73,741 research outputs found
Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans
We have used whole genome paired-end Illumina sequence data to identify
tandem duplications in 20 isofemale lines of D. yakuba, and 20 isofemale lines
of D. simulans and performed genome wide validation with PacBio long molecule
sequencing. We identify 1,415 tandem duplications that are segregating in D.
yakuba as well as 975 duplications in D. simulans, indicating greater variation
in D. yakuba. Additionally, we observe high rates of secondary deletions at
duplicated sites, with 8% of duplicated sites in D. simulans and 17% of sites
in D. yakuba modified with deletions. These secondary deletions are consistent
with the action of the large loop mismatch repair system acting to remove
polymorphic tandem duplication, resulting in rapid dynamics of gain and loss in
duplicated alleles and a richer substrate of genetic novelty than has been
previously reported. Most duplications are present in only single strains,
suggesting deleterious impacts are common. D. simulans shows larger numbers of
whole gene duplications in comparison to larger proportions of gene fragments
in D. yakuba. D. simulans displays an excess of high frequency variants on the
X chromosome, consistent with adaptive evolution through duplications on the D.
simulans X or demographic forces driving duplicates to high frequency. We
identify 78 chimeric genes in D. yakuba and 38 chimeric genes in D. simulans,
as well as 143 cases of recruited non-coding sequence in D. yakuba and 96 in D.
simulans, in agreement with rates of chimeric gene origination in D.
melanogaster. Together, these results suggest that tandem duplications often
result in complex variation beyond whole gene duplications that offers a rich
substrate of standing variation that is likely to contribute both to
detrimental phenotypes and disease, as well as to adaptive evolutionary change.Comment: Revised Version- Accepted at Molecular Biology and Evolutio
Occurrence of LINE, gypsy-like, and copia-like retrotransposons in the clonally propagated sweet potato (Ipomoea batatas L.)
Retrotransposons are a class of transposable elements that represent a major fraction of the repetitive DNA of most eukaryotes. Their abundance stems from their expansive replication strategies. We screened and isolated sequence fragments of long terminal repeat (LTR), gypsy-like reverse transcriptase (rt) and gypsy-like envelope (env) domains, and two partial sequences of non-LTR retrotransposons, long interspersed element (LINE), in the clonally propagated allohexaploid sweet potato (Ipomoea batatas (L.) Lam.) genome. Using dot-blot hybridization, these elements were found to be present in the ~1597 Mb haploid sweet potato genome with copy numbers ranging from ~50 to ~4100 as observed in the partial LTR (IbLtr-1) and LINE (IbLi-1) sequences, respectively. The continuous clonal propagation of sweet potato may have contributed to such a multitude of copies of some of these genomic elements. Interestingly, the isolated gypsy-like env and gypsy-like rt sequence fragments, IbGy-1 (~2100 copies) and IbGy-2 (~540 copies), respectively, were found to be homologous to the Bagy-2 cDNA sequences of barley (Hordeum vulgare L.). Although the isolated partial sequences were found to be homologous to other transcriptionally active elements, future studies are required to determine whether they represent elements that are transcriptionally active under normal and (or) stressful conditions
Are we there yet? : reliably estimating the completeness of plant genome sequences
Genome sequencing is becoming cheaper and faster thanks to the introduction of next-generation sequencing techniques. Dozens of new plant genome sequences have been released in recent years, ranging from small to gigantic repeat-rich or polyploid genomes. Most genome projects have a dual purpose: delivering a contiguous, complete genome assembly and creating a full catalog of correctly predicted genes. Frequently, the completeness of a species' gene catalog is measured using a set of marker genes that are expected to be present. This expectation can be defined along an evolutionary gradient, ranging from highly conserved genes to species-specific genes. Large-scale population resequencing studies have revealed that gene space is fairly variable even between closely related individuals, which limits the definition of the expected gene space, and, consequently, the accuracy of estimates used to assess genome and gene space completeness. We argue that, based on the desired applications of a genome sequencing project, different completeness scores for the genome assembly and/or gene space should be determined. Using examples from several dicot and monocot genomes, we outline some pitfalls and recommendations regarding methods to estimate completeness during different steps of genome assembly and annotation
Miniature transposable sequences are frequently mobilized in the bacterial plant pathogen Pseudomonas syringae pv. phaseolicola
Mobile genetic elements are widespread in Pseudomonas syringae, and often associate with virulence genes. Genome
reannotation of the model bean pathogen P. syringae pv. phaseolicola 1448A identified seventeen types of insertion
sequences and two miniature inverted-repeat transposable elements (MITEs) with a biased distribution, representing 2.8%
of the chromosome, 25.8% of the 132-kb virulence plasmid and 2.7% of the 52-kb plasmid. Employing an entrapment vector
containing sacB, we estimated that transposition frequency oscillated between 2.661025 and 1.161026, depending on the
clone, although it was stable for each clone after consecutive transfers in culture media. Transposition frequency was similar
for bacteria grown in rich or minimal media, and from cells recovered from compatible and incompatible plant hosts,
indicating that growth conditions do not influence transposition in strain 1448A. Most of the entrapped insertions
contained a full-length IS801 element, with the remaining insertions corresponding to sequences smaller than any
transposable element identified in strain 1448A, and collectively identified as miniature sequences. From these, fragments
of 229, 360 and 679-nt of the right end of IS801 ended in a consensus tetranucleotide and likely resulted from one-ended
transposition of IS801. An average 0.7% of the insertions analyzed consisted of IS801 carrying a fragment of variable size
from gene PSPPH_0008/PSPPH_0017, showing that IS801 can mobilize DNA in vivo. Retrospective analysis of complete
plasmids and genomes of P. syringae suggests, however, that most fragments of IS801 are likely the result of reorganizations
rather than one-ended transpositions, and that this element might preferentially contribute to genome flexibility by
generating homologous regions of recombination. A further miniature sequence previously found to affect host range
specificity and virulence, designated MITEPsy1 (100-nt), represented an average 2.4% of the total number of insertions
entrapped in sacB, demonstrating for the first time the mobilization of a MITE in bacteria
A versatile quantum walk resonator with bright classical light
In a Quantum Walk (QW) the "walker" follows all possible paths at once
through the principle of quantum superposition, differentiating itself from
classical random walks where one random path is taken at a time. This
facilitates the searching of problem solution spaces faster than with classical
random walks, and holds promise for advances in dynamical quantum simulation,
biological process modelling and quantum computation. Current efforts to
implement QWs have been hindered by the complexity of handling single photons
and the inscalability of cascading approaches. Here we employ a versatile and
scalable resonator configuration to realise quantum walks with bright classical
light. We experimentally demonstrate the versatility of our approach by
implementing a variety of QWs, all with the same experimental platform, while
the use of a resonator allows for an arbitrary number of steps without scaling
the number of optics. Our approach paves the way for practical QWs with bright
classical light and explicitly makes clear that quantum walks with a single
walker do not require quantum states of light
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