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Hybrid assembly may be used to resolve ambiguities that exist in genomes previously assembled using second generation sequencing. Short second generation reads have also been used to correct errors that exist in the long third generation reads.
In bioinformatics, hybrid genome assembly refers to utilizing various sequencing technologies to achieve the task of assembling a genome from fragmented, sequenced DNA resulting from shotgun sequencing. Genome assembly presents one of the most challenging tasks in genome sequencing as most modern DNA sequencing technologies can only produce reads that are, on average, 25-300 base pairs in length.[1] This is orders of magnitude smaller than the average size of a genome (the genome of the octoploid plant Paris japonica is 149 billion base pairs[2]). This assembly is computationally difficult and has some inherent challenges, one of these challenges being that genomes often contain complex tandem repeats of sequences that can be thousands of base pairs in length.[3] These repeats can be long enough that second generation sequencing reads are not long enough to bridge the repeat, and, as such, determining the location of each repeat in the genome can be difficult.[4] Resolving these tandem repeats can be accomplished by utilizing long third generation sequencing reads, such as those obtained using the PacBio RS DNA sequencer. These sequences are, on average, 10,000-15,000 base pairs in length and are long enough to span most repeated regions.[5] Using a hybrid approach to this process can increase the fidelity of assembling tandem repeats by being able to accurately place them along a linear scaffold and make the process more computationally efficient.
^Pellicer, Jaume, Fay, Michael F., & Leitch, Ilia J. (2010). The largest eukaryotic genome of them all? Botanical Journal of the Linnean Society, 164(1), 10-15. doi:10.1111/j.1095-8339.2010.01072.x
^Alkan, C., Sajjadian, S., & Eichler, E. (2011). Limitations of next-generation genome sequence assembly. Nature Methods, 8.
^Koren, S., Harhay, G., Smith, P., Bono, J., Harhay, D., Mcvey, S., . . . Phillippy, A. (2013). Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology.
a subset of the whole genome. A number of algorithmical problems differ between genome and EST assembly. For instance, genomes often have large amounts...
A plant genomeassembly represents the complete genomic sequence of a plant species, which is assembled into chromosomes and other organelles by using...
the genome) phenomena such as epistasis (effect of one gene on another), pleiotropy (one gene affecting more than one trait), heterosis (hybrid vigour)...
Zhang Q, Nie X, Sun Y, Zhang Z, et al. (September 2019). "Hybrid de novo genomeassembly of Chinese chestnut (Castanea mollissima)". GigaScience. 8 (9)...
Genome editing, or genome engineering, or gene editing, is a type of genetic engineering in which DNA is inserted, deleted, modified or replaced in the...
that of humans. As of 2018, assembly of the axolotl genome (32Gb) displaced loblolly pine as the largest assembled genome. The loblolly pine was selected...
sequencing large genomes, but its assembly is complex and difficult, particularly with sequence repeats often causing gaps in genomeassembly. Most sequencing...
Gibbon Network and Research Lab Gibbon Conservation Alliance Gibbon Rehabilitation Project View the nomLeu3 genomeassembly in the UCSC Genome Browser....
"Hybridassembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm". Genome Research...
Re-sequencing Group sequences specific regions of genomes using several different methods including PCR as well as hybrid selection techniques. Transcriptomes: The...
2018). "Genome Survey of the Freshwater Mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) Using a Hybrid De Novo Assembly Approach". Genome Biology...
different). While the scope, purpose and process are totally different, a genomeassembly can be viewed as the "ultimate" form of physical map, in that it provides...
than females. A detailed map of hybrid incompatibility sites for the C. briggsae genome was generated in 2015. Hybrid male inviability primarily manifests...
The genomeassembly is 42.73 Mbp, with a predicted number of 12789 genes. The second genome is from S. lacrymans S7.3 (v2.0). The genomeassembly is 47...
Bohlmann J, Birol I. (2015). "Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation". Genome Biology and Evolution. 8 (1): 29–41. doi:10...
to be a hybrid of P. lactiflora and P. veitchii, although being a diploid with 10 chromosomes. P. emodi and P. sterniana are diploid hybrids of P. lactiflora...
Estefanía; McFadden, Catherine S (2019). "A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome". GigaScience. 8 (4). doi:10.1093/gigascience/giz026...
Red Junglefowl View the red junglefowl genome in Ensembl View the galGal4 genomeassembly in the UCSC Genome Browser. Gallus bankiva (illustration) in...
cerevisiae. To overcome this problem a C. albicans specific two-hybrid system was developed. The genome of C. albicans is highly dynamic, contributed by the different...
novel traits, radiation hybrid lines have been established, where maize chromosome segments have been introgressed into the oat genome. This technique – which...
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