Cytogenetic Map of Pummelo and Chromosome Evolution of True Citrus Species and the Hybrid Sweet Orange

Pummelo (Citrus maxima) is considered as one of the true citrus species. Together with mandarin (C. reticulata), it gave rise to the hybrid sweet orange (C. sinensis) and other important citrus crops. Although these species have 2n = 18, each has a unique heterochromatin distribution. The aims of this study were to identify chromosome homoeologies between pummelo and other true citrus species, to investigate the karyotypic changes involved in the chromosomal evolution between true citrus and to shed light into the origin of sweet orange hybrid karyotype. Mitotic metaphase chromosomes of pummelo and sweet orange were double stained with the fluorochromes CMA/DAPI (Chromomycin A3/4’-6-diamidino-2-phenylindole), and identified by FISH (Fluorescence in Situ Hybridization) with chromosome-specific BAC (Bacterial Artificial Chromosome) markers. The results were compared to previously established cytogenetic maps of mandarin, C. medica and Poncirus trifoliata. Only chromosomes 1, 4 and 8 were maintained unaltered among species, with chromosomes 2 and 3 being among the least conserved in heterochromatin distribution. BACs were conserved in position among homoeologs and the markers mapped to chromosomes 2 and 3 indicated that sweet orange karyotype largely conserved one chromosome from pummelo and one from mandarin. Despite conserved synteny, expansion and contraction of heterochromatic blocks accounted for the differences between karyotypes, even between the hybrid sweet orange and pummelo.

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Integration of mandarin (Citrus reticulata) cytogenetic map with its genome sequence

Genome ◽

10.1139/gen-2020-0046 ◽

2020 ◽

Vol 63 (9) ◽

pp. 437-444

Author(s):

Sandra Mendes ◽

Thallita Régis ◽

Javier Terol ◽

Walter dos Santos Soares Filho ◽

Manuel Talon ◽

...

Keyword(s):

Sweet Orange ◽

Artificial Chromosome ◽

Chromosomal Evolution ◽

Fruit Production ◽

Citrus Reticulata ◽

Cytogenetic Map ◽

Structural Genomic ◽

Dapi Banding ◽

Complex Relationships ◽

Bac Fish

Citrus is an extremely important genus in terms of world fruit production. Despite its economic importance and the small genome sizes of its species (2n = 18, 1C = 430 ± 68 Mbp), entire genomic assemblies have only recently become available for some of its representatives. Together with the previous CMA/DAPI banding and fluorescence in situ hybridization (FISH) in the group, these data are important for understanding the complex relationships between its species and for assisting breeding programs. To anchor genomic data with the cytogenetic map of mandarin (Citrus reticulata), the parental species of several economically important hybrids such as sweet orange and clementine, 18 BAC (bacterial artificial chromosome) clones were used. Eleven clementine BACs were positioned by BAC-FISH, doubling the number of chromosome markers so far available for BAC-FISH in citrus. Additionally, six previously mapped BACs were end-sequenced, allowing, together with one BAC previously sequenced, their assignment to scaffolds and the subsequent integration of chromosomes and the genome assembly. This study therefore established correlations between mandarin scaffolds and chromosomes, allowing further structural genomic and comparative study with the sweet orange genome, as well as insights into the chromosomal evolution of the group.

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Detection of myc translocations in lymphoma cells by fluorescence in situ hybridization with yeast artificial chromosomes

Blood ◽

10.1182/blood.v85.8.2132.bloodjournal8582132 ◽

1995 ◽

Vol 85 (8) ◽

pp. 2132-2138 ◽

Cited By ~ 23

Author(s):

ML Veronese ◽

M Ohta ◽

J Finan ◽

PC Nowell ◽

CM Croce

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Yeast Artificial Chromosome ◽

Human Lymphocytes ◽

Artificial Chromosome ◽

Chromosome 8 ◽

Metaphase Chromosomes ◽

Artificial Chromosomes ◽

Myc Gene

Translocations involving chromosome 8 at band q24 and one of the Ig loci on chromosomes 14q32, 22q11, and 2p11 are the hallmark of Burkitt's lymphoma (BL). It has been previously observed that the exact localization of the breakpoints at chromosome 8q24 can vary significantly from patient to patient, scattering over a distance of more than 300 kb upstream of c-myc and about 300 kb downstream of c-myc. To generate probes for fluorescence in situ hybridization (FISH) that detect most c-myc translocations, we screened a yeast artificial chromosome (YAC) library from normal human lymphocytes by colony hybridization, using three markers surrounding the c-myc gene as probes. We obtained 10 YAC clones ranging in size between 500 and 200 kb. Two nonchimeric clones were used for FISH on several BL cell lines and patient samples with different breakpoints at 8q24. Our results show that the YAC clones detected translocations scattered along approximately 200 kb in both metaphase chromosomes and interphase nuclei. The sensitivity, rapidity, and feasibility in nondividing cells render FISH an important diagnostic tool. Furthermore, the use of large DNA fragments such as YACs greatly simplifies the detection of translocations with widely scattered breakpoints such as these seen in BL.

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Isoenzymatic polymorphism in Citrus spp. and Poncirus trifoliata (L.) Raf. (Rutaceae)

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000100030 ◽

2000 ◽

Vol 23 (1) ◽

pp. 163-168 ◽

Cited By ~ 12

Author(s):

Valdenice Moreira Novelli ◽

Marcos Antonio Machado ◽

Catalina Romero Lopes

Keyword(s):

Leucine Aminopeptidase ◽

Sweet Orange ◽

High Variability ◽

Poncirus Trifoliata ◽

Polymorphism Analysis ◽

Citrus Species ◽

Shikimate Dehydrogenase ◽

Phosphogluconate Dehydrogenase ◽

Enzymatic Systems ◽

Citrus Spp

Isoenzymatic polymorphism analysis was used to determine genetic variability among species and hybrids of Citrus spp. and one accession of Poncirus trifoliata (L.) Raf. Ten enzymatic systems aspartate aminotransferase (AAT), acid phosphatase (ACP), leucine aminopeptidase (LAP), 6-phosphogluconate dehydrogenase (6-PGD), isocitrate dehydrogenase (IDH), phosphoglucoisomerase (PGI), phosphoglucomutase (PGM), diaphorase (DIA), shikimate dehydrogenase (SKD) and peroxidase (PRX) were analyzed. Twenty loci and 48 alleles were identified. Sweet orange cultivars (C. sinensis (L). Osbeck) showed the highest polymorphism with the largest number of heterozygous loci, although the alleles of those loci were the same in all cultivars, with the exception of Westin and Lima graúda. Mandarins (C. reticulata Blanco) exhibited diverse patterns, whereas Poncirus trifoliata (L.) Raf. showed high variability with all Citrus species and hybrids. Exclusive phenotypes were observed in some enzymatic systems, and similar patterns were found among interspecific hybrids and their putative parents.

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

Genome ◽

10.1139/g05-069 ◽

2005 ◽

Vol 48 (6) ◽

pp. 1093-1103 ◽

Cited By ~ 23

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.

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Integrated karyotyping of sorghum by in situ hybridization of landed BACs

Genome ◽

10.1139/g01-141 ◽

2002 ◽

Vol 45 (2) ◽

pp. 402-412 ◽

Cited By ~ 58

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.

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

Frontiers in Marine Science ◽

10.3389/fmars.2021.741230 ◽

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.

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In situ localization of yeast artificial chromosome sequences on tomato and potato metaphase chromosomes

Chromosome Research ◽

10.1007/bf02263677 ◽

1996 ◽

Vol 4 (4) ◽

pp. 277-281 ◽

Cited By ~ 13

Author(s):

Jörg Fuchs ◽

Dorothee-U. Kloos ◽

Martin W. Ganal ◽

Ingo Schubert

Keyword(s):

Yeast Artificial Chromosome ◽

Artificial Chromosome ◽

Metaphase Chromosomes

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DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100122885 ◽

1992 ◽

Vol 50 (1) ◽

pp. 496-497

Author(s):

Barbara Trask ◽

Susan Allen ◽

Anne Bergmann ◽

Mari Christensen ◽

Anne Fertitta ◽

...

Keyword(s):

In Situ Hybridization ◽

Dna Sequence ◽

Dna Sequences ◽

Dual Band ◽

Nick Translation ◽

Metaphase Chromosomes ◽

Band Pass ◽

Texas Red ◽

Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

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Genome of a citrus rootstock and global DNA demethylation caused by heterografting

Horticulture Research ◽

10.1038/s41438-021-00505-2 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Yue Huang ◽

Yuantao Xu ◽

Xiaolin Jiang ◽

Huiwen Yu ◽

Huihui Jia ◽

...

Keyword(s):

Sweet Orange ◽

Epigenetic Modification ◽

Epigenetic Modifications ◽

Genetic Effects ◽

Dna Demethylation ◽

Poncirus Trifoliata ◽

Protein Coding ◽

Horticultural Crops ◽

Citrus Rootstock ◽

Methylome Analysis

AbstractGrafting is an ancient technique used for plant propagation and improvement in horticultural crops for at least 1,500 years. Citrus plants, with a seed-to-seed cycle of 5–15 years, are among the fruit crops that were probably domesticated by grafting. Poncirus trifoliata, a widely used citrus rootstock, can promote early flowering, strengthen stress tolerance, and improve fruit quality via scion–rootstock interactions. Here, we report its genome assembly using PacBio sequencing. We obtained a final genome of 303 Mb with a contig N50 size of 1.17 Mb and annotated 25,680 protein-coding genes. DNA methylome and transcriptome analyses indicated that the strong adaptability of P. trifoliata is likely attributable to its special epigenetic modification and expression pattern of resistance-related genes. Heterografting by using sweet orange as scion and P. trifoliata as rootstock and autografting using sweet orange as both scion and rootstock were performed to investigate the genetic effects of the rootstock. Single-base methylome analysis indicated that P. trifoliata as a rootstock caused DNA demethylation and a reduction in 24-nt small RNAs (sRNAs) in scions compared to the level observed with autografting, implying the involvement of sRNA-mediated graft-transmissible epigenetic modifications in citrus grafting. Taken together, the assembled genome for the citrus rootstock and the analysis of graft-induced epigenetic modifications provide global insights into the genetic effects of rootstock–scion interactions and grafting biology.

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A thin, deformable, high-performance supercapacitor implant that can be biodegraded and bioabsorbed within an animal body

Science Advances ◽

10.1126/sciadv.abe3097 ◽

2021 ◽

Vol 7 (2) ◽

pp. eabe3097

Author(s):

Hongwei Sheng ◽

Jingjing Zhou ◽

Bo Li ◽

Yuhang He ◽

Xuetao Zhang ◽

...

Keyword(s):

High Performance ◽

Electronic Devices ◽

Form Factors ◽

Time Frame ◽

Water Soluble ◽

Two Dimensional ◽

Medical Electronics ◽

Thin Structure ◽

Shed Light

It has been an outstanding challenge to achieve implantable energy modules that are mechanically soft (compatible with soft organs and tissues), have compact form factors, and are biodegradable (present for a desired time frame to power biodegradable, implantable medical electronics). Here, we present a fully biodegradable and bioabsorbable high-performance supercapacitor implant, which is lightweight and has a thin structure, mechanical flexibility, tunable degradation duration, and biocompatibility. The supercapacitor with a high areal capacitance (112.5 mF cm−2 at 1 mA cm−2) and energy density (15.64 μWh cm−2) uses two-dimensional, amorphous molybdenum oxide (MoOx) flakes as electrodes, which are grown in situ on water-soluble Mo foil using a green electrochemical strategy. Biodegradation behaviors and biocompatibility of the associated materials and the supercapacitor implant are systematically studied. Demonstrations of a supercapacitor implant that powers several electronic devices and that is completely degraded after implantation and absorbed in rat body shed light on its potential uses.

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