scholarly journals Meiotic effects of MSH4 copy number variation support an adaptive role for post-polyploidy gene loss

2018 ◽  
Author(s):  
Adrián Gonzalo ◽  
Marie-Odile Lucas ◽  
Catherine Marquis ◽  
Andrew Lloyd ◽  
Eric Jenczewski
Keyword(s):  
Chromosome Segregation ◽  
Meiotic Recombination ◽  
Copy Number ◽  
Gene Loss ◽  
Duplicate Gene ◽  
Single Copy ◽  
Homologous Chromosomes ◽  
Evolutionary Forces ◽  
Copy Numbers ◽  
Number Variation

ABSTRACTMany eukaryotes descend from polyploid ancestors that experienced massive duplicate gene loss. This genomic erosion is particularly strong for duplicated (meiotic) recombination genes that return to a single copy more rapidly than genome average following polyploidy. To better understand the evolutionary forces underlying duplicate loss, we analysed how varying copy numbers of MSH4, an essential meiotic recombination gene, influences crossover formation in allotetraploid Brassica napus. We show that faithful chromosome segregation and crossover frequencies between homologous chromosomes are unchanged with MSH4 duplicate loss; by contrast, crossovers between homoeologous chromosomes (which result in genomic rearrangements) decrease with reductions in MSH4 copy number. We also found that inter-homoeologue crossovers originate almost exclusively from the MSH4-dependent crossover pathway. Limiting the efficiency of this pathway by decreasing the copy number of key meiotic recombination genes could therefore contribute to adaptation to polyploidy, by promoting regular chromosome segregation and genomic stability.

scholarly journals Convergent evolution of polyploid genomes from across the eukaryotic tree of life

2021 ◽  
Author(s):  
Yue Hao ◽  
Jonathon Fleming ◽  
Joanna Petterson ◽  
Eric Lyons ◽  
Patrick P. Edger ◽  
...  
Keyword(s):  
High Frequency ◽  
Gene Loss ◽  
Relative Rate ◽  
Duplicate Gene ◽  
Single Copy ◽  
Selective Constraint ◽  
Diploid Hybrid ◽  
Hybrid Species ◽  
Evolutionary Forces ◽  
Modern Species

By modeling the homoeologous gene losses that occurred in fifty genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes or yeasts. The models suggest these events were nearly all allopolyploidies, with two distinct progenitors contributing to the modern species. We show that many of the events show a relative rate of duplicate gene loss prior to the first post-polyploidy speciation that is significantly higher than in later phases of their evolution. The relatively low selective constraint seen for the single-copy genes these losses produced lead us to suggest that most of the purely selectively neutral duplicate gene losses occur in the immediate post-polyploid period. We also find ongoing and extensive reciprocal gene losses (RGL; alternative losses of duplicated ancestral genes) between these genomes. With the exception of a handful of closely related taxa, all of these polyploid organisms are separated from each other by tens to thousands of reciprocal gene losses. As a result, it is very unlikely that viable diploid hybrid species could form between these taxa, since matings between such hybrids would tend to produce offspring lacking essential genes. It is therefore possible that the relatively high frequency of recurrent polyploidies in some lineages may be due to the ability of new polyploidies to bypass RGL barriers.

scholarly journals Copy Number Variations of Four Y-Linked Genes in Swamp Buffaloes

Animals ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 31
Author(s):  
Ting Sun ◽  
Quratulain Hanif ◽  
Hong Chen ◽  
Chuzhao Lei ◽  
Ruihua Dang
Keyword(s):  
Y Chromosome ◽  
Copy Number ◽  
Water Buffalo ◽  
Single Copy ◽  
Copy Number Variations ◽  
Tetratricopeptide Repeat ◽  
Dead Box ◽  
Complex Phenotypes ◽  
Swamp Buffaloes ◽  
Number Variation

Copy number variation (CNV), a significant source of genetic diversity in the mammalian Y chromosome, is associated with the development of many complex phenotypes, such as spermatogenesis and male fertility. The contribution of Y-linked CNVs has been studied in various species, however, water buffalo has not been explored in this area and the genetic information still remains unknown. The aim of the current study was to investigate the CNVs of four Y-linked genes, including, sex determining Region of Y-Chromosome (SRY), ubiquitously transcribed tetratricopeptide repeat gene protein on the chromosome Y (UTY), DEAD-box helicase 3 Y-linked (DDX3Y, also known as DBY), and oral-facial-digital syndrome 1 Y-linked (OFD1Y) in 254 swamp buffaloes from 15 populations distributed across China, Vietnam, and Laos using quantitative real-time PCR (qPCR). Our results revealed the prevalence of a single-copy UTY gene in buffaloes. The DBY and OFD1Y represented CNVs among and within different buffalo breeds. The SRY showed CNVs only in Vietnamese and Laotian buffaloes. In conclusion, this study indicated that DBY, OFD1Y, and SRY showed CNVs, while the UTY was a single-copy gene in swamp buffaloes.

scholarly journals Salivary AMY1 Copy Number Variation Modifies Age-Related Type 2 Diabetes Risk

2020 ◽  
Vol 66 (5) ◽  
pp. 718-726
Author(s):  
Yuwei Liu ◽  
Caren E Smith ◽  
Laurence D Parnell ◽  
Yu-Chi Lee ◽  
Ping An ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Copy Number Variation ◽  
Metabolic Pathway ◽  
Copy Number ◽  
Lipid Lowering ◽  
Pathway Enrichment Analysis ◽  
Copy Numbers ◽  
Number Variation ◽  
The Relationship

Abstract Background Copy number variation (CNV) in the salivary amylase gene (AMY1) modulates salivary α-amylase levels and is associated with postprandial glycemic traits. Whether AMY1-CNV plays a role in age-mediated change in insulin resistance (IR) is uncertain. Methods We measured AMY1-CNV using duplex quantitative real-time polymerase chain reaction in two studies, the Boston Puerto Rican Health Study (BPRHS, n = 749) and the Genetics of Lipid-Lowering Drug and Diet Network study (GOLDN, n = 980), and plasma metabolomic profiles in the BPRHS. We examined the interaction between AMY1-CNV and age by assessing the relationship between age with glycemic traits and type 2 diabetes (T2D) according to high or low copy numbers of the AMY1 gene. Furthermore, we investigated associations between metabolites and interacting effects of AMY1-CNV and age on T2D risk. Results We found positive associations of IR with age among subjects with low AMY1-copy-numbers in both studies. T2D was marginally correlated with age in participants with low AMY1-copy-numbers but not with high AMY1-copy-numbers in the BPRHS. Metabolic pathway enrichment analysis identified the pentose metabolic pathway based on metabolites that were associated with both IR and the interactions between AMY1-CNV and age. Moreover, in older participants, high AMY1-copy-numbers tended to be associated with lower levels of ribonic acid, erythronic acid, and arabinonic acid, all of which were positively associated with IR. Conclusions We found evidence supporting a role of AMY1-CNV in modifying the relationship between age and IR. Individuals with low AMY1-copy-numbers tend to have increased IR with advancing age.

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 Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error

2017 ◽  
Vol 284 (1859) ◽  
pp. 20170425 ◽  
Author(s):  
Chundi Wang ◽  
Tengteng Zhang ◽  
Yurui Wang ◽  
Laura A. Katz ◽  
Feng Gao ◽  
...  
Keyword(s):  
Single Cell ◽  
Copy Number ◽  
Sequence Variation ◽  
Ssu Rdna ◽  
Copy Numbers ◽  
Number Variation ◽  
The Impact ◽  
Rdna Copy ◽  
Rdna Polymorphism ◽  
Rdna Copy Number

Small subunit ribosomal DNA (SSU rDNA) is widely used for phylogenetic inference, barcoding and other taxonomy-based analyses. Recent studies indicate that SSU rDNA of ciliates may have a high level of sequence variation within a single cell, which impacts the interpretation of rDNA-based surveys. However, sequence variation can come from a variety of sources including experimental errors, especially the mutations generated by DNA polymerase in PCR. In the present study, we explore the impact of four DNA polymerases on sequence variation and find that low-fidelity polymerases exaggerate the estimates of single-cell sequence variation. Therefore, using a polymerase with high fidelity is essential for surveys of sequence variation. Another source of variation results from errors during amplification of SSU rDNA within the polyploidy somatic macronuclei of ciliates. To investigate further the impact of SSU rDNA copy number variation, we use a high-fidelity polymerase to examine the intra-individual SSU rDNA polymorphism in ciliates with varying levels of macronuclear amplification: Halteria grandinella , Blepharisma americanum and Strombidium stylifer . We estimate the rDNA copy numbers of these three species by single-cell quantitative PCR. The results indicate that: (i) sequence variation of SSU rDNA within a single cell is authentic in ciliates, but the level of intra-individual SSU rDNA polymorphism varies greatly among species; (ii) rDNA copy numbers vary greatly among species, even those within the same class; (iii) the average rDNA copy number of Halteria grandinella is about 567 893 (s.d. = 165 481), which is the highest record of rDNA copy number in ciliates to date; and (iv) based on our data and the records from previous studies, it is not always true in ciliates that rDNA copy numbers are positively correlated with cell or genome size.

scholarly journals Plasmodium copy number variation scan: gene copy numbers evaluation in haploid genomes

2016 ◽  
Vol 15 (1) ◽  
Author(s):  
Johann Beghain ◽  
Anne-Claire Langlois ◽  
Eric Legrand ◽  
Laura Grange ◽  
Nimol Khim ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Gene Copy ◽  
Copy Numbers ◽  
Number Variation ◽  
Gene Copy Numbers

scholarly journals Eight Y chromosome genes show copy number variations in horses

2018 ◽  
Vol 61 (3) ◽  
pp. 263-270
Author(s):  
Haoyuan Han ◽  
Xin Zhang ◽  
Xiaocheng Zhao ◽  
Xiaoting Xia ◽  
Chuzhao Lei ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Copy Number ◽  
Distribution Patterns ◽  
Single Copy ◽  
Copy Number Variations ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Specific Transcript ◽  
Copy Numbers ◽  
The Impact

Abstract. Copy number variations (CNVs), which represent a significant source of genetic diversity on the Y chromosome in mammals, have been shown to be associated with the development of many complex phenotypes, such as reproduction and male fertility. The occurrence of CNVs has been confirmed on the Y chromosome in horses. However, the copy numbers (CNs) of Equus caballus Y chromosome (ECAY) genes are largely unknown. To demonstrate the copy number variations of Y chromosome genes in horses, the quantitative real-time polymerase chain reaction (qPCR) method was applied to measure the CNVs of the eukaryotic translation initiation factor 1A Y (EIF1AY), equine testis-specific transcript on Y 1 (ETSTY1), equine testis-specific transcript on Y 4 (ETSTY4), equine testis-specific transcript on Y 5 (ETSTY5), equine transcript Y4 (ETY4), ubiquitin activating enzyme Y (UBE1Y), sex determining region Y (SRY), and inverted repeat 2 Y (YIR2) across 14 Chinese domestic horse breeds in this study. Our results revealed that these eight genes were multi-copy; furthermore, some of the well acknowledged single-copy genes such as SRY and EIF1AY were found to be multi-copy in this research. The median copy numbers (MCNs) varied among different breeds for the same gene. The CNVs of Y chromosome genes showed different distribution patterns among Chinese horse breeds, indicating the impact of natural selection on copy numbers. Our results will provide fundamental information for future functional studies.

scholarly journals High levels of copy number variation of ampliconic genes across major human Y haplogroups

2017 ◽  
Author(s):  
Danling Ye ◽  
Arslan Zaidi ◽  
Marta Tomaszkiewicz ◽  
Corey Liebowitz ◽  
Michael DeGiorgio ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Y Chromosome ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Families ◽  
Digital Pcr ◽  
Gene Copy ◽  
Copy Numbers ◽  
Number Variation ◽  
Gene Copy Numbers

AbstractDue to its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100 males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared by males from very different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according to major Y haplogroups. Overall, only three gene families (DATZ, RBMY, TSPY) showed significant differences in copy number among major Y haplogroups, and the haplogroup of an individual could not be predicted based on his ampliconic gene copy numbers. Finally, we found a significant correlation between copy number variation and individual’s height (for three gene families), but not between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.

scholarly journals Evolutionary and functional analysis of RBMY1 gene copy number variation on the human Y chromosome

2019 ◽  
Vol 28 (16) ◽  
pp. 2785-2798 ◽  
Author(s):  
Wentao Shi ◽  
Sandra Louzada ◽  
Marina Grigorova ◽  
Andrea Massaia ◽  
Elena Arciero ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Y Chromosome ◽  
Sperm Motility ◽  
Copy Number ◽  
Population Variation ◽  
Gene Copy ◽  
Copy Numbers ◽  
Fish Samples ◽  
Number Variation ◽  
Fibre Fish

Abstract Human RBMY1 genes are located in four variable-sized clusters on the Y chromosome, expressed in male germ cells and possibly associated with sperm motility. We have re-investigated the mutational background and evolutionary history of the RBMY1 copy number distribution in worldwide samples and its relevance to sperm parameters in an Estonian cohort of idiopathic male factor infertility subjects. We estimated approximate RBMY1 copy numbers in 1218 1000 Genomes Project phase 3 males from sequencing read-depth, then chose 14 for valid ation by multicolour fibre-FISH. These fibre-FISH samples provided accurate calibration standards for the entire panel and led to detailed insights into population variation and mutational mechanisms. RBMY1 copy number worldwide ranged from 3 to 13 with a mode of 8. The two larger proximal clusters were the most variable, and additional duplications, deletions and inversions were detected. Placing the copy number estimates onto the published Y-SNP-based phylogeny of the same samples suggested a minimum of 562 mutational changes, translating to a mutation rate of 2.20 × 10−3 (95% CI 1.94 × 10−3 to 2.48 × 10−3) per father-to-son Y-transmission, higher than many short tandem repeat (Y-STRs), and showed no evidence for selection for increased or decreased copy number, but possible copy number stabilizing selection. An analysis of RBMY1 copy numbers among 376 infertility subjects failed to replicate a previously reported association with sperm motility and showed no significant effect on sperm count and concentration, serum follicle stimulating hormone (FSH), luteinizing hormone (LH) and testosterone levels or testicular and semen volume. These results provide the first in-depth insights into the structural rearrangements underlying RBMY1 copy number variation across diverse human lineages.

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