scholarly journals Comparison of Karyotypes in Two Hybridizing Passerine Species: Conserved Chromosomal Structure but Divergence in Centromeric Repeats

2021 ◽  
Vol 12 ◽  
Author(s):  
Manon Poignet ◽  
Martina Johnson Pokorná ◽  
Marie Altmanová ◽  
Zuzana Majtánová ◽  
Dmitry Dedukh ◽  
...  
Keyword(s):  
Copy Number ◽  
Chromosomal Rearrangements ◽  
Repetitive Sequences ◽  
Chromosome Morphology ◽  
Comparative Genomic ◽  
Structural Variations ◽  
Chromosomal Structure ◽  
Meiotic Chromosomes ◽  
Passerine Species ◽  
Number Variation

Changes in chromosomal structure involving chromosomal rearrangements or copy number variation of specific sequences can play an important role in speciation. Here, we explored the chromosomal structure of two hybridizing passerine species; the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia), using conventional cytogenetic approaches, immunostaining of meiotic chromosomes, fluorescence in situ hybridization as well as comparative genomic hybridization (CGH). We found that the two nightingale species show conserved karyotypes with the same diploid chromosome number of 2n = 84. In addition to standard chromosomes, both species possessed a small germline restricted chromosome of similar size as a microchromosome. Just a few subtle changes in chromosome morphology were observed between the species, suggesting that only a limited number of chromosomal rearrangements occurred after the species divergence. The interspecific CGH experiment suggested that the two nightingale species might have diverged in centromeric repetitive sequences in most macro- and microchromosomes. In addition, some chromosomes showed changes in copy number of centromeric repeats between the species. The observation of very similar karyotypes in the two nightingale species is consistent with a generally slow rate of karyotype evolution in birds. The divergence of centromeric sequences between the two species could theoretically cause meiotic drive or reduced fertility in interspecific hybrids. Nevertheless, further studies are needed to evaluate the potential role of chromosomal structural variations in nightingale speciation.

scholarly journals Structural genome analysis in cultivated potato taxa

2019 ◽  
Vol 133 (3) ◽  
pp. 951-966 ◽  
Author(s):  
Maria Kyriakidou ◽  
Sai Reddy Achakkagari ◽  
José Héctor Gálvez López ◽  
Xinyi Zhu ◽  
Chen Yu Tang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Agronomic Traits ◽  
Genomic Variation ◽  
Sequencing Data ◽  
Structural Variations ◽  
Structural Genomic ◽  
Ploidy Levels ◽  
Cultivated Potato ◽  
Number Variation

Abstract Key message Twelve potato accessions were selected to represent two principal views on potato taxonomy. The genomes were sequenced and analyzed for structural variation (copy number variation) against three published potato genomes. Abstract The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X–5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.

scholarly journals Copy Number Variation of Multiple Genes in SAPHO Syndrome

2019 ◽  
Vol 47 (9) ◽  
pp. 1323-1329
Author(s):  
Changlong Guo ◽  
Xin Tian ◽  
Feifei Han ◽  
Lihong Liu ◽  
Jianen Gao ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Candidate Genes ◽  
Copy Number ◽  
Nuclear Family ◽  
Sapho Syndrome ◽  
Unknown Etiology ◽  
Comparative Genomic ◽  
Number Variation ◽  
And Control ◽  
Control Samples

Objective.SAPHO (synovitis, acne, pustulosis, hyperostosis, osteitis) syndrome is a type of rare chronic aseptic inflammation of unknown etiology. To date, no research to our knowledge has reported copy number variation (CNV) of genes that could affect predisposition to SAPHO syndrome. We investigated the association between CNV profile and SAPHO syndrome.Methods.We used array comparative genomic hybridization (CGH) to screen for CNV in a nuclear family including 2 patients and a healthy control. We then validated the copy numbers of candidate genes found in the array CGH assay and other candidate genes by TaqMan real-time PCR in 360 case and control samples.Results.Ten regions from 8 chromosomes were found to have abnormal gene copies in the nuclear family, so the CNV of candidate genes (ADAM5, CSF2RA, IL3RA, and 9 other genes) were tested by TaqMan PCR. Significant copy number loss of CSF2RA (p = 0.000) and NOD2 (p = 0.005), and significant copy number gain of MEGF6 (p = 0.002) and ADAM5 (p = 0.000) were seen in patients with SAPHO compared with controls at the a = 0.05 level. There were no differences in the other 8 candidate genes between patient and control samples (p > 0.05).Conclusion.Our study established the first association between CNV in CSF2RA, NOD2, MEGF6, and ADAM5 and SAPHO syndrome. These findings may offer insight into the pathogenesis of SAPHO and provide the basis for improved diagnosis and treatment.

Comparative Genomic Hybridization to Dna Microarrays

1997 ◽  
Vol 3 (S2) ◽  
pp. 205-206
Author(s):  
D. Pinkel ◽  
R. Segraves ◽  
D. Sudar ◽  
L. van Vliet ◽  
S. Clark ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Dna Microarrays ◽  
Suppressor Gene ◽  
Comparative Genomic ◽  
Cancer Genes ◽  
Genomic Hybridization ◽  
Metaphase Chromosomes ◽  
Number Variation ◽  
Genetic Events

Comparative genomic hybridization (CGH), which involves the simultaneous hybridization of differentially labeled total genomic DNA from test cells and reference normal cells to metaphase chromosomes, has been used extensively to screen tumor genomes for regions of DNA sequence copy number variation. Analysis of these hybridizations requires quantitative analysis of the ratio of intensities of the fluorescent hybridization signals as a function of position along the chromosomes, which basically serve as a convenient genetic map. The ratios need to be measured very accurately since changes of about ± 20% from the average for the genome indicate important genetic events. Widespread use of CGH over the past several years has identified numerous regions of the genome that may contain currently unknown cancer genes. For example, regions of increased copy number may indicate sites of oncogenes, while regions of copy number decrease relative to average for the genome may signify the presence of a tumor suppressor gene.

Array-based comparative genomic hybridization and copy number variation in cancer research

2006 ◽  
Vol 115 (3-4) ◽  
pp. 262-272 ◽  
Author(s):  
E.K. Cho ◽  
J. Tchinda ◽  
J.L. Freeman ◽  
Y.-J. Chung ◽  
W.W. Cai ◽  
...  
Keyword(s):  
Cancer Research ◽  
Copy Number Variation ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Number Variation

scholarly journals Measurement of DNA sequence copy number variation using comparative genomic hybridization to microarrays

10.1038/14259 ◽  
1999 ◽  
Vol 23 (S3) ◽  
pp. 30-30
Author(s):  
D.G. Albertson ◽  
R. Segraves ◽  
B. Huey ◽  
X. Zhang ◽  
J. Palmer ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Dna Sequence ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Number Variation

scholarly journals Absence of AVPR2 copy number variation in eunatremic and dysnatremic subjects in non-Hispanic Caucasian populations

2010 ◽  
Vol 40 (3) ◽  
pp. 121-127 ◽  
Author(s):  
Yi Fu ◽  
Zhan Chen ◽  
Alexandra I. F. Blakemore ◽  
Eric Orwoll ◽  
David M. Cohen
Keyword(s):  
Water Balance ◽  
Copy Number Variation ◽  
Serum Sodium ◽  
Water Conservation ◽  
Copy Number ◽  
Osteoporotic Fractures ◽  
Sodium Concentration ◽  
Serum Sodium Concentration ◽  
Comparative Genomic ◽  
Number Variation

Copy number variation (CNV) is increasingly recognized as a source of phenotypic variation among humans. We hypothesized that a CNV in the human arginine vasopressin receptor-2 gene ( AVPR2) would be associated with serum sodium concentration based on the following lines of evidence: 1) the protein product of the AVPR2 gene is essential for renal water conservation; 2) mutations in the AVPR2 gene are associated with aberrant water balance in humans; 3) heritability of serum sodium concentration may be greater in females than in males; 4) the AVPR2 gene is X-linked; and 5) a common CNV spanning the AVPR2 gene was recently described in a non-Hispanic Caucasian population. We developed a highly reproducible assay for AVPR2 CNV. Among 279 subjects with measured serum sodium concentration in the Offspring Cohort of the Framingham Heart Study, no subjects exhibited CNV at the AVPR2 locus. Among 517 subjects in the Osteoporotic Fractures in Men Study (MrOS)—including 152 with hyponatremia and 183 with hypernatremia—no subjects with CNV at the AVPR2 locus were identified. CNV at the AVPR2 locus could not be independently confirmed, and CNV at the AVPR2 gene is unlikely to influence systemic water balance on a population-wide basis in non-Hispanic Caucasian subjects. A novel AVPR2 single nucleotide polymorphism affecting the reporter hybridization site gave rise to an artifactually low copy number signal (i.e., less than unity) in one male African American subject. Reanalysis of the original comparative genomic hybridization data revealed bona fide CNVs flanking—but not incorporating—the AVPR2 gene, consistent with our new genotyping data.

scholarly journals Genomic Alterations and Complex Subclonal Architecture in Sporadic GH-Secreting Pituitary Adenomas

2018 ◽  
Vol 103 (5) ◽  
pp. 1929-1939 ◽  
Author(s):  
Mirella Hage ◽  
Say Viengchareun ◽  
Erika Brunet ◽  
Chiara Villa ◽  
Dominique Pineau ◽  
...  
Keyword(s):  
Pituitary Adenomas ◽  
Copy Number ◽  
Chromosomal Rearrangements ◽  
Comparative Genomic ◽  
Fish Analysis ◽  
Dna Copy Number ◽  
Distinct Cell ◽  
Two Samples ◽  
High Degree ◽  
Gnas Mutation

Abstract Purpose The molecular pathogenesis of growth hormone-secreting pituitary adenomas is not fully understood. Cytogenetic alterations might serve as alternative driver events in GNAS mutation–negative somatotroph tumors. Experimental Design We performed cytogenetic profiling of pituitary adenomas obtained from 39 patients with acromegaly and four patients with sporadic gigantism by using array comparative genomic hybridization analysis. We explored intratumor DNA copy-number heterogeneity in two tumor samples by using DNA fluorescence in situ hybridization (FISH). Results Based on copy-number profiles, we found two groups of adenomas: a low–copy-number alteration (CNA) group (<12% of genomic disruption, 63% of tumors) and a high-CNA group (24% to 45% of genomic disruption, 37% of tumors). Arm-level CNAs were the most common abnormalities. GNAS mutation–positive adenomas belonged exclusively to the low-CNA group, whereas a subgroup of GNAS mutation–negative adenomas had a high degree of genomic disruption. We detected chromothripsis-related CNA profiles in two adenoma samples from an AIP mutation–positive patient with acromegaly and a patient with sporadic gigantism. RNA sequencing of these two samples identified 17 fusion transcripts, most of which resulted from chromothripsis-related chromosomal rearrangements. DNA FISH analysis of these samples demonstrated a subclonal architecture with up to six distinct cell populations in each tumor. Conclusion Somatotroph pituitary adenomas display substantial intertumor and intratumor DNA copy-number heterogeneity, as revealed by variable CNA profiles and complex subclonal architecture. The extensive cytogenetic burden in a subgroup of GNAS mutation–negative somatotroph adenomas points to an alternative tumorigenic pathway linked to genomic instability.

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