scholarly journals Frequency and Spectrum of Mutations Induced by Gamma Rays Revealed by Phenotype Screening and Whole-Genome Re-Sequencing in Arabidopsis thaliana

2022 ◽  
Vol 23 (2) ◽  
pp. 654
Author(s):  
Yan Du ◽  
Zhuo Feng ◽  
Jie Wang ◽  
Wenjie Jin ◽  
Zhuanzi Wang ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Gamma Rays ◽  
Large Scale ◽  
Mutation Frequency ◽  
Mutation Screening ◽  
Whole Genome ◽  
Single Base ◽  
Small Indels ◽  
Phenotype Screening ◽  
Mutagenic Effects

Genetic variations are an important source of germplasm diversity, as it provides an allele resource that contributes to the development of new traits for plant breeding. Gamma rays have been widely used as a physical agent for mutation creation in plants, and their mutagenic effect has attracted extensive attention. However, few studies are available on the comprehensive mutation profile at both the large-scale phenotype mutation screening and whole-genome mutation scanning. In this study, biological effects on M1 generation, large-scale phenotype screening in M2 generation, as well as whole-genome re-sequencing of seven M3 phenotype-visible lines were carried out to comprehensively evaluate the mutagenic effects of gamma rays on Arabidopsis thaliana. A total of 417 plants with visible mutated phenotypes were isolated from 20,502 M2 plants, and the phenotypic mutation frequency of gamma rays was 2.03% in Arabidopsis thaliana. On average, there were 21.57 single-base substitutions (SBSs) and 11.57 small insertions and deletions (InDels) in each line. Single-base InDels accounts for 66.7% of the small InDels. The genomic mutation frequency was 2.78 × 10−10/bp/Gy. The ratio of transition/transversion was 1.60, and 64.28% of the C > T events exhibited the pyrimidine dinucleotide sequence; 69.14% of the small InDels were located in the sequence with 1 to 4 bp terminal microhomology that was used for DNA end rejoining, while SBSs were less dependent on terminal microhomology. Nine genes, on average, were predicted to suffer from functional alteration in each re-sequenced line. This indicated that a suitable mutation gene density was an advantage of gamma rays when trying to improve elite materials for one certain or a few traits. These results will aid the full understanding of the mutagenic effects and mechanisms of gamma rays and provide a basis for suitable mutagen selection and parameter design, which can further facilitate the development of more controlled mutagenesis methods for plant mutation breeding.

Comparative study of mutations induced by carbon-ion beams and gamma-ray irradiations in Arabidopsis thaliana at the genome-wide scale.

2021 ◽  
pp. 451-458
Author(s):  
Li-bin Zhou ◽  
Yan Du ◽  
Zhuo Feng ◽  
Tao Cui ◽  
Xia Chen ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Gamma Rays ◽  
Gamma Ray ◽  
Mutation Breeding ◽  
Ion Beams ◽  
Single Base ◽  
Carbon Ion ◽  
Sequencing Platform ◽  
Genome Wide ◽  
Wide Scale

Abstract Mutation breeding induced by irradiation with highly energetic photons and ion beams is one of the important methods to improve plant varieties, but the mutagenic effects and molecular mechanisms are often not entirely clear. Traditional research is focused on phenotype screening, chromosome aberration tests and genetic variation analysis of specific genes. The whole genome sequencing technique provides a new method to understand and undertake the comprehensive identification of mutations caused by irradiations with different linear energy transfer (LET). In this study, ten Arabidopsis thaliana M3 lines induced by carbon-ion beams (CIB) and ten M3 lines induced by gamma-rays were re-sequenced by using the Illumina HiSeq sequencing platform, and the single base substitutions (SBSs) and small insertions or deletions (indels) were analysed comparatively. It was found that the ratio of SBSs to small indels for M3 lines induced by CIB was 2.57:1, whereas the ratio was 1.78:1 for gamma-rays. The ratios of deletions to insertions for carbon ions and gamma-rays were 4.8:1 and 2.8:1, respectively. The single-base indels were more prevalent than those equal to or greater than 2 bp in both CIB and gamma-ray induced M3 lines. Among the detected SBSs, the ratio of transitions to transversions induced by carbon-ion irradiation was 1.01 and 1.42 for gamma-rays; these values differ greatly from the 2.41 reported for spontaneous substitutions. This study provides novel data on molecular characteristics of CIB and gamma-ray induced mutations at the genome-wide scale. It can also provide valuable clues for explaining the potential mechanism of plant mutation breeding by irradiations with different LETs.

RADIO-SENSITIVITY IN RAGI (ELEUSINE CORACANA)

1969 ◽  
Vol 11 (2) ◽  
pp. 254-265 ◽  
Author(s):  
J. V. Goud ◽  
K. Muraleedharan Nayar ◽  
M. Goalkrishna Rao
Keyword(s):  
Gamma Irradiation ◽  
Gamma Rays ◽  
Mutation Frequency ◽  
Radiation Effect ◽  
Wide Spectrum ◽  
Eleusine Coracana ◽  
Seed Fertility ◽  
Acute Dosage ◽  
Mutagenic Effects ◽  
Radio Sensitivity

Dry seeds of three varieties of ragi (Eleusine coracana) were subjected to gamma irradiation with acute dosage of 20 Kr and 30 Kr. The mutagenic effects of gamma rays in the M1 generation and the mutation frequency with regard to chlorophyll and viable mutations in the M2 generation were studied.The LD50 appears to be around 30 Kr for ragi, although there are enormous varietal differences. Purna is the least and H22 the most sensitive to gamma irradiation in the M1 generation. There is a direct correlation between the radiation effect produced as measured by seedling growth, pollen fertility and seed fertility with the dosage used. Multivalent formation, lagging chromosomes and stickiness, etc. were observed in meiotic studies in the M1 generation.The frequency of chlorophyll mutations was less in populations irradiated with 30 Kr than with 20 Kr. A wide spectrum and a high frequency of viable mutations were produced in Purna. The mutation frequency (viable + chlorophyll) increased with the dosage. The 200 isolated viable mutations included many agronomic types which are useful either directly or in conventional plant breeding.

0306 Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 146-146
Author(s):  
D. M. Bickhart ◽  
L. Xu ◽  
J. L. Hutchison ◽  
J. B. Cole ◽  
D. J. Null ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Copy Number ◽  
Large Scale ◽  
Copy Number Variants ◽  
Whole Genome

scholarly journals Modeling Gamma-Ray SEDs and Angular Extensions of Extreme TeV Blazars from Intergalactic Proton-Initiated Cascades in Contemporary Astrophysical EGMF Models

Universe ◽  
2021 ◽  
Vol 7 (7) ◽  
pp. 220
Author(s):  
Emil Khalikov
Keyword(s):  
Gamma Rays ◽  
Large Scale ◽  
Gamma Ray ◽  
High Energy ◽  
Cascade Model ◽  
Point Sources ◽  
Spectral Energy ◽  
Observation Data ◽  
Cherenkov Telescopes ◽  
The Universe

The intrinsic spectra of some distant blazars known as “extreme TeV blazars” have shown a hint at an anomalous hardening in the TeV energy region. Several extragalactic propagation models have been proposed to explain this possible excess transparency of the Universe to gamma-rays starting from a model which assumes the existence of so-called axion-like particles (ALPs) and the new process of gamma-ALP oscillations. Alternative models suppose that some of the observable gamma-rays are produced in the intergalactic cascades. This work focuses on investigating the spectral and angular features of one of the cascade models, the Intergalactic Hadronic Cascade Model (IHCM) in the contemporary astrophysical models of Extragalactic Magnetic Field (EGMF). For IHCM, EGMF largely determines the deflection of primary cosmic rays and electrons of intergalactic cascades and, thus, is of vital importance. Contemporary Hackstein models are considered in this paper and compared to the model of Dolag. The models assumed are based on simulations of the local part of large-scale structure of the Universe and differ in the assumptions for the seed field. This work provides spectral energy distributions (SEDs) and angular extensions of two extreme TeV blazars, 1ES 0229+200 and 1ES 0414+009. It is demonstrated that observable SEDs inside a typical point spread function of imaging atmospheric Cherenkov telescopes (IACTs) for IHCM would exhibit a characteristic high-energy attenuation compared to the ones obtained in hadronic models that do not consider EGMF, which makes it possible to distinguish among these models. At the same time, the spectra for IHCM models would have longer high energy tails than some available spectra for the ALP models and the universal spectra for the Electromagnetic Cascade Model (ECM). The analysis of the IHCM observable angular extensions shows that the sources would likely be identified by most IACTs not as point sources but rather as extended ones. These spectra could later be compared with future observation data of such instruments as Cherenkov Telescope Array (CTA) and LHAASO.

scholarly journals High prevalence of TP53 loss and whole-genome doubling in early-onset colorectal cancer

2021 ◽  
Author(s):  
Jeong Eun Kim ◽  
Jaeyong Choi ◽  
Chang-Ohk Sung ◽  
Yong Sang Hong ◽  
Sun Young Kim ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Early Onset ◽  
Large Scale ◽  
Late Onset ◽  
Age Groups ◽  
The Cancer Genome Atlas ◽  
Whole Genome ◽  
Genome Doubling ◽  
Whole Genome Doubling ◽  
Early Onset Colorectal Cancer

AbstractThe global incidence of early-onset colorectal cancer (EO-CRC) is rapidly rising. However, the reason for this rise in incidence as well as the genomic characteristics of EO-CRC remain largely unknown. We performed whole-exome sequencing in 47 cases of EO-CRC and targeted deep sequencing in 833 cases of CRC. Mutational profiles of EO-CRC were compared with previously published large-scale studies. EO-CRC and The Cancer Genome Atlas (TCGA) data were further investigated according to copy number profiles and mutation timing. We classified colorectal cancer into three subgroups: the hypermutated group consisted of mutations in POLE and mismatch repair genes; the whole-genome doubling group had early functional loss of TP53 that led to whole-genome doubling and focal oncogene amplification; the genome-stable group had mutations in APC and KRAS, similar to conventional colon cancer. Among non-hypermutated samples, whole-genome doubling was more prevalent in early-onset than in late-onset disease (54% vs 38%, Fisher’s exact P = 0.04). More than half of non-hypermutated EO-CRC cases involved early TP53 mutation and whole-genome doubling, which led to notable differences in mutation frequencies between age groups. Alternative carcinogenesis involving genomic instability via loss of TP53 may be related to the rise in EO-CRC.

Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 141-155 ◽  
Author(s):  
H H Yan ◽  
J Mudge ◽  
D-J Kim ◽  
R C Shoemaker ◽  
D R Cook ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Glycine Max ◽  
Medicago Truncatula ◽  
Physical Mapping ◽  
Large Scale ◽  
Sequence Similarity ◽  
Artificial Chromosome ◽  
Bac Contig ◽  
Cross Hybridization ◽  
Bac Contigs

To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.Key words: Glycine max, Medicago truncatula, Arabidopsis thaliana, conserved microsynteny, genome duplication.

scholarly journals A Phylogenomic Supertree of Birds

Diversity ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 109 ◽  
Author(s):  
Rebecca T. Kimball ◽  
Carl H. Oliveros ◽  
Ning Wang ◽  
Noor D. White ◽  
F. Keith Barker ◽  
...  
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Bird Species ◽  
Divide And Conquer ◽  
Clear Understanding ◽  
Whole Genome ◽  
Efficient Manner ◽  
Sequence Capture ◽  
Branch Lengths ◽  
Supertree Methods

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.

scholarly journals Comparison of Whole-Genome Sequences from Two Colony Morphovars of Burkholderia pseudomallei

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Pei-Tan Hsueh ◽  
Yao-Shen Chen ◽  
Hsi-Hsu Lin ◽  
Pei-Ju Liu ◽  
Wen-Fan Ni ◽  
...  
Keyword(s):  
Burkholderia Pseudomallei ◽  
Repeated Sequences ◽  
Whole Genome ◽  
Genome Sequences ◽  
Single Base

The entire genomes of two isogenic morphovars (vgh16W and vgh16R) of Burkholderia pseudomallei were sequenced. A comparison of the sequences from both strains indicates that they show 99.99% identity, are composed of 22 tandem repeated sequences with <100 bp of indels, and have 199 single-base variants.

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