scholarly journals Assessment of an organ-specific de novo transcriptome of the nematode trap-crop, Solanum sisymbriifolium

2018 ◽  
Author(s):  
Alexander Q Wixom ◽  
N Carol Casavant ◽  
Joseph C Kuhl ◽  
Fangming Xiao ◽  
Louise-Marie Dandurand ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Globodera Pallida ◽  
Smrt Sequencing ◽  
Trap Crop ◽  
Site Analysis ◽  
Organ Specific ◽  
Disproportionate Number ◽  
Single Time Point ◽  
Solanum Sisymbriifolium

AbstractSolanum sisymbriifolium, also known as “Litchi Tomato” or “Sticky Nightshade,” is an undomesticated and poorly researched plant related to potato and tomato. Unlike the latter species, S. sisymbriifolium induces eggs of the cyst nematode, Globodera pallida, to hatch and migrate into its roots, but then arrests further nematode maturation. In order to provide researchers with a partial blueprint of its genetic make-up so that the mechanism of this response might be identified, we used single molecule real time (SMRT) sequencing to compile a high quality de novo transcriptome of 41,189 unigenes drawn from individually sequenced bud, root, stem, and leaf RNA populations. Functional annotation and BUSCO analysis showed that this transcriptome was surprisingly complete, even though it represented genes expressed at a single time point. By sequencing the 4 organ libraries separately, we found we could get a reliable snapshot of transcript distributions in each organ. A divergent site analysis of the merged transcriptome indicated that this species might have undergone a recent genome duplication and re-diploidization. Further analysis indicated that the plant then retained a disproportionate number of genes associated with photosynthesis and amino acid metabolism in comparison to genes with characteristics of R-proteins or involved in secondary metabolism. The former processes may have given S. sisymbriifolium a bigger competitive advantage than the latter did.

scholarly journals Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium

2018 ◽  
Vol 8 (7) ◽  
pp. 2135-2143 ◽  
Author(s):  
Alexander Q. Wixom ◽  
N. Carol Casavant ◽  
Joseph C. Kuhl ◽  
Fangming Xiao ◽  
Louise-Marie Dandurand ◽  
...  
Keyword(s):  
De Novo ◽  
De Novo Transcriptome ◽  
Trap Crop ◽  
Organ Specific ◽  
Solanum Sisymbriifolium

scholarly journals Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing

2014 ◽  
Author(s):  
Konstantin Berlin ◽  
Sergey Koren ◽  
Chen-Shan Chin ◽  
James Drake ◽  
Jane M Landolin ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Locality Sensitive Hashing ◽  
Model Organisms ◽  
Smrt Sequencing ◽  
High Coverage ◽  
Celera Assembler ◽  
Single Molecule Sequencing ◽  
Long Reads ◽  
Long Read

We report reference-grade de novo assemblies of four model organisms and the human genome from single-molecule, real-time (SMRT) sequencing. Long-read SMRT sequencing is routinely used to finish microbial genomes, but the available assembly methods have not scaled well to larger genomes. Here we introduce the MinHash Alignment Process (MHAP) for efficient overlapping of noisy, long reads using probabilistic, locality-sensitive hashing. Together with Celera Assembler, MHAP was used to reconstruct the genomes of Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, and human from high-coverage SMRT sequencing. The resulting assemblies include fully resolved chromosome arms and close persistent gaps in these important reference genomes, including heterochromatic and telomeric transition sequences. For D. melanogaster, MHAP achieved a 600-fold speedup relative to prior methods and a cloud computing cost of a few hundred dollars. These results demonstrate that single-molecule sequencing alone can produce near-complete eukaryotic genomes at modest cost.

scholarly journals Complete Genome Sequence of Pseudomonas aeruginosa Phage-Resistant Variant PA1RG

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Gang Li ◽  
Shuguang Lu ◽  
Mengyu Shen ◽  
Shuai Le ◽  
Yinling Tan ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequence ◽  
Single Molecule ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
De Novo ◽  
Smrt Sequencing ◽  
Sequence Coverage ◽  
Resistant Variant ◽  
Defense Systems

Bacteria have evolved several defense systems against phage predation. Here, we report the 6,500,439-bp complete genome sequence of the Pseudomonas aeruginosa phage-resistant variant PA1RG. Single-molecule real-time (SMRT) sequencing and de novo assembly revealed a single contig with 320-fold sequence coverage.

scholarly journals Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information

2019 ◽  
Author(s):  
Hui-Su Kim ◽  
Sungwon Jeon ◽  
Changjae Kim ◽  
Yeon Kyung Kim ◽  
Yun Sung Cho ◽  
...  
Keyword(s):  
Human Genome ◽  
Single Molecule ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Low Cost ◽  
Cost Effective ◽  
Sequencing Data ◽  
Smrt Sequencing ◽  
Human Genome Assembly

AbstractBackgroundLong DNA reads produced by single molecule and pore-based sequencers are more suitable for assembly and structural variation discovery than short read DNA fragments. For de novo assembly, PacBio and Oxford Nanopore Technologies (ONT) are favorite options. However, PacBio’s SMRT sequencing is expensive for a full human genome assembly and costs over 40,000 USD for 30x coverage as of 2019. ONT PromethION sequencing, on the other hand, is one-twelfth the price of PacBio for the same coverage. This study aimed to compare the cost-effectiveness of ONT PromethION and PacBio’s SMRT sequencing in relation to the quality.FindingsWe performed whole genome de novo assemblies and comparison to construct an improved version of KOREF, the Korean reference genome, using sequencing data produced by PromethION and PacBio. With PromethION, an assembly using sequenced reads with 64x coverage (193 Gb, 3 flowcell sequencing) resulted in 3,725 contigs with N50s of 16.7 Mbp and a total genome length of 2.8 Gbp. It was comparable to a KOREF assembly constructed using PacBio at 62x coverage (188 Gbp, 2,695 contigs and N50s of 17.9 Mbp). When we applied Hi-C-derived long-range mapping data, an even higher quality assembly for the 64x coverage was achieved, resulting in 3,179 scaffolds with an N50 of 56.4 Mbp.ConclusionThe pore-based PromethION approach provides a good quality chromosome-scale human genome assembly at a low cost with long maximum contig and scaffold lengths and is more cost-effective than PacBio at comparable quality measurements.

scholarly journals Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information

GigaScience ◽  
2019 ◽  
Vol 8 (12) ◽  
Author(s):  
Hui-Su Kim ◽  
Sungwon Jeon ◽  
Changjae Kim ◽  
Yeon Kyung Kim ◽  
Yun Sung Cho ◽  
...  
Keyword(s):  
Human Genome ◽  
Single Molecule ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Low Cost ◽  
Cost Effective ◽  
Sequencing Data ◽  
Smrt Sequencing ◽  
Human Genome Assembly

Abstract Background Long DNA reads produced by single-molecule and pore-based sequencers are more suitable for assembly and structural variation discovery than short-read DNA fragments. For de novo assembly, Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) are the favorite options. However, PacBio's SMRT sequencing is expensive for a full human genome assembly and costs more than $40,000 US for 30× coverage as of 2019. ONT PromethION sequencing, on the other hand, is 1/12 the price of PacBio for the same coverage. This study aimed to compare the cost-effectiveness of ONT PromethION and PacBio's SMRT sequencing in relation to the quality. Findings We performed whole-genome de novo assemblies and comparison to construct an improved version of KOREF, the Korean reference genome, using sequencing data produced by PromethION and PacBio. With PromethION, an assembly using sequenced reads with 64× coverage (193 Gb, 3 flowcell sequencing) resulted in 3,725 contigs with N50s of 16.7 Mb and a total genome length of 2.8 Gb. It was comparable to a KOREF assembly constructed using PacBio at 62× coverage (188 Gb, 2,695 contigs, and N50s of 17.9 Mb). When we applied Hi-C–derived long-range mapping data, an even higher quality assembly for the 64× coverage was achieved, resulting in 3,179 scaffolds with an N50 of 56.4 Mb. Conclusion The pore-based PromethION approach provided a high-quality chromosome-scale human genome assembly at a low cost with long maximum contig and scaffold lengths and was more cost-effective than PacBio at comparable quality measurements.

scholarly journals Evaluation of Solanum sisymbriifolium as a Potential Inoculum Source of Verticillium dahliae and Colletotrichum coccodes

Plant Disease ◽  
2017 ◽  
Vol 101 (7) ◽  
pp. 1300-1305 ◽  
Author(s):  
Z. A. Frederick ◽  
T. F. Cummings ◽  
C. R. Brown ◽  
R. A. Quick ◽  
D. A. Johnson
Keyword(s):  
Verticillium Dahliae ◽  
Potato Cultivar ◽  
Potato Production ◽  
Globodera Pallida ◽  
Colletotrichum Coccodes ◽  
Herbaceous Plant ◽  
Trap Crop ◽  
Inoculum Source ◽  
Russet Norkotah ◽  
Solanum Sisymbriifolium

Solanum sisymbriifolium, the litchi tomato, is a perennial herbaceous plant from South America that is used as a trap crop to reduce soilborne populations of the pale cyst nematode Globodera pallida, an important potato pathogen. Possible interactions of soilborne potato pathogens Verticillium dahliae and Colletotrichum coccodes with litchi tomato are unknown, yet important for potato production if litchi tomato is to be planted as a trap crop. The goal of this research was to quantitatively assess if litchi tomato is a potential inoculum source for C. coccodes and V. dahliae by comparing colony forming units (CFU) observed in litchi tomato to susceptible and resistant potato cultivars. The potato cvs. Alturas (P = 0.0003), Ranger Russet (P = 0.0193), and Russet Norkotah (P = 0.0022) produced more CFUs of the potato pathotype of V. dahliae than litchi tomato the first of two years of greenhouse trials. Significantly more CFUs of the potato pathotype of V. dahliae were quantified from stems and roots of only cv. Russet Norkotah compared with litchi tomato (P = 0.0001) in the second year. The CFUs for C. coccodes varied between litchi tomato and the potato cvs., perhaps due to varying levels of resistance since litchi tomato is from a selected intermated seed source. Based on these data, the effect of litchi tomato in rotation with potato is likely to have limited effect on the proliferation of V. dahliae or C. coccodes populations in the soil when compared with a susceptible potato cultivar.

scholarly journals De Novo Genome Assembly of a Plasmodium falciparum NF54 Clone Using Single-Molecule Real-Time Sequencing

2018 ◽  
Vol 6 (5) ◽  
Author(s):  
Jessica M. Bryant ◽  
Sebastian Baumgarten ◽  
Audrey Lorthiois ◽  
Christine Scheidig-Benatar ◽  
Aurélie Claës ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Real Time ◽  
Single Molecule ◽  
Malaria Parasite ◽  
De Novo ◽  
Severe Form ◽  
Smrt Sequencing ◽  
Sequencing Technology ◽  
De Novo Genome Assembly ◽  
Human Malaria Parasite

ABSTRACT Plasmodium falciparum is the species of human malaria parasite that causes the most severe form of the disease. Here, we used single-molecule real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) to sequence, assemble de novo , and annotate the genome of a P. falciparum NF54 clone.

scholarly journals Initial responses of the trap‐crop, Solanum sisymbriifolium , to Globodera pallida invasions

2020 ◽  
Vol 13 (2) ◽  
Author(s):  
Alexander Q. Wixom ◽  
N. Carol Casavant ◽  
Timothy J. Sonnen ◽  
Joseph C. Kuhl ◽  
Fangming Xiao ◽  
...  
Keyword(s):  
Globodera Pallida ◽  
Trap Crop ◽  
Solanum Sisymbriifolium

scholarly journals Whole-Genome Assembly of Klebsiella pneumoniae Coproducing NDM-1 and OXA-232 Carbapenemases Using Single-Molecule, Real-Time Sequencing

2014 ◽  
Vol 58 (10) ◽  
pp. 5947-5953 ◽  
Author(s):  
Yohei Doi ◽  
Tracy H. Hazen ◽  
Matthew Boitano ◽  
Yu-Chih Tsai ◽  
Tyson A. Clark ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Real Time ◽  
Single Molecule ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Mercury Resistance ◽  
Whole Genome ◽  
Smrt Sequencing ◽  
Single Chromosome ◽  
Content Type

ABSTRACTThe whole-genome sequence of a carbapenem-resistantKlebsiella pneumoniaestrain, PittNDM01, which coproduces NDM-1 and OXA-232 carbapenemases, was determined in this study. The use of single-molecule, real-time (SMRT) sequencing provided a closed genome in a single sequencing run.K. pneumoniaePittNDM01 has a single chromosome of 5,348,284 bp and four plasmids: pPKPN1 (283,371 bp), pPKPN2 (103,694 bp), pPKPN3 (70,814 bp), and pPKPN4 (6,141 bp). The contents of the chromosome were similar to that of theK. pneumoniaereference genome strain MGH 78578, with the exception of a large inversion spanning 23.3% of the chromosome. In contrast, three of the four plasmids are unique. The plasmid pPKPN1, an IncHI1B-like plasmid, carries theblaNDM-1,armA, andqnrB1genes, along with tellurium and mercury resistance operons.blaNDM-1is carried on a unique structure in which Tn125is further bracketed by IS26downstream of a class 1 integron. The IncFIA-like plasmid pPKPN3 also carries an array of resistance elements, includingblaCTX-M-15and a mercury resistance operon. The ColE-type plasmid pPKPN4 carryingblaOXA-232is identical to a plasmid previously reported from France. SMRT sequencing was useful in resolving the complex bacterial genomic structures in thede novoassemblies.

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