6 vs. 2) in hyperdiploid than in non-hyperdiploid patients, but size median of these losses (3.33 Mb vs. 19.6 Mb) and gains (36.1 Mb vs. 63.5 Mb) was smaller in hyperdiploid than in non-hyperdiploid patients. Moreover, we found one MGUS patient who has progressed to MM and required therapy after 6 months from MGUS diagnosis. Genome-wide profile of MGUS patient was especially unique by high number of structural changes (n=11) compared to other 15 MGUS patients with structural CNAs (median 1; 1 – 6). MGUS patient’s profile showed hyperdiploidy (gains of chromosomes 3, 5, 9, 11, 15 and 19), losses of chromosomes 8, 13 and Y, 7 segmental losses in areas 1p34.2-p13.1, 6p23, 6q12-q27, 7q36.3, 12p12.1-p11.23, 12q12, 12q21.2-q23.3 and 4 segmental gains in areas 6p25.3-p23, 6p23-p11.1, 6q11.1-q12, Xq21.33-q28. In addition, gains and losses, which included whole or large parts of chromosomes, showed unusual profile associated with other alterations. These findings have suggested a complex karyotype. Summary In our study we have optimized protocol of array-CGH analysis from amplified DNA and we have used it in first 37 MGUS patients. We found there are various chromosomal changes (numerical, whole-arm and segmental) in more than half of MGUS patients. Similar to MM, hyperdiploid and non-hyperdiploid genetic subgroups were identified. We also described one MGUS case with unique genome-wide profile indicating unfavourable prognosis. Support NT13492, NT13190, NT11154, OPVK CZ.1.07/2.3.00/20.0183, MSM0021622434, GAP304/10/1395 Disclosures: No relevant conflicts of interest to declare.

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