High-Resolution Pachytene Chromosome Mapping of Bacterial Artificial Chromosomes Anchored by Genetic Markers Reveals the Centromere Location and the Distribution of Genetic Recombination Along Chromosome 10 of Rice

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1749-1757 ◽  
Author(s):  
Zhukuan Cheng ◽  
Gernot G Presting ◽  
C Robin Buell ◽  
Rod A Wing ◽  
Jiming Jiang
Keyword(s):  
Large Scale ◽  
Genetic Recombination ◽  
Physical Map ◽  
Rice Chromosome ◽  
Resolving Power ◽  
Pachytene Chromosome ◽  
Chromosome 10 ◽  
Bac Clone ◽  
Fish Mapping ◽  
Artificial Chromosomes

AbstractLarge-scale physical mapping has been a major challenge for plant geneticists due to the lack of techniques that are widely affordable and can be applied to different species. Here we present a physical map of rice chromosome 10 developed by fluorescence in situ hybridization (FISH) mapping of bacterial artificial chromosome (BAC) clones on meiotic pachytene chromosomes. This physical map is fully integrated with a genetic linkage map of rice chromosome 10 because each BAC clone is anchored by a genetically mapped restriction fragment length polymorphism marker. The pachytene chromosome-based FISH mapping shows a superior resolving power compared to the somatic metaphase chromosome-based methods. The telomere-centromere orientation of DNA clones separated by 40 kb can be resolved on early pachytene chromosomes. Genetic recombination is generally evenly distributed along rice chromosome 10. However, the highly heterochromatic short arm shows a lower recombination frequency than the largely euchromatic long arm. Suppression of recombination was found in the centromeric region, but the affected region is far smaller than those reported in wheat and barley. Our FISH mapping effort also revealed the precise genetic position of the centromere on chromosome 10.

scholarly journals Physical and Genetic Mapping in the GrassesLolium perenneandFestuca pratensis

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 315-324 ◽  
Author(s):  
J King ◽  
I P Armstead ◽  
I S Donnison ◽  
H M Thomas ◽  
R N Jones ◽  
...  
Keyword(s):  
Large Scale ◽  
Physical Map ◽  
Rice Chromosome ◽  
Nucleolar Organizer ◽  
Physical Distance ◽  
Chromosome 1 ◽  
Grass Species ◽  
Nucleolar Organizer Regions ◽  
Single Chromosome ◽  
Large Scale Analysis

AbstractA single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line (2n = 2x = 14). In this line recombination occurs throughout the length of the F. pratensis/L. perenne bivalent. The F. pratensis chromosome and recombinants between it and its L. perenne homeologue can be visualized using genomic in situ hybridization (GISH). GISH junctions represent the physical locations of sites of recombination, enabling a range of recombinant chromosomes to be used for physical mapping of the introgressed F. pratensis chromosome. The physical map, in conjunction with a genetic map composed of 104 F. pratensis-specific amplified fragment length polymorphisms (AFLPs), demonstrated: (1) the first large-scale analysis of the physical distribution of AFLPs; (2) variation in the relationship between genetic and physical distance from one part of the F. pratensis chromosome to another (e.g., variation was observed between and within chromosome arms); (3) that nucleolar organizer regions (NORs) and centromeres greatly reduce recombination; (4) that coding sequences are present close to the centromere and NORs in areas of low recombination in plant species with large genomes; and (5) apparent complete synteny between the F. pratensis chromosome and rice chromosome 1.

scholarly journals A novel high-accuracy genome assembly method utilizing a high-throughput workflow

2020 ◽  
Author(s):  
Qingdong Zeng ◽  
Wenjin Cao ◽  
Liping Xing ◽  
Guowei Qin ◽  
Jianhui Wu ◽  
...  
Keyword(s):  
High Throughput ◽  
Genome Assembly ◽  
Large Scale ◽  
Sequence Data ◽  
Physical Map ◽  
Bac Library ◽  
High Accuracy ◽  
Biological Research ◽  
Bac Clone ◽  
Assembly Method

AbstractAcross domains of biological research using genome sequence data, high-quality reference genome sequences are essential for characterizing genetic variation and understanding the genetic basis of phenotypes. However, the construction of genome assemblies for various species is often hampered by complexities of genome organization, especially repetitive and complex sequences, leading to mis-assembly and missing regions. Here, we describe a high-throughput gold standard genome assembly workflow using a large-scale bacterial artificial chromosome (BAC) library with a refined two-step pooling strategy and the Lamp assembler algorithm. This strategy minimizes the laborious processes of physical map construction and clone-by-clone sequencing, enabling inexpensive sequencing of several thousand BAC clones. By applying this strategy with a minimum tiling path BAC clone library for the short arm of chromosome 2D (2DS) of bread wheat, 98% of BAC sequences, covering 92.7% of the 2DS chromosome, were assembled correctly for this species with a highly complex and repetitive genome. We also identified 48 large mis-assemblies in the reference wheat genome assembly (IWGSC RefSeq v1.0) and corrected these large mis-assemblies in addition to filling 92.2% of the gaps in RefSeq v1.0. Our 2DS assembly represents a new benchmark for the assembly of complex genomes with both high accuracy and efficiency.

scholarly journals Heterogeneity in Rates of Recombination Across the Mouse Genome

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 537-548 ◽  
Author(s):  
Michael W Nachman ◽  
Gary A Churchill
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Large Scale ◽  
Physical Map ◽  
Genetic Maps ◽  
Recombination Rates ◽  
Physical Maps ◽  
Genomic Patterns ◽  
Mary Lyon ◽  
Microsatellite Linkage

Abstract If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.

scholarly journals The SAMI Galaxy Survey: the third and final data release

2021 ◽  
Author(s):  
Scott M Croom ◽  
Matt S Owers ◽  
Nicholas Scott ◽  
Henry Poetrodjojo ◽  
Brent Groves ◽  
...  
Keyword(s):  
Large Scale ◽  
Resolving Power ◽  
Stellar Kinematics ◽  
New Era ◽  
Optical Wavelength ◽  
Astronomical Optics ◽  
Data Release ◽  
Gas Ionization ◽  
Release Data ◽  
First Time

Abstract We have entered a new era where integral-field spectroscopic surveys of galaxies are sufficiently large to adequately sample large-scale structure over a cosmologically significant volume. This was the primary design goal of the SAMI Galaxy Survey. Here, in Data Release 3 (DR3), we release data for the full sample of 3068 unique galaxies observed. This includes the SAMI cluster sample of 888 unique galaxies for the first time. For each galaxy, there are two primary spectral cubes covering the blue (370–570 nm) and red (630–740 nm) optical wavelength ranges at spectral resolving power of R = 1808 and 4304 respectively. For each primary cube, we also provide three spatially binned spectral cubes and a set of standardized aperture spectra. For each galaxy, we include complete 2D maps from parameterized fitting to the emission-line and absorption-line spectral data. These maps provide information on the gas ionization and kinematics, stellar kinematics and populations, and more. All data are available online through Australian Astronomical Optics (AAO) Data Central.

scholarly journals Cross-Species RNAi Rescue Platform in Drosophila melanogaster

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 1165-1173 ◽  
Author(s):  
Shu Kondo ◽  
Matthew Booker ◽  
Norbert Perrimon
Keyword(s):  
Cell Culture ◽  
Drosophila Melanogaster ◽  
Large Scale ◽  
Transgenic Animals ◽  
Selection Marker ◽  
Bacterial Artificial Chromosomes ◽  
Loss Of Function ◽  
Artificial Chromosomes ◽  
Target Effects

RNAi-mediated gene knockdown in Drosophila melanogaster is a powerful method to analyze loss-of-function phenotypes both in cell culture and in vivo. However, it has also become clear that false positives caused by off-target effects are prevalent, requiring careful validation of RNAi-induced phenotypes. The most rigorous proof that an RNAi-induced phenotype is due to loss of its intended target is to rescue the phenotype by a transgene impervious to RNAi. For large-scale validations in the mouse and Caenorhabditis elegans, this has been accomplished by using bacterial artificial chromosomes (BACs) of related species. However, in Drosophila, this approach is not feasible because transformation of large BACs is inefficient. We have therefore developed a general RNAi rescue approach for Drosophila that employs Cre/loxP-mediated recombination to rapidly retrofit existing fosmid clones into rescue constructs. Retrofitted fosmid clones carry a selection marker and a phiC31 attB site, which facilitates the production of transgenic animals. Here, we describe our approach and demonstrate proof-of-principle experiments showing that D. pseudoobscura fosmids can successfully rescue RNAi-induced phenotypes in D. melanogaster, both in cell culture and in vivo. Altogether, the tools and method that we have developed provide a gold standard for validation of Drosophila RNAi experiments.

scholarly journals Disentangling AGN and starburst activities in NGC 6240 from an X-ray perspective

2014 ◽  
Vol 10 (S312) ◽  
pp. 36-38
Author(s):  
Junfeng Wang
Keyword(s):  
Active Galactic Nuclei ◽  
Large Scale ◽  
Imaging Spectroscopy ◽  
Galactic Nuclei ◽  
Resolving Power ◽  
High Excitation ◽  
X Ray ◽  
Supermassive Black Hole ◽  
X Ray Imaging ◽  
High Temperature Gas

AbstractThe circum-nuclear region in an active galaxy is often complex with presence of high excitation gas, collimated radio outflow, and star formation activities, besides the actively accreting supermassive black hole. The unique spatial resolving power of Chandra X-ray imaging spectroscopy enables more investigations to disentangle the active galactic nuclei and starburst activities. For galaxies in the throes of a violent merging event such as NGC6240, we were able to resolve the high temperature gas surrounding its binary active black holes and discovered a large scale soft X-ray halo.

Isolation and structural analysis of a 1.2-megabase N-myc amplicon from a human neuroblastoma

1992 ◽  
Vol 12 (12) ◽  
pp. 5563-5570
Author(s):  
S S Schneider ◽  
J L Hiemstra ◽  
B A Zehnbauer ◽  
P Taillon-Miller ◽  
D L Le Paslier ◽  
...  
Keyword(s):  
Cell Line ◽  
Gene Amplification ◽  
De Novo ◽  
Physical Map ◽  
Neuroblastoma Cell ◽  
Neuroblastoma Cell Line ◽  
Chromosome 2 ◽  
Human Neuroblastoma ◽  
Artificial Chromosomes ◽  
Yeast Artificial Chromosomes

Oncogene amplification is observed frequently in human cancers, but little is known about the mechanism of gene amplification or the structure of amplified DNA in tumor cells. We have studied the N-myc amplified domain from a representative neuroblastoma cell line, SMS-KAN, and compared the map of the amplicon in this cell line with that seen in normal DNA. The SMS-KAN cell line DNA was cloned into yeast artificial chromosomes (YACs), and clones were identified by screening the YAC library with amplified DNA probes that were obtained previously (B. Zehnbauer, D. Small, G. M. Brodeur, R. Seeger, and B. Vogelstein, Mol. Cell. Biol. 8:522-530, 1988). In addition, YAC clones corresponding to the normal N-myc locus on chromosome 2 were obtained by screening two normal human YAC libraries with these probes, and the restriction maps of the two sets of overlapping YACs were compared. Our results suggest that the amplified domain in this cell line is a approximately 1.2-Mb circular molecule with a head-to-tail configuration, and the physical map of the normal N-myc locus generally is conserved in the amplicon. These results provide a physical map of the amplified domain of a neuroblastoma cell line that has de novo amplification of an oncogene. The head-to-tail organization, the general conservation of the normal physical map in the amplicon, and the extrachromosomal location of the amplified DNA are most consistent with the episome formation-plus-segregation mechanism of gene amplification in these tumors.

scholarly journals Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Yang Song ◽  
Yong Zhang ◽  
Zhenzhi Han ◽  
Wen Xu ◽  
Jinbo Xiao ◽  
...  
Keyword(s):  
Large Scale ◽  
Genetic Recombination ◽  
Mainland China ◽  
Clinical Manifestations ◽  
Foot And Mouth Disease ◽  
Capsid Gene ◽  
Global Epidemic ◽  
Public Health Burden ◽  
Coxsackievirus A6 ◽  
Fast Spreading

Abstract Hand, foot, and mouth disease (HFMD) is a common global epidemic. From 2008 onwards, many HFMD outbreaks caused by coxsackievirus A6 (CV-A6) have been reported worldwide. Since 2013, with a dramatically increasing number of CV-A6-related HFMD cases, CV-A6 has become the predominant HFMD pathogen in mainland China. Phylogenetic analysis based on the VP1 capsid gene revealed that subtype D3 dominated the CV-A6 outbreaks. Here, we performed a large-scale (near) full-length genetic analysis of global and Chinese CV-A6 variants, including 158 newly sequenced samples collected extensively in mainland China between 2010 and 2018. During the global transmission of subtype D3 of CV-A6, the noncapsid gene continued recombining, giving rise to a series of viable recombinant hybrids designated evolutionary lineages, and each lineage displayed internal consistency in both genetic and epidemiological features. The emergence of lineage –A since 2005 has triggered CV-A6 outbreaks worldwide, with a rate of evolution estimated at 4.17 × 10−3 substitutions site-1 year−1 based on a large number of monophyletic open reading frame sequences, and created a series of lineages chronologically through varied noncapsid recombination events. In mainland China, lineage –A has generated another two novel widespread lineages (–J and –L) through recombination within the enterovirus A gene pool, with robust estimates of occurrence time. Lineage –A, –J, and –L infections presented dissimilar clinical manifestations, indicating that the conservation of the CV-A6 capsid gene resulted in high transmissibility, but the lineage-specific noncapsid gene might influence pathogenicity. Potentially important amino acid substitutions were further predicted among CV-A6 variants. The evolutionary phenomenon of noncapsid polymorphism within the same subtype observed in CV-A6 was uncommon in other leading HFMD pathogens; such frequent recombination happened in fast-spreading CV-A6, indicating that the recovery of deleterious genomes may still be ongoing within CV-A6 quasispecies. CV-A6-related HFMD outbreaks have caused a significant public health burden and pose a great threat to children’s health; therefore, further surveillance is greatly needed to understand the full genetic diversity of CV-A6 in mainland China.

Large‐Scale BAC Clone Restriction Digest Fingerprinting

2007 ◽  
Vol 53 (1) ◽  
Author(s):  
Carrie A. Mathewson ◽  
Jacqueline E. Schein ◽  
Marco A. Marra
Keyword(s):  
Large Scale ◽  
Bac Clone ◽  
Restriction Digest

A paracentric inversion suppresses genetic recombination at the FON3 locus with breakpoints corresponding to sequence gaps on rice chromosome 11L

2006 ◽  
Vol 277 (3) ◽  
pp. 263-272 ◽  
Author(s):  
Li Jiang ◽  
Wenli Zhang ◽  
Zhihui Xia ◽  
Guanghuai Jiang ◽  
Qian Qian ◽  
...  
Keyword(s):  
Genetic Recombination ◽  
Rice Chromosome ◽  
Paracentric Inversion
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