scholarly journals Extreme copy number variation at a tRNA ligase affecting phenology and fitness in yellow monkeyflowers

2018 ◽  
Author(s):  
Thom Nelson ◽  
Patrick Monnahan ◽  
Mariah McIntosh ◽  
Findley R. Finseth ◽  
Kayli Anderson ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Molecular Mechanisms ◽  
Wild Population ◽  
Intermediate Frequency ◽  
Single Copy ◽  
Multiple Traits ◽  
Fluctuating Selection ◽  
Mendelian Segregation ◽  
Number Variation

AbstractCopy number variation (CNV) is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on a tRNA ligase gene (Migut.N02091; RLG1a) exhibiting unprecedented, and fitness-relevant, CNV within an annual population of the yellow monkeyflower Mimulus guttatus. RLG1a variation was associated with multiple traits in pooled population sequencing (PoolSeq) scans of phenotypic and phenological cohorts. Resequencing of inbred lines revealed intermediate frequency three-copy variants of RLG1a (trip+; 5/35 = 14%), and trip+ lines exhibited elevated RLG1a expression under multiple conditions. trip+ carriers, in addition to being over-represented in late-flowering and large-flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment (P < 0.05). In wild population samples, we discovered an additional rare RLG1a variant (high+) that carries 250-300 copies of RLG1a totaling ∼5.7Mb (20-40% of a chromosome). In the progeny of a high+ carrier, Mendelian segregation of diagnostic alleles and qPCR-based copy counts indicate that high+ is a single tandem array unlinked from the single copy RLG1a locus. In the wild, high+ carriers had highest fitness in two particularly dry and/or hot years (2015 and 2017; both p < 0.01), while single copy individuals were twice as fecund as either CNV type in a lush year (2016: p < 0.005). Our results demonstrate fluctuating selection on CNVs affecting phenological traits in a wild population, suggest that plant tRNA ligases mediate stress-responsive life-history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.

scholarly journals Copy number variation ofTdDofcontrols solid-stemmed architecture in wheat

2020 ◽  
Vol 117 (46) ◽  
pp. 28708-28718
Author(s):  
Kirby T. Nilsen ◽  
Sean Walkowiak ◽  
Daoquan Xiang ◽  
Peng Gao ◽  
Teagen D. Quilichini ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Triticum Turgidum ◽  
Single Copy ◽  
Gene Encoding ◽  
Wheat Stem Sawfly ◽  
Number Variation ◽  
Stem Solidness ◽  
Stem Development ◽  
Chromosome 3B

Stem solidness is an important agronomic trait of durum (Triticum turgidumL. var.durum) and bread (Triticum aestivumL.) wheat that provides resistance to the wheat stem sawfly. This dominant trait is conferred by theSSt1locus on chromosome 3B. However, the molecular identity and mechanisms underpinning stem solidness have not been identified. Here, we demonstrate that copy number variation ofTdDof, a gene encoding a putative DNA binding with one finger protein, controls the stem solidness trait in wheat. Using map-based cloning, we localizedTdDofto within a physical interval of 2.1 Mb inside theSSt1locus. Molecular analysis revealed that hollow-stemmed wheat cultivars such as Kronos carry a single copy ofTdDof, whereas solid-stemmed cultivars such as CDC Fortitude carry multiple identical copies of the gene. Deletion of allTdDofcopies from CDC Fortitude resulted in the loss of stem solidness, whereas the transgenic overexpression ofTdDofrestored stem solidness in theTdDofdeletion mutantpithless1and conferred stem solidness in Kronos. In solid-stemmed cultivars, increasedTdDofexpression was correlated with the down-regulation of genes whose orthologs have been implicated in programmed cell death (PCD) in other species. Anatomical and histochemical analyses revealed that hollow-stemmed lines had stronger PCD-associated signals in the pith cells compared to solid-stemmed lines, which suggests copy number-dependent expression ofTdDofcould be directly or indirectly involved in the negative regulation of PCD. These findings provide opportunities to manipulate stem development in wheat and other monocots for agricultural or industrial purposes.

scholarly journals Copy number variation, increased gene expression, and molecular mechanisms of neurofascin in lung cancer

2017 ◽  
Vol 56 (9) ◽  
pp. 2076-2085 ◽  
Author(s):  
Johanna Samulin Erdem ◽  
Yke Jildouw Arnoldussen ◽  
Vidar Skaug ◽  
Aage Haugen ◽  
Shanbeh Zienolddiny
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Molecular Mechanisms ◽  
Number Variation

scholarly journals Amplification of theInsulin-Like Growth Factor 1 ReceptorGene Is a Rare Event in Adrenocortical Adenocarcinomas: Searching for Potential Mechanisms of Overexpression

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Tamaya Castro Ribeiro ◽  
Alexander Augusto Jorge ◽  
Madson Q. Almeida ◽  
Beatriz Marinho de Paula Mariani ◽  
Mirian Yumi Nishi ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Real Time ◽  
Real Time Pcr ◽  
Adrenocortical Carcinoma ◽  
Copy Number ◽  
Molecular Mechanisms ◽  
Prognostic Biomarker ◽  
Rare Event ◽  
Adrenocortical Tumors ◽  
Number Variation

Context.IGF1Roverexpression appears to be a prognostic biomarker of metastatic pediatric adrenocortical tumors. However, the molecular mechanisms that are implicated in its upregulation remain unknown.Aim. To investigate the potential mechanisms involved inIGF1Roverexpression.Patients and Methods. We studied 64 adrenocortical tumors.IGF1Rcopy number variation was determined in all patients using MLPA and confirmed using real time PCR. In a subgroup of 32 patients, automatic sequencing was used to identifyIGF1Rallelic variants and the expression of microRNAs involved inIGF1Rregulation by real time PCR.Results.IGF1Ramplification was detected in an adrenocortical carcinoma that was diagnosed in a 46-year-old woman with Cushing’s syndrome and virilization.IGF1Roverexpression was demonstrated in this case. In addition, gene amplification of otherlociwas identified in this adrenocortical malignant tumor, but noIGF1Rcopy number variation was evidenced in the remaining cases. Automatic sequencing revealed three known polymorphisms but they did not correlate with its expression. Expression of miR-100, miR-145, miR-375, and miR-126 did not correlate withIGF1Rexpression.Conclusion. We demonstrated amplification and overexpression ofIGF1Rgene in only one adrenocortical carcinoma, suggesting that these combined events are uncommon. In addition,IGF1Rpolymorphisms and abnormal microRNA expression did not correlate withIGF1Rupregulation in adrenocortical tumors.

scholarly journals Gene copy-number polymorphism in nature

2010 ◽  
Vol 277 (1698) ◽  
pp. 3213-3221 ◽  
Author(s):  
Daniel R. Schrider ◽  
Matthew W. Hahn
Keyword(s):  
Natural Selection ◽  
Copy Number Variation ◽  
Copy Number ◽  
Molecular Mechanisms ◽  
Copy Number Variants ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Phenotypic Differences ◽  
Sequencing Technologies ◽  
Number Variation

Differences between individuals in the copy-number of whole genes have been found in every multicellular species examined thus far. Such differences result in unique complements of protein-coding genes in all individuals, and have been shown to underlie adaptive phenotypic differences. Here, we review the evidence for copy-number variants (CNVs), focusing on the methods used to detect them and the molecular mechanisms responsible for generating this type of variation. Although there are multiple technical and computational challenges inherent to these experimental methods, next-generation sequencing technologies are making such experiments accessible in any system with a sequenced genome. We further discuss the connection between copy-number variation within species and copy-number divergence between species, showing that these values are exactly what one would expect from similar comparisons of nucleotide polymorphism and divergence. We conclude by reviewing the growing body of evidence for natural selection on copy-number variants. While it appears that most genic CNVs—especially deletions—are quickly eliminated by selection, there are now multiple studies demonstrating a strong link between copy-number differences at specific genes and phenotypic differences in adaptive traits. We argue that a complete understanding of the molecular basis for adaptive natural selection necessarily includes the study of copy-number variation.

Identification of Novel Germline and Tumor-Specific Nucleotide Variants and Copy Number Variation in Clival Chordomas by Exome Sequencing

2015 ◽  
Vol 76 (S 01) ◽  
Author(s):  
Georgios Zenonos ◽  
Peter Howard ◽  
Maureen Lyons-Weiler ◽  
Wang Eric ◽  
William LaFambroise ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Exome Sequencing ◽  
Copy Number ◽  
Number Variation ◽  
Specific Nucleotide

The impact of paralog genes: detection of copy number variation in spinal muscle atrophy patients

BIOCELL ◽  
2018 ◽  
Vol 42 (3) ◽  
pp. 87-91 ◽  
Author(s):  
Sergio LAURITO ◽  
Juan A. CUETO ◽  
Jimena PEREZ ◽  
Mar韆 ROQU�
Keyword(s):  
Copy Number Variation ◽  
Muscle Atrophy ◽  
Copy Number ◽  
Number Variation ◽  
The Impact
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