The Rice Genome Structure as a Trail from the Past to Beyond

2008 ◽  
pp. 131-142 ◽  
Author(s):  
T. Sasaki
Keyword(s):  
Genome Structure ◽  
Rice Genome ◽  
The Past

A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 32-37 ◽  
Author(s):  
Shoko Saji ◽  
Yosuke Umehara ◽  
Baltazar A Antonio ◽  
Hiroko Yamane ◽  
Hiroshi Tanoue ◽  
...  
Keyword(s):  
Genetic Map ◽  
Dna Markers ◽  
Yeast Artificial Chromosome ◽  
Physical Map ◽  
Genome Structure ◽  
Rice Genome ◽  
Artificial Chromosome ◽  
Physical Length ◽  
Rice Chromosomes ◽  
Yac Contig

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.Key words: physical mapping, YAC contig, rice genome, rice chromosomes.

scholarly journals The Toolbox for Untangling Chromosome Architecture in Immune Cells

2021 ◽  
Vol 12 ◽  
Author(s):  
Shuai Liu ◽  
Keji Zhao
Keyword(s):  
Gene Expression ◽  
Immune Cells ◽  
Spatial Organization ◽  
Chromosome Structure ◽  
Immune Cell ◽  
Genome Structure ◽  
Chromosome Architecture ◽  
The Past ◽  
Important Player ◽  
The Way

The code of life is not only encrypted in the sequence of DNA but also in the way it is organized into chromosomes. Chromosome architecture is gradually being recognized as an important player in regulating cell activities (e.g., controlling spatiotemporal gene expression). In the past decade, the toolbox for elucidating genome structure has been expanding, providing an opportunity to explore this under charted territory. In this review, we will introduce the recent advancements in approaches for mapping spatial organization of the genome, emphasizing applications of these techniques to immune cells, and trying to bridge chromosome structure with immune cell activities.

scholarly journals Genome Diversity in Maize

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Victor Llaca ◽  
Matthew A. Campbell ◽  
Stéphane Deschamps
Keyword(s):  
Structural Variation ◽  
Genome Structure ◽  
Primate Species ◽  
Maize Genome ◽  
Genome Diversity ◽  
Model Species ◽  
The Past ◽  
Genome Complexity ◽  
Genome Wide ◽  
Sequencing Platforms

Zea mays (maize) has historically been used as a model species for genetics, development, physiology and more recently, genome structure. The maize genome is complex with striking intraspecific variation in gene order, repetitive DNA content, and allelic content exceeding the levels observed between primate species. Maize genome complexity is primarily driven by polyploidization and explosive amplification of LTR retrotransposons, with the counteracting effect of unequal and illegitimate crossover. Transposable elements have been shown to capture genic content, create chimeras, and amplify those sequences via transposition. New sequencing platforms and hybridization-based strategies have appeared over the past decade which are being applied to maize and providing the first genome-wide comprehensive view of structural variation and will provide the basis for investigating the interplay between repeats and genes as well as the amount of species level diversity within maize.

scholarly journals Dasheng: A Recently Amplified Nonautonomous Long Terminal Repeat Element That Is a Major Component of Pericentromeric Regions in Rice

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1293-1305 ◽  
Author(s):  
Ning Jiang ◽  
Zhirong Bao ◽  
Svetlana Temnykh ◽  
Zhukuan Cheng ◽  
Jiming Jiang ◽  
...  
Keyword(s):  
Copy Number ◽  
Genomic Sequence ◽  
Rice Genome ◽  
Sequence Information ◽  
Fish Analysis ◽  
Transposon Display ◽  
The Past ◽  
Rice Chromosomes ◽  
Rice Genomic Sequence ◽  
Bac End Sequence

Abstract A new and unusual family of LTR elements, Dasheng, has been discovered in the genome of Oryza sativa following database searches of ~100 Mb of rice genomic sequence and 78 Mb of BAC-end sequence information. With all of the cis-elements but none of the coding domains normally associated with retrotransposons (e.g., gag, pol), Dasheng is a novel nonautonomous LTR element with high copy number. Over half of the ~1000 Dasheng elements in the rice genome are full length (5.6–8.6 kb), and 60% are estimated to have amplified in the past 500,000 years. Using a modified AFLP technique called transposon display, 215 elements were mapped to all 12 rice chromosomes. Interestingly, more than half of the mapped elements are clustered in the heterochromatic regions around centromeres. The distribution pattern was further confirmed by FISH analysis. Despite clustering in heterochromatin, Dasheng elements are not nested, suggesting their potential value as molecular markers for these marker-poor regions. Taken together, Dasheng is one of the highest-copy-number LTR elements and one of the most recent elements to amplify in the rice genome.

scholarly journals Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses

2017 ◽  
Author(s):  
Judit J Pénzes ◽  
Soledad Marsile-Medun ◽  
Mavis Agbandje-McKenna ◽  
Robert James Gifford
Keyword(s):  
Genome Structure ◽  
Structural Features ◽  
Capsid Gene ◽  
Phylogenetic Placement ◽  
The Past ◽  
A Genome ◽  
Genome Features ◽  
Mole Vole ◽  
Domain Iii ◽  
High Degree

ABSTRACTAmdoparvoviruses (familyParvoviridae:genusAmdoparvovirus) infect carnivores, and are a major cause of morbidity and mortality in farmed animals. In this study, we systematically screened animal genomes to identify PVe disclosing a high degree of similarity to amdoparvoviruses, and investigated their genomic, phylogenetic and protein structural features. We report the first examples of full-length, amdoparvovirus-derived PVe in the genome of the Transcaucasian mole vole (Ellobius lutescens). Furthermore, we identify four further PVe in mammal and reptile genomes that are intermediate between amdoparvoviruses and their sister genus (Protoparvovirus) in terms of their phylogenetic placement and genomic features. In particular, we identify a genome-length PVe in the genome of a pit viper (Protobothrops mucrosquamatus) that is more like a protoparvovirus than an amdoparvovirus in terms of its phylogenetic placement and the structural features of its capsid protein (as revealed by homology modeling), yet exhibits characteristically amdoparvovirus-like genome features including: (i) a putative middle ORF gene; (ii) a capsid gene that lacks a phospholipase A2 (PLA2) domain; (iii) a genome structure consistent with an amdoparvovirus-like mechanism of capsid gene expression. Our findings indicate that amdoparvovirus host range has extended to rodents in the past, and that parvovirus lineages possessing a mixture of proto- and amdoparvovirus-like characteristics have circulated in the past. In addition, we show that PVe in the mole vole and pit viper encode intact, expressible replicase genes that have potentially been co-opted or exapted in these host species.

scholarly journals Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome

2012 ◽  
Vol 2012 ◽  
pp. 1-8
Author(s):  
P. C. Sharma ◽  
Manish Roorkiwal ◽  
Atul Grover
Keyword(s):  
Selection Bias ◽  
Evolutionary Dynamics ◽  
Rice Genome ◽  
Purifying Selection ◽  
Comprehensive Analysis ◽  
Segmental Duplications ◽  
Genome Sequences ◽  
The Public ◽  
The Past ◽  
Made In

Little data is available on microsatellite dynamics in the duplicated regions of the rice genome, even though efforts have been made in the past to align genome sequences of its two sub-species. Based on the coordinates of duplicated sequences in the indica genome as available in the public domain, we identified microsatellites in these regions. CCG and GAAAA repeats occurred most frequently. In all, 259 microsatellites could be identified in the duplicated sequences using the criteria of minimum 90% alignability spread over a minimum of 1 Kb sequence. More than 25% of the repeats in duplicated regions occurred in the genic sequences. Only 45 (17%) of these 259 microsatellites were found conserved in the duplicated paralogues. Among these repeats, 40% maintained both sequence and length conservation. The effect of mutability of nearby regions could also be clearly seen in microsatellite regions. The overall purpose of this study was to investigate, whether microsatellites follow an independent course of evolutionary dynamics subsequent to events like genome reshuffling that simply drives these elements to different locations in the genome. To the best of our knowledge, this is the first comprehensive analysis of microsatellite conservation in the duplicated regions of any genome.

scholarly journals Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Agnieszka A. Golicz ◽  
Prem L. Bhalla ◽  
David Edwards ◽  
Mohan B. Singh
Keyword(s):  
Meiotic Recombination ◽  
Recombination Rate ◽  
Sequence Variation ◽  
Genome Structure ◽  
Rice Genome ◽  
Three Dimensional ◽  
3D Genome ◽  
Cellular Processes ◽  
Eukaryotic Species ◽  
Topologically Associated Domains

AbstractGenomes of many eukaryotic species have a defined three-dimensional architecture critical for cellular processes. They are partitioned into topologically associated domains (TADs), defined as regions of high chromatin inter-connectivity. While TADs are not a prominent feature of A. thaliana genome organization, they have been reported for other plants including rice, maize, tomato and cotton and for which TAD formation appears to be linked to transcription and chromatin epigenetic status. Here we show that in the rice genome, sequence variation and meiotic recombination rate correlate with the 3D genome structure. TADs display increased SNP and SV density and higher recombination rate compared to inter-TAD regions. We associate the observed differences with the TAD epigenetic landscape, TE composition and an increased incidence of meiotic crossovers.

scholarly journals Applications of the CRISPR/Cas9 System for Rice Grain Quality Improvement: Perspectives and Opportunities

2019 ◽  
Vol 20 (4) ◽  
pp. 888 ◽  
Author(s):  
Sajid Fiaz ◽  
Shakeel Ahmad ◽  
Mehmood Noor ◽  
Xiukang Wang ◽  
Afifa Younas ◽  
...  
Keyword(s):  
Quality Improvement ◽  
Genome Editing ◽  
Reverse Genetics ◽  
Grain Quality ◽  
Rice Genome ◽  
Targeted Mutagenesis ◽  
High Yield ◽  
Genomic Alteration ◽  
Rice Grain ◽  
The Past

Grain quality improvement is a key target for rice breeders, along with yield. It is a multigenic trait that is simultaneously influenced by many factors. Over the past few decades, breeding for semi-dwarf cultivars and hybrids has significantly contributed to the attainment of high yield demands but reduced grain quality, which thus needs the attention of researchers. The availability of rice genome sequences has facilitated gene discovery, targeted mutagenesis, and revealed functional aspects of rice grain quality attributes. Some success has been achieved through the application of molecular markers to understand the genetic mechanisms for better rice grain quality; however, researchers have opted for novel strategies. Genomic alteration employing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) for reverse genetics has opened new avenues of research in the life sciences, including for rice grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting. Over the past few years many genes that are related to various aspects of rice grain quality have been successfully edited via CRISPR/Cas9 technology. Interestingly, studies on functional genomics at larger scales have become possible because of the availability of GETs. In this review, we discuss the progress made in rice by employing the CRISPR/Cas9 editing system and its eminent applications. We also elaborate possible future avenues of research with this system, and our understanding regarding the biological mechanism of rice grain quality improvement.

scholarly journals Inferences on the Genome Structure of Progenitor Maize Through Comparative Analysis of Rice, Maize and the Domesticated Panicoids

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 453-473 ◽  
Author(s):  
William A Wilson ◽  
Sandra E Harrington ◽  
Wendy L Woodman ◽  
Michael Lee ◽  
Mark E Sorrells ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
Genome Structure ◽  
Rice Genome ◽  
Maize Genome ◽  
Linkage Groups ◽  
Comparative Maps ◽  
Rice Chromosomes ◽  
Modern Maize ◽  
New Evidence ◽  
Rice Genetic

Abstract Corn and rice genetic linkage map alignments were extended and refined by the addition of 262 new, reciprocally mapped maize cDNA loci. Twenty chromosomal rearrangements were identified in maize relative to rice and these included telomeric fusions between rice linkage groups, nested insertion of rice linkage groups, intrachromosomal inversions, and a nonreciprocal translocation. Maize genome evolution was inferred relative to other species within the Panicoideae and a progenitor maize genome with eight linkage groups was proposed. Conservation of composite linkage groups indicates that the tetrasomic state arose during maize evolution either from duplication of one progenitor corn genome (autoploidy) or from a cross between species that shared the composite linkages observed in modern maize (alloploidy). New evidence of a quadruplicated homeologous segment on maize chromosomes 2 and 10, and 3 and 4, corresponded to the internally duplicated region on rice chromosomes 11 and 12 and suggested that this duplication in the rice genome predated the divergence of the Panicoideae and Oryzoideae subfamilies. Charting of the macroevolutionary steps leading to the modern maize genome clarifies the interpretation of intercladal comparative maps and facilitates alignments and genomic cross-referencing of genes and phenotypes among grass family members.

scholarly journals Metabolic Interdependence of Obligate Intracellular Bacteria and Their Insect Hosts

2004 ◽  
Vol 68 (4) ◽  
pp. 745-770 ◽  
Author(s):  
Evelyn Zientz ◽  
Thomas Dandekar ◽  
Roy Gross
Keyword(s):  
Metabolic Pathways ◽  
Genome Structure ◽  
Tsetse Flies ◽  
Intracellular Bacteria ◽  
Obligate Intracellular ◽  
The Past ◽  
Evolution Of Metabolic Pathways ◽  
Obligate Intracellular Bacteria ◽  
Evolutionary Consequences ◽  
Endosymbiotic Microorganisms

SUMMARY Mutualistic associations of obligate intracellular bacteria and insects have attracted much interest in the past few years due to the evolutionary consequences for their genome structure. However, much less attention has been paid to the metabolic ramifications for these endosymbiotic microorganisms, which have to compete with but also to adapt to another metabolism—that of the host cell. This review attempts to provide insights into the complex physiological interactions and the evolution of metabolic pathways of several mutualistic bacteria of aphids, ants, and tsetse flies and their insect hosts.

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