Analysis of Brachypodium genomes with genome-wide optical maps
Genome, 2018 Brachypodium distachyon (n = 5) is a diploid and has been widely used as a genetic model. Brachypodium stacei (n = 10) and B. hybridum (n = 15) are species that are related to B. distachyon, leading to an hypothesis that they are part of a polyploid series based on x = 5. Several lines of evidence suggest that this hypothesis is incorrect and that the
Zhu, Tingting +7 more
openaire +3 more sources
nanotatoR: a tool for enhanced annotation of genomic structural variants
BMC Genomics, 2021 Background Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently
Surajit Bhattacharya +3 more
doaj +1 more source
Optical mapping of the Fusarium oxysporum f. sp. melongenae genome [PDF]
Journal of Basic Microbiology, 2021 Abstract Optical mapping approaches are widely preferred and applied in different branches of genomic studies because of their accuracy, low cost, and high efficiency. In the current study, a sequence orientation of the Fusarium oxysporum f.
Duygu Ates +2 more
openaire +6 more sources
Are we there yet? : reliably estimating the completeness of plant genome sequences [PDF]
, 2016 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.
Ruttink, Tom +2 more
core +3 more sources
SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner [PDF]
, 2013 To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of
Chang Yu +16 more
core +6 more sources
Draft genome sequence of Pseudomonas moraviensis R28-S [PDF]
, 2014 We report the draft genome sequence of Pseudomonas moraviensis R28-S, isolated from the municipal wastewater treatment plant of Moscow, ID. The strain carries a native mercury resistance plasmid, poorly maintains introduced IncP-1 antibiotic resistance ...
De Gelder, Leen +8 more
core +1 more source
Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with
mBio, 2014 Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations.
Colin Raeside +10 more
doaj +1 more source
A Powerful New Quantitative Genetics Platform, Combining Caenorhabditis elegans High-Throughput Fitness Assays with a Large Collection of Recombinant Strains. [PDF]
, 2015 The genetic variants underlying complex traits are often elusive even in powerful model organisms such as Caenorhabditis elegans with controlled genetic backgrounds and environmental conditions.
Andersen, Erik C +7 more
core +2 more sources
A clone-free, single molecule map of the domestic cow (Bos taurus) genome. [PDF]
, 2015 BackgroundThe cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals.
Bechner, Michael +11 more
core +1 more source
Recombining your way out of trouble: the genetic architecture of hybrid fitness under environmental stress [PDF]
, 2020 Hybridization between species is a fundamental evolutionary force that can both promote and delay adaptation. There is a deficit in our understanding of the genetic basis of hybrid fitness, especially in non-domesticated organisms.
Bendixsen, D. +5 more
core +1 more source