Mapping barley Ds insertions using wheat deletion lines reveals high insertion frequencies in gene-rich regions with high to moderate recombination rates

Genome ◽  
2009 ◽  
Vol 52 (6) ◽  
pp. 566-575 ◽  
Author(s):  
Harpinder S. Randhawa ◽  
Jaswinder Singh ◽  
Peggy G. Lemaux ◽  
Kulvinder S. Gill
Keyword(s):  
Gene Cloning ◽  
Single Copy ◽  
Gene Density ◽  
Targeted Mutagenesis ◽  
Recombination Rates ◽  
Transposition Frequency ◽  
Deletion Lines ◽  
Gene Distribution ◽  
Flanking Sequences ◽  
Large Genomes

Gene distribution is highly uneven in the large genomes of barley and wheat; however, location, order, and gene density of gene-containing regions are very similar between the two genomes. Flanking sequences from 35 unique, single-copy, barley Ds insertion events were physically mapped using wheat nullisomic-tetrasomic, ditelosomic, and deletion lines. Of the 35 sequences, 23 (66%) detected 34 loci mapping on all 7 homoeologous wheat groups. Seven sequences were not mapped owing to lack of polymorphism and the remaining 5 (14%) were barley-specific. All 34 loci physically mapped to the previously identified gene-rich regions (GRRs) of wheat, making the contained genes candidates for targeted mutagenesis by remobilization. Transpositions occurred preferentially into GRRs with higher recombination rates. The GRRs containing 17 of the 23 Ds insertions accounted for 60%–89% of the respective arm’s recombination. The remaining 6 (17%) insertions mapped to GRRs with <15% of the arm’s recombination. Overall, kb/cM estimates for the Ds-containing GRRs were twofold higher than those for regions without insertions. These results suggest that all genes may be targeted by transposon-based gene cloning, although the transposition frequency for genes present in recombination-poor regions is significantly less than that present in highly recombinogenic regions.

Restriction Fragment Length Polymorphism and Divergence in the Genomic Regions of High and Low Recombination in Self-Fertilizing and Cross-Fertilizing Aegilops Species

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 423-434
Author(s):  
Jan Dvorřák ◽  
Ming-Cheng Luo ◽  
Zu-Li Yang
Keyword(s):  
Related Species ◽  
Gene Diversity ◽  
Single Copy ◽  
Species Variation ◽  
Recombination Rates ◽  
Distal Chromosome ◽  
Phylogenetic Status ◽  
Average Gene ◽  
Genomic Regions ◽  
Chromosome Regions

Abstract RFLP was investigated at 52 single-copy gene loci among six species of Aegilops, including both cross-fertilizing and self-fertilizing species. Average gene diversity (H) was found to correlate with the level of outcrossing. No relationship was found between H and the phylogenetic status of a species. In all six species, the level of RFLP at a locus was a function of the position of the locus on the chromosome and the recombination rate in the neighborhood of the locus. Loci in the proximal chromosome regions, which show greatly reduced recombination rates relative to the distal regions, were significantly less variable than loci in the distal chromosome regions in all six species. Variation in recombination rates was also reflected in the haplotype divergence between closely related species; loci in the chromosome regions with low recombination rates were found to be diverged less than those in the chromosome regions with high recombination rates. This relationship was not found among the more distantly related species.

scholarly journals Focal Distribution of Baculovirus IE1 Triggered by Its Binding to the hr DNA Elements

2005 ◽  
Vol 79 (1) ◽  
pp. 39-46 ◽  
Author(s):  
Toshihiro Nagamine ◽  
Yu Kawasaki ◽  
Tetsutaro Iizuka ◽  
Shogo Matsumoto
Keyword(s):  
Fluorescent Protein ◽  
Direct Repeat ◽  
Single Copy ◽  
Targeted Mutagenesis ◽  
Homologous Region ◽  
Focus Formation ◽  
Primary Determinant ◽  
Dna Elements ◽  
Species Specific ◽  
Green Fluorescent

ABSTRACT In BmN cells infected with the baculovirus Bombyx mori nucleopolyhedrovirus (BmNPV), IE1, a principal transcriptional activator, localizes to sites of viral DNA replication. IE1 initially displays focal distribution in BmNPV-infected cells prior to DNA synthesis, whereas the protein expressed by transfection with the ie1 gene is distributed throughout the nucleoplasm instead of localized to discrete subnuclear structures. To identify the inducer of focus formation for IE1, we conducted transfection experiments with an IE1-GFP construct and found that cotransfection with genomic DNA fragments bearing the homologous region (hr) sequences caused the formation of IE1-green fluorescent protein (GFP) foci. The transfection of insect cells with a single plasmid containing exclusively the hr3 sequence and the IE1-GFP gene was sufficient to form IE1-GFP foci. These results suggest that hr elements are a primary determinant of the focal distribution of IE1. An analysis of a series of hr3 deletion mutants showed that a single copy of the direct repeat could induce the formation of IE1 foci. Targeted mutagenesis within the hr-binding domain of IE1-GFP caused impairment of the hr-dependent IE1 localization, suggesting that binding of IE1 to the hr elements is essential for the onset of IE1 focus formation. The observation of BmNPV IE1 foci in non-BmNPV-susceptible cells suggests that no species-specific factors are required for hr-dependent IE1 focus formation.

Defective zonae pellucidae in Zp2-null mice disrupt folliculogenesis, fertility and development

Development ◽  
2001 ◽  
Vol 128 (7) ◽  
pp. 1119-1126 ◽  
Author(s):  
T.L. Rankin ◽  
M. O'Brien ◽  
E. Lee ◽  
K. Wigglesworth ◽  
J. Eppig ◽  
...  
Keyword(s):  
Zona Pellucida ◽  
Embryonic Stem ◽  
Single Copy ◽  
Targeted Mutagenesis ◽  
Developmental Competence ◽  
Normal Male ◽  
Null Mouse ◽  
Developmental Potential ◽  
Early Embryos

All vertebrate eggs are surrounded by an extracellular matrix. This matrix is known as the zona pellucida in mammals and is critically important for the survival of growing oocytes, successful fertilization and the passage of early embryos through the oviduct. The mouse zona pellucida is composed of three glycoproteins (ZP1, ZP2 and ZP3), each encoded by a single copy gene. Using targeted mutagenesis in embryonic stem cells, Zp2-null mouse lines have been established. ZP1 and ZP3 proteins continue to be synthesized and form a thin zona matrix in early follicles that is not sustained in pre-ovulatory follicles. The abnormal zona matrix does not affect initial folliculogenesis, but there is a significant decrease in the number of antral stage follicles in ovaries isolated from mice lacking a zona pellucida. Few eggs are detected in the oviduct after stimulation with gonadotropins, and no two-cell embryos are recovered after mating Zp2-null females with normal male mice. The structural defect is more severe than that observed in Zp1-null mice, which have decreased fecundity, but not quite as severe as that observed in Zp3-null mice, which never form a visible zona pellucida and are sterile. Although zona-free oocytes matured and fertilized in vitro can progress to the blastocyst stage, the developmental potential of blastocysts derived from either Zp2- or Zp3-null eggs appears compromised and, after transfer to foster mothers, live births have not been observed. Thus, in addition to its role in fertilization and protection of early embryos, these data are consistent with the zona pellucida maintaining interactions between granulosa cells and oocytes during folliculogenesis that are critical to maximize developmental competence of oocytes.

Different chromosomal distribution patterns of radiation-induced interchange breakpoints in barley: First post-treatment mitosis versus viable offspring

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 128-132 ◽  
Author(s):  
G Künzel ◽  
K I Gecheff ◽  
I Schubert
Keyword(s):  
Distribution Patterns ◽  
Gene Density ◽  
Post Treatment ◽  
Recombination Rates ◽  
Chromosomal Distribution ◽  
Chromosome Breaks ◽  
Translocation Breakpoints ◽  
High Gene ◽  
Radiation Induced ◽  
High Gene Density

Translocation breakpoints (TBs) induced by ionizing radiation are nonrandomly distributed along barley chromosomes. When first post-treatment mitoses were evaluated, centromeres and the heterochromatin-containing proximal segments tended to be more than randomly involved, and terminal segments to be less than randomly involved in translocations. Contrary to this, small chromosomal regions in median and distal arm positions, characterized by high recombination rates and high gene density, were identified as preferred sites for the origination of viable translocations, probably due to deviations in chromatin organization. Apparently, the position of a TB has an influence on the rate of viability versus elimination of the carrier cells. Surprisingly, TBs within centromeres and heterochromatin-containing segments seem to be more harmful for survival than those induced in gene-rich regions.Key words: Hordeum vulgare, radiation-induced chromosome breaks, translocation lines, breakpoint distribution.

Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes

1995 ◽  
Vol 11 (2) ◽  
pp. 63-68 ◽  
Author(s):  
Steven D. Tanksley ◽  
Martin W. Ganal ◽  
Gregory B. Martin
Keyword(s):  
Gene Cloning ◽  
Large Genomes

scholarly journals Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)

2019 ◽  
Vol 10 (1) ◽  
pp. 299-309 ◽  
Author(s):  
Rami-Petteri Apuli ◽  
Carolina Bernhardsson ◽  
Bastian Schiffthaler ◽  
Kathryn M. Robinson ◽  
Stefan Jansson ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Map ◽  
Recombination Rate ◽  
Gene Density ◽  
Populus Tremula ◽  
Rate Variation ◽  
Recombination Rates ◽  
Genomic Features ◽  
European Aspen ◽  
Recombination Rate Variation

The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.

scholarly journals Towards population genomics in non-model species with large genomes: a case study of the marine zooplankton Calanus finmarchicus

2019 ◽  
Vol 6 (2) ◽  
pp. 180608 ◽  
Author(s):  
Marvin Choquet ◽  
Irina Smolina ◽  
Anusha K. S. Dhanasiri ◽  
Leocadio Blanco-Bercial ◽  
Martina Kopp ◽  
...  
Keyword(s):  
Population Genomics ◽  
Single Copy ◽  
Calanus Finmarchicus ◽  
Model Species ◽  
Reduced Representation ◽  
Marine Copepod ◽  
Marine Zooplankton ◽  
Sequencing Technologies ◽  
A Genome ◽  
Large Genomes

Advances in next-generation sequencing technologies and the development of genome-reduced representation protocols have opened the way to genome-wide population studies in non-model species. However, species with large genomes remain challenging, hampering the development of genomic resources for a number of taxa including marine arthropods. Here, we developed a genome-reduced representation method for the ecologically important marine copepod Calanus finmarchicus (haploid genome size of 6.34 Gbp). We optimized a capture enrichment-based protocol based on 2656 single-copy genes, yielding a total of 154 087 high-quality SNPs in C. finmarchicus including 62 372 in common among the three locations tested. The set of capture probes was also successfully applied to the congeneric C. glacialis . Preliminary analyses of these markers revealed similar levels of genetic diversity between the two Calanus species, while populations of C. glacialis showed stronger genetic structure compared to C. finmarchicus . Using this powerful set of markers, we did not detect any evidence of hybridization between C. finmarchicus and C. glacialis . Finally, we propose a shortened version of our protocol, offering a promising solution for population genomics studies in non-model species with large genomes.

Mini-Tn7 vectors as genetic tools for single copy gene cloning in Acinetobacter baumannii

2010 ◽  
Vol 82 (3) ◽  
pp. 296-300 ◽  
Author(s):  
Ayush Kumar ◽  
Courtney Dalton ◽  
Jenny Cortez-Cordova ◽  
Herbert P. Schweizer
Keyword(s):  
Acinetobacter Baumannii ◽  
Gene Cloning ◽  
Single Copy ◽  
Single Copy Gene ◽  
Genetic Tools ◽  
Copy Gene

scholarly journals Complete Chloroplast Genome Sequence of Erigeron breviscapus and Characterization of Chloroplast Regulatory Elements

2021 ◽  
Vol 12 ◽  
Author(s):  
Yifan Yu ◽  
Zhen Ouyang ◽  
Juan Guo ◽  
Wen Zeng ◽  
Yujun Zhao ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Regulatory Elements ◽  
Rrna Genes ◽  
Expression Vectors ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flanking Sequences ◽  
Erigeron Breviscapus ◽  
Cp Genome

Erigeron breviscapus is a famous medicinal plant. However, the limited chloroplast genome information of E. breviscapus, especially for the chloroplast DNA sequence resources, has hindered the study of E. breviscapus chloroplast genome transformation. Here, the complete chloroplast (cp) genome of E. breviscapus was reported. This genome was 152,164bp in length, included 37.2% GC content and was structurally arranged into two 24,699bp inverted repeats (IRs) and two single-copy areas. The sizes of the large single-copy region and the small single-copy region were 84,657 and 18,109bp, respectively. The E. breviscapus cp genome consisted of 127 coding genes, including 83 protein coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. For those genes, 95 genes were single copy genes and 16 genes were duplicated in two inverted regions with seven tRNAs, four rRNAs, and five protein coding genes. Then, genomic DNA of E. breviscapus was used as a template, and the endogenous 5' and 3' flanking sequences of the trnI gene and trnA gene were selected as homologous recombinant fragments in vector construction and cloned through PCR. The endogenous 5' flanking sequences of the psbA gene and rrn16S gene, the endogenous 3' flanking sequences of the psbA gene, rbcL gene, and rps16 gene and one sequence element from the psbN-psbH chloroplast operon were cloned, and certain chloroplast regulatory elements were identified. Two homologous recombination fragments and all of these elements were constructed into the cloning vector pBluescript SK (+) to yield a series of chloroplast expression vectors, which harbored the reporter gene EGFP and the selectable marker aadA gene. After identification, the chloroplast expression vectors were transformed into Escherichia coli and the function of predicted regulatory elements was confirmed by a spectinomycin resistance test and fluorescence intensity measurement. The results indicated that aadA gene and EGFP gene were efficiently expressed under the regulation of predicted regulatory elements and the chloroplast expression vector had been successfully constructed, thereby providing a solid foundation for establishing subsequent E. breviscapus chloroplast transformation system and genetic improvement of E. breviscapus.

scholarly journals Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans.

Genetics ◽  
1995 ◽  
Vol 141 (1) ◽  
pp. 159-179 ◽  
Author(s):  
T M Barnes ◽  
Y Kohara ◽  
A Coulson ◽  
S Hekimi
Keyword(s):  
Caenorhabditis Elegans ◽  
Genetic Map ◽  
Recombination Rate ◽  
Physical Map ◽  
Gene Density ◽  
Cdna Clones ◽  
Recombination Rates ◽  
Noncoding Dna ◽  
Physical Size ◽  
C Elegans

Abstract The genetic map of each Caenorhabditis elegans chromosome has a central gene cluster (less pronounced on the X chromosome) that contains most of the mutationally defined genes. Many linkage group termini also have clusters, though involving fewer loci. We examine the factors shaping the genetic map by analyzing the rate of recombination and gene density across the genome using the positions of cloned genes and random cDNA clones from the physical map. Each chromosome has a central gene-dense region (more diffuse on the X) with discrete boundaries, flanked by gene-poor regions. Only autosomes have reduced rates of recombination in these gene-dense regions. Cluster boundaries appear discrete also by recombination rate, and the boundaries defined by recombination rate and gene density mostly, but not always, coincide. Terminal clusters have greater gene densities than the adjoining arm but similar recombination rates. Thus, unlike in other species, most exchange in C. elegans occurs in gene-poor regions. The recombination rate across each cluster is constant and similar; and cluster size and gene number per chromosome are independent of the physical size of chromosomes. We propose a model of how this genome organization arose.

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