Unusual patterns of genetic diversity and gene expression in the maize genome

2009 ◽  
Author(s):  
Li Li
Keyword(s):  
Gene Expression ◽  
Genetic Diversity ◽  
Maize Genome

scholarly journals Chromatin loop anchors contain core structural components of the gene expression machinery in maize

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Stéphane Deschamps ◽  
John A. Crow ◽  
Nadia Chaidir ◽  
Brooke Peterson-Burch ◽  
Sunil Kumar ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Transcriptional Activity ◽  
Spatial Organization ◽  
Regulatory Elements ◽  
Open Chromatin ◽  
Maize Genome ◽  
Chromatin Loop ◽  
Structural Components ◽  
Chromatin Loops

Abstract Background Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that < 7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome.

Histones: genetic diversity and tissue-specific gene expression

1997 ◽  
Vol 107 (1) ◽  
pp. 1-10 ◽  
Author(s):  
D. Doenecke ◽  
W. Albig ◽  
C. Bode ◽  
B. Drabent ◽  
K. Franke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Diversity ◽  
Specific Gene ◽  
Tissue Specific ◽  
Tissue Specific Gene ◽  
Specific Gene Expression

scholarly journals BOX Elements Modulate Gene Expression in Streptococcus pneumoniae: Impact on the Fine-Tuning of Competence Development

2006 ◽  
Vol 188 (23) ◽  
pp. 8307-8312 ◽  
Author(s):  
Eivind Knutsen ◽  
Ola Johnsborg ◽  
Yves Quentin ◽  
Jean-Pierre Claverys ◽  
Leiv Sigve Håvarstein
Keyword(s):  
Gene Expression ◽  
Genetic Diversity ◽  
Streptococcus Pneumoniae ◽  
Competence Development ◽  
Fine Tuning ◽  
Present Evidence ◽  
Genomic Plasticity ◽  
Affect Expression ◽  
Intergenic Regions

ABSTRACT More than 100 BOX elements are randomly distributed in intergenic regions of the pneumococcal genome. Here we demonstrate that these elements can affect expression of neighboring genes and present evidence that they are mobile. Together, our findings show that BOX elements enhance genetic diversity and genomic plasticity in Streptococcus pneumoniae.

Resources for studies of iron walnut (Juglans sigillata) gene expression, genetic diversity, and evolution

2018 ◽  
Vol 14 (4) ◽  
Author(s):  
Xiaojia Feng ◽  
Xiaoying Yuan ◽  
Yiwei Sun ◽  
Yiheng Hu ◽  
Saman Zulfiqar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Diversity ◽  
Juglans Sigillata

scholarly journals Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome

2018 ◽  
Vol 27 (18) ◽  
pp. 3572-3581 ◽  
Author(s):  
Ludovic Dutoit ◽  
Carina F. Mugal ◽  
Paulina Bolívar ◽  
Mi Wang ◽  
Krystyna Nadachowska-Brzyska ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Diversity ◽  
Ficedula Albicollis ◽  
Sexual Antagonism ◽  
Collared Flycatcher

scholarly journals Identification of Structural Variants in Two Novel Genomes of Maize Inbred Lines Possibly Related to Glyphosate Tolerance

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 523
Author(s):  
Medhat Mahmoud ◽  
Joanna Gracz-Bernaciak ◽  
Marek Żywicki ◽  
Wojciech Karłowski ◽  
Tomasz Twardowski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Molecule ◽  
Zea Mays L ◽  
Shikimate Pathway ◽  
High Impact ◽  
Maize Genome ◽  
Structural Variants ◽  
Shikimate Dehydrogenase ◽  
Epsps Gene ◽  
Sequencing Technologies

To study genetic variations between genomes of plants that are naturally tolerant and sensitive to glyphosate, we used two Zea mays L. lines traditionally bred in Poland. To overcome the complexity of the maize genome, two sequencing technologies were employed: Illumina and Single Molecule Real-Time (SMRT) PacBio. Eleven thousand structural variants, 4 million SNPs and approximately 800 thousand indels differentiating the two genomes were identified. Detailed analyses allowed to identify 20 variations within the EPSPS gene, but all of them were predicted to have moderate or unknown effects on gene expression. Other genes of the shikimate pathway encoding bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase and chorismate synthase were altered by variants predicted to have a high impact on gene expression. Additionally, high-impact variants located within the genes involved in the active transport of glyphosate through the cell membrane encoding phosphate transporters as well as multidrug and toxic compound extrusion have been identified.

scholarly journals High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis

2020 ◽  
Vol 47 (3) ◽  
pp. 1589-1603 ◽  
Author(s):  
Marwa Ghonaim ◽  
Ruslan Kalendar ◽  
Hoda Barakat ◽  
Nahla Elsherif ◽  
Naglaa Ashry ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput ◽  
Genetic Similarity ◽  
Maize Genome ◽  
Ltr Retrotransposons ◽  
Maize Germplasm ◽  
Phylogeny Analysis ◽  
Generating Method ◽  
Polymerase Chain Reaction Primers ◽  
Hybrid Lines

AbstractMaize is one of the world’s most important crops and a model for grass genome research. Long terminal repeat (LTR) retrotransposons comprise most of the maize genome; their ability to produce new copies makes them efficient high-throughput genetic markers. Inter-retrotransposon-amplified polymorphisms (IRAPs) were used to study the genetic diversity of maize germplasm. Five LTR retrotransposons (Huck, Tekay, Opie, Ji, and Grande) were chosen, based on their large number of copies in the maize genome, whereas polymerase chain reaction primers were designed based on consensus LTR sequences. The LTR primers showed high quality and reproducible DNA fingerprints, with a total of 677 bands including 392 polymorphic bands showing 58% polymorphism between maize hybrid lines. These markers were used to identify genetic similarities among all lines of maize. Analysis of genetic similarity was carried out based on polymorphic amplicon profiles and genetic similarity phylogeny analysis. This diversity was expected to display ecogeographical patterns of variation and local adaptation. The clustering method showed that the varieties were grouped into three clusters differing in ecogeographical origin. Each of these clusters comprised divergent hybrids with convergent characters. The clusters reflected the differences among maize hybrids and were in accordance with their pedigree. The IRAP technique is an efficient high-throughput genetic marker-generating method.

scholarly journals Evolution of Superinfection Immunity in Cluster A Mycobacteriophages

mBio ◽  
2019 ◽  
Vol 10 (3) ◽  
Author(s):  
Travis N. Mavrich ◽  
Graham F. Hatfull
Keyword(s):  
Gene Expression ◽  
Genetic Diversity ◽  
Defense Mechanism ◽  
Genetic Interactions ◽  
Form Complex ◽  
Lytic Gene ◽  
Regulatory Circuit ◽  
Gene Regulatory ◽  
Cluster A ◽  
Phage Growth

ABSTRACTTemperate phages encode an immunity system to control lytic gene expression during lysogeny. This gene regulatory circuit consists of multiple interacting genetic elements, and although it is essential for controlling phage growth, it is subject to conflicting evolutionary pressures. During superinfection of a lysogen, the prophage’s circuit interacts with the superinfecting phage’s circuit and prevents lytic growth if the two circuits are closely related. The circuitry is advantageous since it provides the prophage with a defense mechanism, but the circuitry is also disadvantageous since it limits the phage’s host range during superinfection. Evolutionarily related phages have divergent, orthogonal immunity systems that no longer interact and are heteroimmune, but we do not understand how immunity systems evolve new specificities. Here, we use a group of Cluster A mycobacteriophages that exhibit a spectrum of genetic diversity to examine how immunity system evolution impacts superinfection immunity. We show that phages with mesotypic (i.e., genetically related but distinct) immunity systems exhibit asymmetric and incomplete superinfection phenotypes. They form complex immunity networks instead of well-defined immunity groups, and mutations conferring escape (i.e., virulence) from homotypic or mesotypic immunity have various escape specificities. Thus, virulence and the evolution of new immune specificities are shaped by interactions with homotypic and mesotypic immunity systems.IMPORTANCEMany aspects regarding superinfection, immunity, virulence, and the evolution of immune specificities are poorly understood due to the lack of large collections of isolated and sequenced phages with a spectrum of genetic diversity. Using a genetically diverse collection of Cluster A phages, we show that the classical and relatively straightforward patterns of homoimmunity, heteroimmunity, and virulence result from interactions between homotypic and heterotypic phages at the extreme edges of an evolutionary continuum of immune specificities. Genetic interactions between mesotypic phages result in more complex mesoimmunity phenotypes and virulence profiles. These results highlight that the evolution of immune specificities can be shaped by homotypic and mesotypic interactions and may be more dynamic than previously considered.

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