scholarly journals Chromosome Identification and Cytogenetic Map Construction of Zhikong Scallop (Chlamys farreri) Based on Fluorescence in situ Hybridization

2021 ◽  
Vol 8 ◽  
Author(s):  
Liping Hu ◽  
Liming Jiang ◽  
Qiang Xing ◽  
Zujing Yang ◽  
Qiang Zhao ◽  
...  
Keyword(s):  
Molecular Breeding ◽  
Repetitive Sequences ◽  
Genomic Analysis ◽  
Artificial Chromosome ◽  
Chlamys Farreri ◽  
Cytogenetic Map ◽  
Zhikong Scallop ◽  
Bac Clones ◽  
Map Construction

Zhikong scallop (Chlamys farreri) is a bivalve species with broad economic and biological value, and an essential species of aquaculture in North China. Recently, efforts have been made to improve knowledge of genome, genetics, and cytogenetics, which is devoted to develop the molecular breeding project for the scallop. In this study, we constructed a cytogenetic map and identified all chromosomes of C. farreri using fluorescence in situ hybridization (FISH). A total of 100 Bacterial Artificial Chromosome (BAC) clones and 27 fosmid clones, including 58 microsatellite marker-anchored BAC clones, 4 genes-anchored BAC clones, 38 random BAC clones, 22 repetitive sequences-anchored fosmid clones, and 5 gene-anchored fosmid clones, were tested as probes, and 69 of them produced specific and stable signal on one pair of chromosomes. Then, multiple co-hybridizations were conducted to distinguish all the submetacentric and subtelocentric chromosomes with similar morphology by the abovementioned chromosome-specific markers. On this basis, a cytogenetic map of C. farreri containing 69 clones was constructed by co-hybridization and karyotype analysis. The markers covered all 19 pairs of chromosomes, and the average number of markers on each chromosome was 3.6. The cytogenetic map provides a platform for genetic and genomic analysis of C. farreri, which facilitates the molecular breeding project of C. farreri and promotes the comparative studies of chromosome evolution in scallops and even bivalves.

Integrated karyotyping of sorghum by in situ hybridization of landed BACs

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 402-412 ◽  
Author(s):  
Jeong-Soon Kim ◽  
Kevin L Childs ◽  
M Nurul Islam-Faridi ◽  
Monica A Menz ◽  
Robert R Klein ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Genetic Manipulation ◽  
Artificial Chromosome ◽  
Linkage Groups ◽  
Cytogenetic Map ◽  
Structural Genomic ◽  
Bac Clones ◽  
Flow Sorting ◽  
Fish Signal

The reliability of genome analysis and proficiency of genetic manipulation are increased by assignment of linkage groups to specific chromosomes, placement of centromeres, and orientation with respect to telomeres. We have endeavored to establish means to enable these steps in sorghum (Sorghum bicolor (L.) Moench), the genome of which contains ca. 780 Mbp spread across n = 10 chromosomes. Our approach relies on fluorescence in situ hybridization (FISH) and integrated structural genomic resources, including large-insert genomic clones in bacterial artificial chromosome (BAC) libraries. To develop robust FISH probes, we selected sorghum BACs by association with molecular markers that map near the ends of linkage groups, in regions inferred to be high in recombination. Overall, we selected 22 BACs that encompass the 10 linkage groups. As a prelude to development of a multiprobe FISH cocktail, we evaluated BAC-derived probes individually and in small groups. Biotin- and digoxygenin-labeled probes were made directly from the BAC clones and hybridized in situ to chromosomes without using suppressive unlabelled C0t-1 DNA. Based on FISH-signal strength and the relative degree of background signal, we judged 19 BAC-derived probes to be satisfactory. Based on their relative position, and collective association with all 10 linkage groups, we chose 17 of the 19 BACs to develop a 17-locus probe cocktail for dual-color detection. FISH of the cocktail allowed simultaneous identification of all 10 chromosomes. The results indicate that linkage and physical maps of sorghum allow facile selection of BAC clones according to position and FISH-signal quality. This capability will enable development of a high-quality molecular cytogenetic map and an integrated genomics system for sorghum, without need of chromosome flow sorting or microdissection. Moreover, transgeneric FISH experiments suggest that the sorghum system might be applicable to other Gramineae.Key words: integrated karyotyping, FISH, sorghum, BAC.

Sequencing and analysis of four BAC clones containing innate immune genes from the Zhikong scallop (Chlamys farreri)

Gene ◽  
2012 ◽  
Vol 502 (1) ◽  
pp. 9-15 ◽  
Author(s):  
Cui Zhao ◽  
Tongwu Zhang ◽  
Xiaojun Zhang ◽  
Songnian Hu ◽  
Jianhai Xiang
Keyword(s):  
Chlamys Farreri ◽  
Innate Immune ◽  
Zhikong Scallop ◽  
Immune Genes ◽  
Bac Clones ◽  
Innate Immune Genes

scholarly journals Development of a sequence-based reference physical map of pea (Pisum sativum L.)

2019 ◽  
Author(s):  
Krishna Kishore Gali ◽  
Bunyamin Tar’an ◽  
Mohammed-Amin Madoui ◽  
Edwin van der Vossen ◽  
Jan van Oeveren ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Positional Cloning ◽  
Physical Map ◽  
Repetitive Sequences ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Bac Clones ◽  
Pooled Dna ◽  
Mapping Technology ◽  
Generation Sequencing

AbstractWhole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. To address the challenges of accurate assembly of the pea genome (~4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. These WGP tags were used to assemble 220,013 BACs into contigs. Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. The average contig size is 0.33 Mbp and the N50 contig size is 0.62 Mbp. WGPTM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. This sequence-based physical map will be useful to assemble the genome sequence of pea. Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest.

Construction of bacterial artificial chromosome libraries for Zhikong Scallop Chlamys farreri

2008 ◽  
Vol 26 (2) ◽  
pp. 215-218
Author(s):  
Yang Zhang ◽  
Xiaojun Zhang ◽  
Chantel F. Scheuring ◽  
Hongbin Zhang ◽  
Fuhua Li ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Artificial Chromosome ◽  
Chlamys Farreri ◽  
Zhikong Scallop

Physical organization of the major duplication on Brassica oleracea chromosome O6 revealed through fluorescence in situ hybridization with Arabidopsis and Brassica BAC probes

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 1093-1103 ◽  
Author(s):  
E C Howell ◽  
S J Armstrong ◽  
G C Barker ◽  
G H Jones ◽  
G J King ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Brassica Oleracea ◽  
Artificial Chromosome ◽  
Genetic Distances ◽  
Chromosome 1 ◽  
Cytogenetic Map ◽  
Inverted Duplication ◽  
Close Relationship

The close relationship between Brassica oleracea and Arabidopsis thaliana has been used to explore the genetic and physical collinearity of the two species, focusing on an inverted segmental chromosome duplication within linkage group O6 of B. oleracea. Genetic evidence suggests that these segments share a common origin with a region of Arabidopsis chromosome 1. Brassica oleracea and Arabidopsis bacterial artificial chromosome probes have been used for fluorescence in situ hybridization analysis of B. oleracea pachytene chromosomes to further characterize the inverted duplication. This has been highly effective in increasing the local resolution of the cytogenetic map. We have shown that the physical order of corresponding genetic markers is highly conserved between the duplicated regions in B. oleracea and the physical lengths of the regions at pachytene are similar, while the genetic distances are considerably different. The physical marker order is also well conserved between Arabidopsis and B. oleracea, with only one short inversion identified. Furthermore, the relative physical distances between the markers in one segment of B. oleracea and Arabidopsis have stayed approximately the same. The efficacy of using fluorescence in situ hybridization, together with other forms of physical and genetic mapping, for elucidating such issues relating to synteny is discussed.Key words: collinearity, cytogenetic map, pachytene chromosomes, Brassica, Arabidopsis.

Comparison of the chromosome maps around a resistance hot spot on chromosome 5 of potato and tomato using BAC-FISH painting

Genome ◽  
2010 ◽  
Vol 53 (2) ◽  
pp. 103-110 ◽  
Author(s):  
Ute C. Achenbach ◽  
Xiaomin Tang ◽  
Agim Ballvora ◽  
Hans de Jong ◽  
Christiane Gebhardt
Keyword(s):  
Hot Spot ◽  
Artificial Chromosome ◽  
Globodera Pallida ◽  
Chromosome 5 ◽  
Physical Size ◽  
Bac Clones ◽  
A Genome ◽  
Chromosome Maps ◽  
Bac Fish

Potato chromosome 5 harbours numerous genes for important qualitative and quantitative traits, such as resistance to the root cyst nematode Globodera pallida and the late blight fungus, Phytophthora infestans . The genes make up part of a “hot spot” for resistances to various pathogens covering a genetic map length of 3 cM between markers GP21 and GP179. We established the physical size and position of this region on chromosome 5 in potato and tomato using fluorescence in situ hybridization (FISH) on pachytene chromosomes. Five potato bacterial artificial chromosome (BAC) clones with the genetically anchored markers GP21, R1-contig (proximal end), CosA, GP179, and StPto were selected, labeled with different fluorophores, and hybridized in a five-colour FISH experiment. Our results showed the location of the BAC clones in the middle of the long arm of chromosome 5 in both potato and tomato. Based on chromosome measurements, we estimate the physical size of the GP21–GP179 interval at 0.85 Mb and 1.2 Mb in potato and tomato, respectively. The GP21–GP179 interval is part of a genome segment known to have inverted map positions between potato and tomato.

A bacterial artificial chromosome (BAC) library of Malus floribunda 821 and contig construction for positional cloning of the apple scab resistance gene Vf

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 1104-1113 ◽  
Author(s):  
Mingliang Xu ◽  
Junqi Song ◽  
Zhukuan Cheng ◽  
Jiming Jiang ◽  
Schuyler S Korban
Keyword(s):  
Positional Cloning ◽  
Apple Scab ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Scab Resistance ◽  
Vf Gene ◽  
Bac Clones ◽  
Malus Floribunda ◽  
Sequence Characterized Amplified Regions

The apple scab resistance gene Vf, originating from the wild species Malus floribunda 821, has been incorporated into a wide variety of apple cultivars through a classical breeding program. With the aim of isolating the Vf gene, a bacterial artificial chromosome (BAC) library consisting of 31 584 clones has been constructed from M. floribunda 821. From the analysis of 88 randomly selected BAC clones, the average insert size is estimated at 125 kb. If it is assumed that the genome size of M. floribunda 821 is 769 Mb/haploid, the library represents about 5× haploid genome equivalents. This provides a 99% probability of finding any specific sequence from this library. PCR-based screening of the library has been carried out using eight random genomic sequence-characterized amplified regions (SCARs), chloroplast- and mitochondria-specific SCARs, and 13 high-density Vf-linked SCAR markers. An average of five positive BAC clones per random SCAR has been obtained, whereas less than 1% of BAC clones are derived from the chloroplast or mitochondrial genomes. Most BAC clones identified with Vf-linked SCAR markers are physically linked. Three BAC contigs along the Vf region have been obtained by assembling physically linked BAC clones based on their fingerprints. The overlapping relatedness of BAC clones has been further confirmed by cytogenetic mapping using fiber fluorescence in situ hybridization (fiber-FISH). The M. floribunda 821 BAC library provides a valuable genetic resource not only for map-based cloning of the Vf gene, but also for finding many other important genes for improving the cultivated apple.Key words: apple, resistance Vf gene, BAC library, sequence-characterized amplified regions (SCARs), fiber fluorescence in situ hybridization (fiber-FISH), positional cloning.

scholarly journals Bacterial Artificial Chromosome-Based Comparative Genomic Analysis Identifies Mycobacterium microti as a Natural ESAT-6 Deletion Mutant

2002 ◽  
Vol 70 (10) ◽  
pp. 5568-5578 ◽  
Author(s):  
Priscille Brodin ◽  
Karin Eiglmeier ◽  
Magali Marmiesse ◽  
Alain Billault ◽  
Thierry Garnier ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Chromosomal Region ◽  
Genomic Analysis ◽  
Direct Repeat ◽  
Artificial Chromosome ◽  
Comparative Genomic ◽  
Minimal Set ◽  
Bac Clones ◽  
Almost All ◽  
Mycobacterium Microti

ABSTRACT Mycobacterium microti is a member of the Mycobacterium tuberculosis complex that causes tuberculosis in voles. Most strains of M. microti are harmless for humans, and some have been successfully used as live tuberculosis vaccines. In an attempt to identify putative virulence factors of the tubercle bacilli, genes that are absent from the avirulent M. microti but present in human pathogen M. tuberculosis or Mycobacterium bovis were searched for. A minimal set of 50 bacterial artificial chromosome (BAC) clones that covers almost all of the genome of M. microti OV254 was constructed, and individual BACs were compared to the corresponding BACs from M. bovis AF2122/97 and M. tuberculosis H37Rv. Comparison of pulsed-field gel-separated DNA digests of BAC clones led to the identification of 10 regions of difference (RD) between M. microti OV254 and M. tuberculosis. A 14-kb chromosomal region (RD1mic) that partly overlaps the RD1 deletion in the BCG vaccine strain was missing from the genomes of all nine tested M. microti strains. This region covers 13 genes, Rv3864 to Rv3876, in M. tuberculosis, including those encoding the potent ESAT-6 and CFP-10 antigens. In contrast, RD5mic, a region that contains three phospholipase C genes (plcA to -C), was missing from only the vole isolates and was present in M. microti strains isolated from humans. Apart from RD1mic and RD5mic other M. microti-specific deleted regions have been identified (MiD1 to MiD3). Deletion of MiD1 has removed parts of the direct repeat region in M. microti and thus contributes to the characteristic spoligotype of M. microti strains.

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