@article{Jiang2019,
author = {Jiang, Jiming},
doi = {10.1007/s10577-019-09607-z},
issn = {0967-3849},
journal = {Chromosome Research},
publisher = {Chromosome Research},
title = {{Fluorescence in situ hybridization in plants: recent developments and future applications}},
year = {2019}
}
@article{Muakrong2018,
abstract = {Jatropha (Jatropha curcas) is an oil-bearing plant used for biodiesel production. Construction of its standard karyotype and identification of the euchromatin/heterochromatin distribution associated with gene expression and meiotic recombination are essential to fully characterize its genome. Here, we developed a J. curcas karyotype based on meiotic pachytene chromosomes. In addition, a karyotype of J. integerrima, a useful species for jatropha breeding, was also constructed. Five out of eleven J. curcas chromosomes were metacentric, but only two were metacentric in J. integerrima. Almost all of the heterochromatin was distributed around the pericentric regions. The interstitial and distal regions were euchromatic without heterochromatic knobs, except for small heterochromatin regions associated with the subtelomeric repeat sequence JcSat1. These pericentric heterochromatin distribution patterns, together with chromosome structure data and the results of FISH probing with rDNA and JcSat1, allowed us to classify all chromosomes of both species. The two species had two 35S rDNA loci and one 5S rDNA locus; one 35S rDNA locus in J. integerrima was located on the interstitial region of the short arms. In addition, JcSat1 was found at only the heterochromatic ends of the J. curcas chromosome, not the J. integerrima chromosome. Despite the same chromosome number, the two pachytene chromosome-based karyotypes suggest variation in chromosome structure and distribution of repetitive DNAs in these two species.},
author = {Muakrong, Narathid and Kikuchi, Shinji and Fukuhara, Shuto and Tanya, Patcharin and Srinives, Peerasak},
doi = {10.1371/journal.pone.0208549},
isbn = {1111111111},
issn = {19326203},
journal = {PLoS ONE},
number = {12},
title = {{Two jatropha karyotypes constructed from meiotic pachytene chromosomes: Pericentric distribution of heterochromatin and variation in repetitive DNAs}},
volume = {13},
year = {2018}
}
@article{Setiawan2018,
author = {Setiawan, Agus Budi and Teo, Chee How and Kikuchi, Shinji and Sassa, Hidenori and Kato, Kenji and Koba, Takato},
doi = {10.11352/scr.21.67},
journal = {Chromosome Science},
pages = {67--73},
title = {{Cytogenetic variation in Cucumis accessions revealed by fluorescence in situ hybridization using ribosomal RNAs genes as the probes}},
volume = {21},
year = {2018}
}
@article{Kalendar2006,
abstract = {Retrotransposons can be used as markers because their integration creates new joints between genomic DNA and their conserved ends. To detect polymorphisms for retrotransposon insertion, marker systems generally rely on PCR amplification between these ends and some component of flanking genomic DNA. We have developed two methods, retrotransposon-microsatellite amplified polymorphism (REMAP) analysis and inter-retrotransposon amplified polymorphism (IRAP) analysis, that require neither restriction enzyme digestion nor ligation to generate the marker bands. The IRAP products are generated from two nearby retrotransposons using outward-facing primers. In REMAP, amplification between retrotransposons proximal to simple sequence repeats (microsatellites) produces the marker bands. Here, we describe protocols for the IRAP and REMAP techniques, including methods for PCR amplification with a single primer or with two primers and for agarose gel electrophoresis of the product using optimal electrophoresis buffers and conditions. This protocol can be completed in 1-2 d.},
author = {Kalendar, Ruslan and Schulman, Alan H.},
doi = {10.1038/nprot.2006.377},
isbn = {1754-2189},
issn = {17542189},
journal = {Nature Protocols},
number = {5},
pages = {2478--2484},
pmid = {17406494},
title = {{IRAP and REMAP for retrotransposon-based genotyping and fingerprinting}},
volume = {1},
year = {2006}
}
@article{Fukui1994,
abstract = {5S rDNA loci have been mapped on barley chromosomes by in situ hybridization using five reciprocal translocation lines. Two kinds of DNA probes covering either the 5S rDNA coding region or the 5S rDNA coding and flanking noncoding regions were used. They were prepared by direct cloning from interphase nuclei and simultaneous direct labeling in PCR. Four 5S rDNA loci were detected in a haploid genome by the 5S rDNA coding region, whereas in addition, the four or six 5S rDNA related sites, depending on the variety used, were revealed by the probe covering the flanking region. The four 5S rDNA loci revealed and mapped on the barley chromosomes: 2 (2I), 3 (3I), 1 (7I), and 4 (4I) were designated 5SRrn-I1, 5SRrn-I2, 5SRrn-I3 and 5SRrn-I4, respectively, in descending order of copy number of 5S rRNA genes.},
author = {Fukui, K and Kamisugi, Y and Sakai, F},
doi = {10.1139/g94-013},
issn = {0831-2796},
journal = {Genome},
number = {1},
pages = {105--111},
pmid = {8181730},
title = {{Physical mapping of 5S rDNA loci by direct-cloned biotinylated probes in barley chromosomes.}},
volume = {37},
year = {1994}
}
@phdthesis{Setiawan2018a,
author = {Setiawan, Agus Budi},
publisher = {Chiba University},
title = {{Molecular cytogenetic studies on satellite DNA and retrotransposon in Cucumis species}},
year = {2018}
}
@article{Koo2010,
abstract = {Chromosomes often serve as one of the most important molecular aspects of studying the evolution of species. Indeed, most of the crucial mutations that led to differentiation of species during the evolution have occurred at the chromosomal level. Furthermore, the analysis of pachytene chromosomes appears to be an invaluable tool for the study of evolution due to its effectiveness in chromosome identification and precise physical gene mapping. By applying fluorescence in situ hybridization of 45S rDNA and CsCent1 probes to cucumber pachytene chromosomes, here, we demonstrate that cucumber chromosomes 1 and 2 may have evolved from fusions of ancestral karyotype with chromosome number n = 12. This conclusion is further supported by the centromeric sequence similarity between cucumber and melon, which suggests that these sequences evolved from a common ancestor. It may be after or during speciation that these sequences were specifically amplified, after which they diverged and specific sequence variants were homogenized. Additionally, a structural change on the centromeric region of cucumber chromosome 4 was revealed by fiber-FISH using the mitochondrial-related repetitive sequences, BAC-E38 and CsCent1. These showed the former sequences being integrated into the latter in multiple regions. The data presented here are useful resources for comparative genomics and cytogenetics of Cucumis and, in particular, the ongoing genome sequencing project of cucumber.},
author = {Koo, Dal-Hoe and Nam, Young-Woo and Choi, Doil and Bang, Jae-Wook and de Jong, Hans and Hur, Yoonkang},
doi = {10.1007/s10577-010-9116-0},
isbn = {0967-3849},
issn = {1573-6849},
journal = {Chromosome research},
number = {3},
pages = {325--336},
pmid = {20198418},
title = {{Molecular cytogenetic mapping of Cucumis sativus and C. melo using highly repetitive DNA sequences.}},
volume = {18},
year = {2010}
}
@article{Wibowo2018,
author = {Wibowo, Ari and Setiawan, Agus Budi and Purwantoro, Aziz and Kikuchi, Shinji and Koba, Takato},
doi = {https://doi.org/10.11352/scr.21.81},
journal = {Chromosome Science},
pages = {81--87},
title = {{Cytological Variation of rRNA Genes and Subtelomeric Repeat Sequences in Indonesian and Japanese Cucumber Accessions}},
volume = {21},
year = {2018}
}
@article{Han2008,
abstract = {We analyzed repeat sequences composition in the genome of cucumber inbred line 9930 using whole-genome shotgun reads. The analysis showed that satellite DNA sequences are the most dominant components in the cucumber genome. The distribution pattern of several tandem repeat sequences (Type I/II, Type III and Type IV) on cucumber chromosomes was visualized using fluorescence in situ hybridization (FISH). The FISH signals of the Type III and 45S rDNA provide useful cytogenetic markers, whose position and fluorescence intensity allow for easy identification of all somatic metaphase chromosomes. A karyotype showing the position and fluorescence intensity of several tandem repeat sequences is constructed. The establishment of this FISH-based karyotype has created the basis for the integration of molecular, genetic and cytogenetic maps in Cucumis sativus and for the ultimate genome sequencing project as well.},
author = {Han, Y. H. and Zhang, Z. H. and Liu, J. H. and Lu, J. Y. and Huang, S. W. and Jin, W. W.},
doi = {10.1159/000151320},
isbn = {1424-859X (Electronic)$\backslash$r1424-8581 (Linking)},
issn = {14248581},
journal = {Cytogenetic and Genome Research},
number = {1},
pages = {80--88},
pmid = {18931490},
title = {{Distribution of the tandem repeat sequences and karyotyping in cucumber (Cucumis sativus L.) by fluorescence in situ hybridization}},
volume = {122},
year = {2008}
}
@article{Gerlach1979,
abstract = {Wheat and barley DNA enriched for ribosomal RNA genes was isolated from actinomycin D-CsCl gradients and used to clone the ribosomal repeating units in the plasraid pAC184. All five chimeric plasmids Isolated which contained wheat rDNA and eleven of the thirteen which had barley rDNA were stable and included full length ribosomal repeating units. Physical maps of all length variants cloned have been constructed using the restriction endonucleases Eco Rl, Bam H1, Bgl II, Hind III and Sal I. Length variation 1n the repeat units was attributed to differences 1n the spacer regions. Comparison of Hae III and Hpa II digestion of cereal rDNAs and the cloned repeats suggests that most methylated cytosines in natural rONA are in -CpG-. Incomplete methylation occurs at specific Bam HI sites in barley DNA. Detectable quantities of ribosomal spacer sequences are not present at any genomic locations other than those of the ribosomal RNA gene repeats.},
author = {Gerlach, W.L. and Bedbrook, J.R.},
doi = {10.1093/nar/7.7.1869},
isbn = {1111111111},
issn = {0305-1048},
journal = {Nucleic Acids Research},
number = {7},
pages = {1869--1885},
title = {{Cloning and characterization of ribosomal RNA genes from wheat and barley}},
volume = {7},
year = {1979}
}
@article{Biscotti2015,
abstract = {Repetitive DNA-sequence motifs repeated hundreds or thousands of times in the genome-makes up the major proportion of all the nuclear DNA in most eukaryotic genomes. However, the significance of repetitive DNA in the genome is not completely understood, and it has been considered to have both structural and functional roles, or perhaps even no essential role. High-throughput DNA sequencing reveals huge numbers of repetitive sequences. Most bioinformatic studies focus on low-copy DNA including genes, and hence, the analyses collapse repeats in assemblies presenting only one or a few copies, often masking out and ignoring them in both DNA and RNA read data. Chromosomal studies are proving vital to examine the distribution and evolution of sequences because of the challenges of analysis of sequence data. Many questions are open about the origin, evolutionary mode and functions that repetitive sequences might have in the genome. Some, the satellite DNAs, are present in long arrays of similar motifs at a small number of sites, while others, particularly the transposable elements (DNA transposons and retrotranposons), are dispersed over regions of the genome; in both cases, sequence motifs may be located at relatively specific chromosome domains such as centromeres or subtelomeric regions. Here, we overview a range of works involving detailed characterization of the nature of all types of repetitive sequences, in particular their organization, abundance, chromosome localization, variation in sequence within and between chromosomes, and, importantly, the investigation of their transcription or expression activity. Comparison of the nature and locations of sequences between more, and less, related species is providing extensive information about their evolution and amplification. Some repetitive sequences are extremely well conserved between species, while others are among the most variable, defining differences between even closely relative species. These data suggest contrasting modes of evolution of repetitive DNA of different types, including selfish sequences that propagate themselves and may even be transferred horizontally between species rather than by descent, through to sequences that have a tendency to amplification because of their sequence motifs, to those that have structural significance because of their bulk rather than precise sequence. Functional consequences of repeats include generation of variability by movement and insertion in the genome {\ldots}},
author = {Biscotti, Maria Assunta and Olmo, Ettore and Heslop-Harrison, J. S (Pat)},
doi = {10.1007/s10577-015-9499-z},
isbn = {1573-6849 (Electronic)$\backslash$r0967-3849 (Linking)},
issn = {15736849},
journal = {Chromosome Research},
number = {3},
pages = {415--420},
pmid = {26514350},
title = {{Repetitive DNA in eukaryotic genomes}},
volume = {23},
year = {2015}
}
@article{Zhang2016,
author = {Zhang, Zhen Tao and Yang, Shu-qiong and Li, Zi-Ang and Zhang, Yun-xia and Wang, Yun-zhu and Cheng, Chun-yan and Li, Ji and Chen, Jin-feng and Lou, Qun-feng},
doi = {10.1139/gen-2015-0207},
issn = {0831-2796},
journal = {Genome},
month = {jul},
number = {7},
pages = {449--457},
title = {{Comparative chromosomal localization of 45S and 5S rDNAs and implications for genome evolution in Cucumis}},
volume = {59},
year = {2016}
}
@article{Schnable2009,
abstract = {We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8{\%} were placed on reference chromosomes. Nearly 85{\%} of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.},
author = {Schnable, Patrick S. and Ware, Doreen and Fulton, Robert S. and Stein, Joshua C. and Wei, Fusheng and Pasternak, Shiran and Liang, Chengzhi and Zhang, Jianwei and Fulton, Lucinda and Graves, Tina A. and Minx, Patrick and Reily, Amy Denise and Courtney, Laura and Kruchowski, Scott S. and Tomlinson, Chad and Strong, Cindy and Delehaunty, Kim and Fronick, Catrina and Courtney, Bill and Rock, Susan M. and Belter, Eddie and Du, Feiyu and Kim, Kyung and Abbott, Rachel M. and Cotton, Marc and Levy, Andy and Marchetto, Pamela and Ochoa, Kerri and Jackson, Stephanie M. and Gillam, Barbara and Chen, Weizu and Yan, Le and Higginbotham, Jamey and Cardenas, Marco and Waligorski, Jason and Applebaum, Elizabeth and Phelps, Lindsey and Falcone, Jason and Kanchi, Krishna and Thane, Thynn and Scimone, Adam and Thane, Nay and Henke, Jessica and Wang, Tom and Ruppert, Jessica and Shah, Neha and Rotter, Kelsi and Hodges, Jennifer and Ingenthron, Elizabeth and Cordes, Matt and Kohlberg, Sara and Sgro, Jennifer and Delgado, Brandon and Mead, Kelly and Chinwalla, Asif and Leonard, Shawn and Crouse, Kevin and Collura, Kristi and Kudrna, Dave and Currie, Jennifer and He, Ruifeng and Angelova, Angelina and Rajasekar, Shanmugam and Mueller, Teri and Lomeli, Rene and Scara, Gabriel and Ko, Ara and Delaney, Krista and Wissotski, Marina and Lopez, Georgina and Campos, David and Braidotti, Michele and Ashley, Elizabeth and Golser, Wolfgang and Kim, Hyeran and Lee, Seunghee and Lin, Jinke and Dujmic, Zeljko and Kim, Woojin and Talag, Jayson and Zuccolo, Andrea and Fan, Chuanzhu and Sebastian, Aswathy and Kramer, Melissa and Spiegel, Lori and Nascimento, Lidia and Zutavern, Theresa and Miller, Beth and Ambroise, Claude and Muller, Stephanie and Spooner, Will and Narechania, Apurva and Ren, Liya and Wei, Sharon and Kumari, Sunita and Faga, Ben and Levy, Michael J. and McMahan, Linda and {Van Buren}, Peter and Vaughn, Matthew W. and Ying, Kai and Yeh, Cheng Ting and Emrich, Scott J. and Jia, Yi and Kalyanaraman, Ananth and Hsia, An Ping and Barbazuk, W. Brad and Baucom, Regina S. and Brutnell, Thomas P. and Carpita, Nicholas C. and Chaparro, Cristian and Chia, Jer Ming and Deragon, Jean Marc and Estill, James C. and Fu, Yan and Jeddeloh, Jeffrey A. and Han, Yujun and Lee, Hyeran and Li, Pinghua and Lisch, Damon R. and Liu, Sanzhen and Liu, Zhijie and Nagel, Dawn Holligan and McCann, Maureen C. and Sanmiguel, Phillip and Myers, Alan M. and Nettleton, Dan and Nguyen, John and Penning, Bryan W. and Ponnala, Lalit and Schneider, Kevin L. and Schwartz, David C. and Sharma, Anupma and Soderlund, Carol and Springer, Nathan M. and Sun, Qi and Wang, Hao and Waterman, Michael and Westerman, Richard and Wolfgruber, Thomas K. and Yang, Lixing and Yu, Yeisoo and Zhang, Lifang and Zhou, Shiguo and Zhu, Qihui and Bennetzen, Jeffrey L. and Dawe, R. Kelly and Jiang, Jiming and Jiang, Ning and Presting, Gernot G. and Wessler, Susan R. and Aluru, Srinivas and Martienssen, Robert A. and Clifton, Sandra W. and McCombie, W. Richard and Wing, Rod A. and Wilson, Richard K.},
doi = {10.1126/science.1178534},
issn = {00368075},
journal = {Science},
number = {5956},
pages = {1112--1115},
title = {{The B73 maize genome: Complexity, diversity, and dynamics}},
volume = {326},
year = {2009}
}
@article{Kuznetsova2017,
abstract = {{\textcopyright} 2017 The Author(s). Background: Most data concerning chromosome organization have been acquired from studies of a small number of model organisms, the majority of which are mammals. In plants with large genomes, the chromosomes are significantly larger than the animal chromosomes that have been studied to date, and it is possible that chromosome condensation in such plants was modified during evolution. Here, we analyzed chromosome condensation and decondensation processes in order to find structural mechanisms that allowed for an increase in chromosome size. Results: We found that anaphase and telophase chromosomes of plants with large chromosomes (average 2C DNA content exceeded 0.8 pg per chromosome) contained chromatin-free cavities in their axial regions in contrast to well-characterized animal chromosomes, which have high chromatin density in the axial regions. Similar to animal chromosomes, two intermediates of chromatin folding were visible inside condensing (during prophase) and decondensing (during telophase) chromosomes of Nigella damascena: approximately 150 nm chromonemata and approximately 300 nm fibers. The spatial folding of the latter fibers occurs in a fundamentally different way than in animal chromosomes, which leads to the formation of chromosomes with axial chromatin-free cavities. Conclusion: Different compaction topology, but not the number of compaction levels, allowed for the evolution of increased chromosome size in plants.},
author = {Kuznetsova, Maria A. and Chaban, Inna A. and Sheval, Eugene V.},
doi = {10.1186/s12870-017-1102-7},
issn = {14712229},
journal = {BMC Plant Biology},
number = {1},
pages = {1--12},
publisher = {BMC Plant Biology},
title = {{Visualization of chromosome condensation in plants with large chromosomes}},
volume = {17},
year = {2017}
}
@article{Setiawan2018b,
abstract = {{\textcopyright} 2018 The Author(s). Background: Detailed karyotyping using metaphase chromosomes in melon (Cucumis melo L.) remains a challenge because of their small chromosome sizes and poor stainability. Prometaphase chromosomes, which are two times longer and loosely condensed, provide a significantly better resolution for fluorescence in situ hybridization (FISH) than metaphase chromosomes. However, suitable method for acquiring prometaphase chromosomes in melon have been poorly investigated. Results: In this study, a modified Carnoy's solution II (MC II) [6:3:1 (v/v) ethanol: acetic acid: chloroform] was used as a pretreatment solution to obtain prometaphase chromosomes. We demonstrated that the prometaphase chromosomes obtained using the MC II method are excellent for karyotyping and FISH analysis. We also observed that a combination of MC II and the modified air dry (ADI) method provides a satisfactory meiotic pachytene chromosome preparation with reduced cytoplasmic background and clear chromatin spreads. Moreover, we demonstrated that pachytene and prometaphase chromosomes of melon and Abelia × grandiflora generate significantly better FISH images when prepared using the method described. We confirmed, for the first time, that Abelia × grandiflora has pairs of both strong and weak 45S ribosomal DNA signals on the short arms of their metaphase chromosomes. Conclusion: The MC II and ADI method are simple and effective for acquiring prometaphase and pachytene chromosomes with reduced cytoplasm background in plants. Our methods provide high-resolution FISH images that can help accelerate molecular cytogenetic research in plants.},
author = {Setiawan, Agus Budi and Teo, Chee How and Kikuchi, Shinji and Sassa, Hidenori and Koba, Takato},
doi = {10.1186/s13039-018-0380-6},
issn = {17558166},
journal = {Molecular Cytogenetics},
keywords = {Abelia × grandiflora,Chloroform,Cucumis melo,FISH,Pachytene,Prometaphase},
title = {{An improved method for inducing prometaphase chromosomes in plants}},
year = {2018}
}
@article{Ganal1986,
abstract = {Cucurbitaceae are characterized by a high copy number for nuclear ribosomal RNA genes. We have investigated the genomic ribosomal DNA (rDNA) of four closely related species of this family with respect to structure, length heterogeneity, and evolution. In Cucumis melo (melon) there are two main length variants of rDNA repeats with 10.7 and 10.55kb. Cucumis sativus (cucumber) shows at least three repeat types with 11.5, 10.5, and 10.2kb. Cucurbita pepo (zucchini) has two different repeat types with 10.0 and 9.3kb. There are also two different repeat types in Cucurbita maxima (pumpkin) of about 11.2 and 10.5kb. Restriction enzyme mapping of the genomic rDNA of these four plants and of cloned repeats of C. sativus shows further heterogeneities which are due to methylation or point mutations. By comparison of the restriction enzyme maps it was possible to trace some evolutionary events in the family of Cucurbitaceae. Some aspects of regulation and function of the middle repetitive rRNA genes (here between 2000 and 10000 copies) are discussed. {\textcopyright} 1986 Springer-Verlag.},
author = {Ganal, Martin and Hemleben, Vera},
doi = {10.1007/BF00984868},
issn = {03782697},
journal = {Plant Systematics and Evolution},
number = {1-2},
pages = {63--77},
title = {{Comparison of the ribosomal RNA genes in four closely related Cucurbitaceae}},
volume = {154},
year = {1986}
}
@article{Cuadrado2008,
abstract = {A significant fraction of the nuclear DNA of all eukaryotes is occupied by simple sequence repeats (SSRs) or microsatellites. This type of sequence has sparked great interest as a means of studying genetic variation, linkage mapping, gene tagging and evolution. Although SSRs at different positions in a gene help determine the regulation of expression and the function of the protein produced, little attention has been paid to the chromosomal organisation and distribution of these sequences, even in model species. This review discusses the main achievements in the characterisation of long-range SSR organisation in the chromosomes of Triticum aestivum L., Secale cereale L., and Hordeum vulgare L. (all members of Triticeae). We have detected SSRs using an improved FISH technique based on the random primer labelling of synthetic oligonucleotides (15-24 bases) in multi-colour experiments. Detailed information on the presence and distribution of AC, AG and all the possible classes of trinucleotide repeats has been acquired. These data have revealed the motif-dependent and non-random chromosome distributions of SSRs in the different genomes, and allowed the correlation of particular SSRs with chromosome areas characterised by specific features (e.g., heterochromatin, euchromatin and centromeres) in all three species. The present review provides a detailed comparative study of the distribution of these SSRs in each of the seven chromosomes of the genomes A, B and D of wheat, H of barley and R of rye. The importance of SSRs in plant breeding and their possible role in chromosome structure, function and evolution is discussed.},
author = {Cuadrado, A. and Cardoso, M. and Jouve, N.},
doi = {10.1159/000121069},
isbn = {1424-8581},
issn = {14248581},
journal = {Cytogenetic and Genome Research},
number = {3-4},
pages = {210--219},
pmid = {18504349},
title = {{Physical organisation of simple sequence repeats (SSRs) in Triticeae: Structural, functional and evolutionary implications}},
volume = {120},
year = {2008}
}
@article{Kubis1998,
author = {Kubis, S E and Heslop-Harrison, J S and Desel, C and Schmidt, T},
journal = {Plant Mol. Biol.},
pages = {821},
title = {{The genomic organisation of non-LTR retrotransposons (LINEs) from three Beta species and five other angiosperms}},
volume = {36},
year = {1998}
}
@article{Kato2009,
author = {Kato, Seiji and Ohmido, Nobuko and Hara, Masaki and Kataoka, Ryouhei and Fukui, Kiichi},
journal = {Chromosome Science},
pages = {43--50},
title = {{Image analysis of small plant chromosomes by using an improved system, CHIAS IV}},
volume = {12},
year = {2009}
}
@article{Markova2010,
abstract = {This review summarizes conventional and recent applications of genomic in situ hybridization (GISH). GISH is a well recognized technique, but its modifications and applications have not been widely used. Here, we show how modifications to the GISH technique can be used as tools to 'paint' plant chromosomes. In addition, we describe novel applications, e.g. how GISH banding could be used for karyotyping plant chromosomes. We further discuss recent phylogenetic applications of GISH that allow a semiquantitative signal analysis and the possibility of comparing and combining this cytogenetic technique with DNA sequence-based phylogenetic trees.},
author = {Markova, M. and Vyskot, B.},
doi = {10.1159/000275796},
issn = {14248581},
journal = {Cytogenetic and Genome Research},
number = {4},
pages = {368--375},
title = {{New horizons of genomic in situ hybridization}},
volume = {126},
year = {2010}
}
@article{Han2015,
abstract = {Chromosome-specific painting is a powerful technique in molecular cytogenetic and genome research. We developed an oligonucleotide (oligo)-based chromosome painting technique in cucumber (Cucumis sativus) that will be applicable in any plant species with a sequenced genome. Oligos specific to a single chromosome of cucumber were identified using a newly developed bioinformatic pipeline and then massively synthesized de novo in parallel. The synthesized oligos were amplified and labeled with biotin or digoxigenin for use in fluorescence in situ hybridization (FISH). We developed three different probes with each containing 23,000-27,000 oligos. These probes spanned 8.3-17 Mb of DNA on targeted cucumber chromosomes and had the densities of 1.5-3.2 oligos per kilobases. These probes produced FISH signals on a single cucumber chromosome and were used to paint homeologous chromosomes in other Cucumis species diverged from cucumber for up to 12 million years. The bulked oligo probes allowed us to track a single chromosome in early stages during meiosis. We were able to precisely map the pairing between cucumber chromosome 7 and chromosome 1 of Cucumis hystrix in a F1 hybrid. These two homeologous chromosomes paired in 71{\%} of prophase I cells but only 25{\%} of metaphase I cells, which may provide an explanation of the higher recombination rates compared to the chiasma frequencies between homeologous chromosomes reported in plant hybrids.},
author = {Han, Yonghua and Zhang, Tao and Thammapichai, Paradee and Weng, Yiqun and Jiang, Jiming},
doi = {10.1534/genetics.115.177642},
issn = {0016-6731},
journal = {Genetics},
number = {3},
pages = {771--779},
pmid = {25971668},
title = {{Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides}},
volume = {200},
year = {2015}
}
@book{Schwarzacher2000,
address = {New York},
author = {Schwarzacher, Trude and Heslop-Harrison, Pat},
publisher = {Springer},
title = {{Practical in situ hyridization}},
year = {2000}
}
@article{Koo2009,
abstract = {Meiotic pachytene chromosome-based fluorescence in situ hybridization (FISH) mapping is one of the most important tools in plant molecular cytogenetic research. Here we report a simple technique that allows stretching of pachytene chromosomes of maize to up to at least 20 times their original size. A modified Carnoy's II fixative (6:1:3 ethanol:chloroform:acetic acid) was used in the procedure, and proved to be key for super-stretching of pachytene chromosomes. We demonstrate that super-stretched pachytene chromosomes provide unprecedented resolution for chromosome-based FISH mapping. DNA probes separated by as little as 50 kb can be resolved on super-stretched chromosomes. A combination of FISH with immunofluorescent detection of 5-methyl cytosine on super-stretched pachytene chromosomes provides a powerful tool to reveal DNA methylation of specific chromosomal domains, especially those associated with highly repetitive DNA sequences.},
author = {Koo, Dal H. and Jiang, Jiming},
doi = {10.1111/j.1365-313X.2009.03881.x},
isbn = {0261-4189 (Print)$\backslash$r0261-4189 (Linking)},
issn = {09607412},
journal = {Plant Journal},
number = {3},
pages = {509--516},
pmid = {19392688},
title = {{Super-stretched pachytene chromosomes for fluorescence in situ hybridization mapping and immunodetection of DNA methylation}},
volume = {59},
year = {2009}
}
@article{Huang2009,
abstract = {Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and 'fresh green' odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system.},
author = {Huang, Sanwen and Li, Ruiqiang and Zhang, Zhonghua and Li, Li and Gu, Xingfang and Fan, Wei and Lucas, William J. and Wang, Xiaowu and Xie, Bingyan and Ni, Peixiang and Ren, Yuanyuan and Zhu, Hongmei and Li, Jun and Lin, Kui and Jin, Weiwei and Fei, Zhangjun and Li, Guangcun and Staub, Jack and Kilian, Andrzej and {Van Der Vossen}, Edwin A.G. and Wu, Yang and Guo, Jie and He, Jun and Jia, Zhiqi and Ren, Yi and Tian, Geng and Lu, Yao and Ruan, Jue and Qian, Wubin and Wang, Mingwei and Huang, Quanfei and Li, Bo and Xuan, Zhaoling and Cao, Jianjun and Asan and Wu, Zhigang and Zhang, Juanbin and Cai, Qingle and Bai, Yinqi and Zhao, Bowen and Han, Yonghua and Li, Ying and Li, Xuefeng and Wang, Shenhao and Shi, Qiuxiang and Liu, Shiqiang and Cho, Won Kyong and Kim, Jae Yean and Xu, Yong and Heller-Uszynska, Katarzyna and Miao, Han and Cheng, Zhouchao and Zhang, Shengping and Wu, Jian and Yang, Yuhong and Kang, Houxiang and Li, Man and Liang, Huiqing and Ren, Xiaoli and Shi, Zhongbin and Wen, Ming and Jian, Min and Yang, Hailong and Zhang, Guojie and Yang, Zhentao and Chen, Rui and Liu, Shifang and Li, Jianwen and Ma, Lijia and Liu, Hui and Zhou, Yan and Zhao, Jing and Fang, Xiaodong and Li, Guoqing and Fang, Lin and Li, Yingrui and Liu, Dongyuan and Zheng, Hongkun and Zhang, Yong and Qin, Nan and Li, Zhuo and Yang, Guohua and Yang, Shuang and Bolund, Lars and Kristiansen, Karsten and Zheng, Hancheng and Li, Shaochuan and Zhang, Xiuqing and Yang, Huanming and Wang, Jian and Sun, Rifei and Zhang, Baoxi and Jiang, Shuzhi and Wang, Jun and Du, Yongchen and Li, Songgang},
doi = {10.1038/ng.475},
isbn = {1546-1718 (Electronic)$\backslash$r1061-4036 (Linking)},
issn = {10614036},
journal = {Nature Genetics},
month = {dec},
number = {12},
pages = {1275--1281},
pmid = {19881527},
title = {{The genome of the cucumber, Cucumis sativus L.}},
volume = {41},
year = {2009}
}
@article{Garcia-Mas2012,
abstract = {We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3{\%} of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site-leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.},
author = {Garcia-Mas, J. and Benjak, A. and Sanseverino, W. and Bourgeois, M. and Mir, G. and Gonzalez, V. M. and Henaff, E. and Camara, F. and Cozzuto, L. and Lowy, E. and Alioto, T. and Capella-Gutierrez, S. and Blanca, J. and Canizares, J. and Ziarsolo, P. and Gonzalez-Ibeas, D. and Rodriguez-Moreno, L. and Droege, M. and Du, L. and Alvarez-Tejado, M. and Lorente-Galdos, B. and Mele, M. and Yang, L. and Weng, Y. and Navarro, A. and Marques-Bonet, T. and Aranda, M. A. and Nuez, F. and Pico, B. and Gabaldon, T. and Roma, G. and Guigo, R. and Casacuberta, J. M. and Arus, P. and Puigdomenech, P.},
doi = {10.1073/pnas.1205415109},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {29},
pages = {11872--11877},
pmid = {22753475},
title = {{The genome of melon (Cucumis melo L.)}},
volume = {109},
year = {2012}
}