Sequence characterization of eccDNA content in glyphosate sensitive and resistant Palmer amaranth from geographically distant populations

The discovery of non-chromosomal circular DNA offers new directions in linking genome structure with function in plant biology. Glyphosate resistance through EPSPS gene copy amplification in Palmer amaranth was due to an autonomously replicating extra-chromosomal circular DNA mechanism (eccDNA). CIDER-Seq analysis of geographically distant glyphosate sensitive (GS) and resistant (GR) Palmer Amaranth ( Amaranthus palmeri ) revealed the presence of numerous small extra-chromosomal circular DNAs varying in size and with degrees of repetitive content, coding sequence, and motifs associated with autonomous replication. In GS biotypes, only a small portion of these aligned to the 399 kb eccDNA replicon, the vehicle underlying gene amplification and genetic resistance to the herbicide glyphosate. The aligned eccDNAs from GS were separated from one another by large gaps in sequence. In GR biotypes, the eccDNAs were present in both abundance and diversity to assemble into a nearly complete eccDNA replicon. Mean sizes of eccDNAs were similar in both biotypes and were around 5kb with larger eccDNAs near 25kb. Gene content for eccDNAs ranged from 0 to 3 with functions that include ribosomal proteins, transport, metabolism, and general stress response genetic elements. Repeat content among smaller eccDNAs indicate a potential for recombination into larger structures. Genomic hotspots were also identified in the Palmer amaranth genome with a disposition for gene focal amplifications as eccDNA. The presence of eccDNA may serve as a reservoir of genetic heterogeneity in this species and may be functionally important for survival.

Download Full-text

Varying Tolerance to Glyphosate in a Population of Palmer Amaranth with Low EPSPS Gene Copy Number

American Journal of Plant Sciences ◽

10.4236/ajps.2013.412297 ◽

2013 ◽

Vol 04 (12) ◽

pp. 2400-2408 ◽

Cited By ~ 2

Author(s):

Neal D. Teaster ◽

Robert E. Hoagland

Keyword(s):

Copy Number ◽

Gene Copy Number ◽

Palmer Amaranth ◽

Gene Copy ◽

Epsps Gene

Download Full-text

Extrachromosomal Circular DNA: Current Knowledge and Implications for CNS Aging and Neurodegeneration

International Journal of Molecular Sciences ◽

10.3390/ijms21072477 ◽

2020 ◽

Vol 21 (7) ◽

pp. 2477 ◽

Cited By ~ 3

Author(s):

Quratul Ain ◽

Christian Schmeer ◽

Diane Wengerodt ◽

Otto W. Witte ◽

Alexandra Kretz

Keyword(s):

Dna Repair ◽

Current Knowledge ◽

Critical Role ◽

Regional Distribution ◽

Gene Copy Number ◽

Gene Copy ◽

Extrachromosomal Dna ◽

Circular Dna ◽

Age Related ◽

Circular Dnas

Still unresolved is the question of how a lifetime accumulation of somatic gene copy number alterations impact organ functionality and aging and age-related pathologies. Such an issue appears particularly relevant in the broadly post-mitotic central nervous system (CNS), where non-replicative neurons are restricted in DNA-repair choices and are prone to accumulate DNA damage, as they remain unreplaced over a lifetime. Both DNA injuries and consecutive DNA-repair strategies are processes that can evoke extrachromosomal circular DNA species, apparently from either part of the genome. Due to their capacity to amplify gene copies and related transcripts, the individual cellular load of extrachromosomal circular DNAs will contribute to a dynamic pool of additional coding and regulatory chromatin elements. Analogous to tumor tissues, where the mosaicism of circular DNAs plays a well-characterized role in oncogene plasticity and drug resistance, we suggest involvement of the “circulome” also in the CNS. Accordingly, we summarize current knowledge on the molecular biogenesis, homeostasis and gene regulatory impacts of circular extrachromosomal DNA and propose, in light of recent discoveries, a critical role in CNS aging and neurodegeneration. Future studies will elucidate the influence of individual extrachromosomal DNA species according to their sequence complexity and regional distribution or cell-type-specific abundance.

Download Full-text

Effect of EPSPS Gene Copy Number and Glyphosate Selection on Fitness of Glyphosate-Resistant Bassia Scoparia in The Field

10.21203/rs.3.rs-155310/v1 ◽

2021 ◽

Author(s):

Charlemagne Ajoc Lim ◽

Prashant Jha ◽

Vipan Kumar ◽

Alan T. Dyer

Keyword(s):

Sugar Beet ◽

Seed Production ◽

Great Plains ◽

Copy Number ◽

Gene Copy Number ◽

Reproductive Traits ◽

Gene Copy ◽

Epsps Gene ◽

Gene Copies

Abstract The widespread evolution of glyphosate-resistant (GR) Bassia scoparia in the U.S. Great Plains poses a serious threat to the long-term sustainability of GR sugar beet. Glyphosate resistance in B. scoparia is due to an increase in the EPSPS (5-enolpyruvyl-shikimate-3-phosphate) gene copy number. The variation in EPSPS gene copies among individuals from within a single GR B. scoparia population indicated a differential response to glyphosate selection. We tested the hypothesis of reduced GR B. scoparia fitness (reproductive traits) to increasing glyphosate rates (applied as single or sequential applications) potentially experienced within a GR sugar beet field. The variation in EPSPS gene copy number and total glyphosate rate (single or sequential applications) did not influence any of the reproductive traits of GR B. scoparia, except seed production. Sequential applications of glyphosate with a total rate of 2,214 g ae ha− 1 or higher prevented seed production in B. scoparia plants with 2–4 (low levels of resistance) and 5–6 (moderate levels of resistance) EPSPS gene copies. Timely sequential applications of glyphosate (full recommended rates) can potentially slow down the evolution of GR B. scoparia with low to moderate levels of resistance (2–6 EPSPS gene copies), but any survivors (highly-resistant individuals with ≥ 8 EPSPS gene copies) need to be mechanically removed before flowering from GR sugar beet fields. This research warrants the need to adopt ecologically based, multi-tactic strategies to reduce exposure of B. scoparia to glyphosate in GR sugar beet.

Download Full-text

Unstable amplification of two extrachromosomal elements in alpha-difluoromethylornithine-resistant Leishmania donovani.

Molecular and Cellular Biology ◽

10.1128/mcb.12.12.5499 ◽

1992 ◽

Vol 12 (12) ◽

pp. 5499-5507 ◽

Cited By ~ 21

Author(s):

S Hanson ◽

S M Beverley ◽

W Wagner ◽

B Ullman

Keyword(s):

Gene Amplification ◽

Leishmania Donovani ◽

Molecular Mechanisms ◽

Gene Copy Number ◽

Gene Copy ◽

Unstable Gene ◽

Extrachromosomal Elements ◽

Circular Dnas ◽

Amplification Mechanism

We describe the first example of unstable gene amplification consisting of linear extrachromosomal DNAs in drug-resistant eukaryotic cells. alpha-Difluoromethylornithine (DFMO)-resistant Leishmania donovani with an amplified ornithine decarboxylase (ODC) gene copy number contained two new extrachromosomal DNAs, both present in 10 to 20 copies. One of these was a 140-kb linear DNA (ODC140-L) on which all of the amplified copies of the odc gene were located. The second was a 70-kb circular DNA (ODC70-C) containing an inverted repeat but lacking the odc gene. Both ODC140-L and ODC70-C were derived from a preexisting wild-type chromosome, probably by a conservative amplification mechanism. Both elements were unstable in the absence of DFMO, and their disappearance coincided with a decrease in ODC activity and an increase in DFMO growth sensitivity. These results suggest the possibility that ODC70-C may play a role in DFMO resistance. These data expand the diversity of known amplification mechanisms in eukaryotes to include the simultaneous unstable amplification of both linear and circular DNAs. Further characterization of these molecules will provide insights into the molecular mechanisms underlying gene amplification, including the ability of linear amplified DNAs to acquire telomeres and the determinants of chromosomal stability.

Download Full-text

Extensive gene deletions in Japanese patients with Diamond-Blackfan anemia

Blood ◽

10.1182/blood-2011-07-368662 ◽

2012 ◽

Vol 119 (10) ◽

pp. 2376-2384 ◽

Cited By ~ 37

Author(s):

Madoka Kuramitsu ◽

Aiko Sato-Otsubo ◽

Tomohiro Morio ◽

Masatoshi Takagi ◽

Tsutomu Toki ◽

...

Keyword(s):

Ribosomal Proteins ◽

Single Nucleotide Polymorphism Array ◽

Gene Copy Number ◽

Japanese Patients ◽

Large Deletion ◽

Gene Copy ◽

Easy Method ◽

Diamond Blackfan Anemia ◽

Large Deletions ◽

Novel Approach

Abstract Fifty percent of Diamond-Blackfan anemia (DBA) patients possess mutations in genes coding for ribosomal proteins (RPs). To identify new mutations, we investigated large deletions in the RP genes RPL5, RPL11, RPL35A, RPS7, RPS10, RPS17, RPS19, RPS24, and RPS26. We developed an easy method based on quantitative-PCR in which the threshold cycle correlates to gene copy number. Using this approach, we were able to diagnose 7 of 27 Japanese patients (25.9%) possessing mutations that were not detected by sequencing. Among these large deletions, similar results were obtained with 6 of 7 patients screened with a single nucleotide polymorphism array. We found an extensive intragenic deletion in RPS19, including exons 1-3. We also found 1 proband with an RPL5 deletion, 1 patient with an RPL35A deletion, 3 with RPS17 deletions, and 1 with an RPS19 deletion. In particular, the large deletions in the RPL5 and RPS17 alleles are novel. All patients with a large deletion had a growth retardation phenotype. Our data suggest that large deletions in RP genes comprise a sizable fraction of DBA patients in Japan. In addition, our novel approach may become a useful tool for screening gene copy numbers of known DBA genes.

Download Full-text

Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA

Nucleic Acids Research ◽

10.1093/nar/gkz725 ◽

2019 ◽

Vol 47 (18) ◽

pp. 9741-9760 ◽

Cited By ~ 3

Author(s):

V Talya Yerlici ◽

Michael W Lu ◽

Carla R Hoge ◽

Richard V Miller ◽

Rafik Neme ◽

...

Keyword(s):

Transposable Elements ◽

Genome Rearrangement ◽

Genome Instability ◽

Genome Rearrangements ◽

Circular Dna ◽

Dna Elimination ◽

Circular Dnas ◽

Bona Fide ◽

Polymerase Chain ◽

2D Gel

Abstract Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular DNA molecules across the genome to gain insight into its processes of programmed genome rearrangement. We recovered thousands of circularly excised Tc1/mariner-type transposable elements and high confidence non-repetitive germline-limited loci. We verified their bona fide circular topology using circular DNA deep-sequencing, 2D gel electrophoresis and inverse polymerase chain reaction. In contrast to the precise circular excision of transposable elements, we report widespread heterogeneity in the circular excision of non-repetitive germline-limited loci. We also demonstrate that circular DNAs are transcribed in Oxytricha, producing rearrangement-specific long non-coding RNAs. The programmed formation of thousands of eccDNA molecules makes Oxytricha a model system for studying nucleic acid topology. It also suggests involvement of eccDNA in programmed genome rearrangement.

Download Full-text

Variable Inheritance of AmplifiedEPSPSGene Copies in Glyphosate-Resistant Palmer Amaranth (Amaranthus palmeri)

Weed Science ◽

10.1017/wsc.2018.65 ◽

2018 ◽

Vol 67 (2) ◽

pp. 176-182 ◽

Cited By ~ 6

Author(s):

Darci A. Giacomini ◽

Philip Westra ◽

Sarah M. Ward

Keyword(s):

Copy Number ◽

Single Gene ◽

Gene Copy Number ◽

Transgressive Segregation ◽

Palmer Amaranth ◽

Gene Copy ◽

Amaranthus Palmeri ◽

Gene Copies ◽

Central United States ◽

Free Environment

AbstractGlyphosate-resistant (GR) Palmer amaranth (Amaranthus palmeriS. Watson) is considered one of the most troublesome weeds in the southern and central United States, but results of previous research to determine the mode of inheritance of this trait have been conflicting and inconclusive. In this study, we examined segregation patterns ofEPSPSgene-copy numbers in F1and F2generations ofA. palmeriand found no evidence of a Mendelian single-gene pattern of inheritance. Transgressive segregation for copy number was exhibited by several F1and all of the F2families, most likely the product ofEPSPScopy-number variation within each plant. This variation was confirmed by assaying gene-copy number across clonal generations and among individual shoots on the same plant, demonstrating thatEPSPSamplification levels vary significantly within a single plant. Increases and decreases in copy number occurred in a controlled, stress-free environment in the absence of glyphosate, indicating thatEPSPSgene amplification is a random and variable process within the plant. The ability ofA. palmerito gain or loseEPSPSgene copies is a valuable adaptive trait, allowing this species to respond rapidly to selection pressures and changing environments.

Download Full-text