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Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

Inanc Birol, Anthony Raymond, Shaun D. Jackman, Stephen Pleasance, Robin Coope, Greg A. Taylor, Macaire Man Saint Yuen, Christopher I. Keeling, Dana Brand, Benjamin P. Vandervalk, Heather Kirk, Pawan Pandoh (+12 others)
2013 Computer applications in the biosciences : CABIOS  
Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software.  ...  Availability: The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435.  ...  ACKNOWLEDGEMENTS The authors would like to thank the British Columbia Cancer Agency, Michael Smith Genome Sciences Centre for Illumina sequencing and targeted BAC Sanger sequencing and the Institute for  ... 
doi:10.1093/bioinformatics/btt178 pmid:23698863 pmcid:PMC3673215 fatcat:eynaukdczfai5etzkkb22fejoi

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation

Shaun D. Jackman, René L. Warren, Ewan A. Gibb, Benjamin P. Vandervalk, Hamid Mohamadi, Justin Chu, Anthony Raymond, Stephen Pleasance, Robin Coope, Mark R. Wildung, Carol E. Ritland, Jean Bousquet (+3 others)
2015 Genome Biology and Evolution  
The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS.  ...  The informatics methodology presented in this study should prove useful to assemble organellar genomes of other plant species using whole-genome shotgun sequencing data.  ...  Acknowledgments This work was supported by Genome Canada, Genome British Columbia, and Genome Quebec as part of the SMarTForests Project (www.smartforests.ca last accessed 17 Dec 2015).  ... 
doi:10.1093/gbe/evv244 pmid:26645680 pmcid:PMC4758241 fatcat:73qfjmhc35amlc64ozqj4nqjci

Genomics of a phylum distant from flowering plants: conifers

Kermit Ritland
2012 Tree Genetics & Genomes  
I highlight both the advantages and disadvantages for conifers as model organism for genomics. With advances of new high-throughput sequencing technologies, we are at a watershed in conifer genomics.  ...  The genomes of coniferous species are very large, among the largest of any nonpolyploid plant species.  ...  Acknowledgments I thank David Neale and Bert Abbott for their comments on drafts, John MacKay for discussions about conifer genomics, Steven Jones and Inanc Birol for teaching me the latest about sequence  ... 
doi:10.1007/s11295-012-0497-4 fatcat:q7scnkvobfcnrnodi7y4mbeobm

Insights into Conifer Giga-Genomes

A. R. De La Torre, I. Birol, J. Bousquet, P. K. Ingvarsson, S. Jansson, S. J. M. Jones, C. I. Keeling, J. MacKay, O. Nilsson, K. Ritland, N. Street, A. Yanchuk (+2 others)
2014 Plant Physiology  
Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda  ...  Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture.  ...  Following early releases of the white spruce (Picea glauca) and loblolly pine (Pinus taeda) genome sequences in public databases (e.g.  ... 
doi:10.1104/pp.114.248708 pmid:25349325 fatcat:6uzukfusaffrnbd27asgqxljeq

A White Spruce Gene Catalog for Conifer Genome Analyses

Philippe Rigault, Brian Boyle, Pierre Lepage, Janice E.K. Cooke, Jean Bousquet, John J. MacKay
2011 Plant Physiology  
A gene catalog was developed for the conifer tree Picea glauca (white spruce) through large-scale expressed sequence tag sequencing and full-length cDNA sequencing to facilitate genome characterizations  ...  Genomic sample sequencing at 8.5% of the 19.8-Gb P. glauca genome identified 1,495 clusters representing highly repeated sequences among the cDNA clusters.  ...  ACKNOWLEDGMENTS We are grateful for the provision of trace sequence files from the Treenomix project by J. Bohlmann and collaborators (University of British Columbia). We thank V. Jacobi, I.  ... 
doi:10.1104/pp.111.179663 pmid:21730200 pmcid:PMC3165865 fatcat:mwlp6srybze2bj3wjn5j3jq3ne

Prospects for Genomic Research in Forestry

K. V. Krutovsky
2014 Sibirskij Lesnoj Žurnal  
Their whole genome sequencing, assembly and annotation will allow us to understand the evolution of the complex ancient giant conifer genomes that are 4 times larger in larch and 7–9 times larger in pines  ...  Genomic studies will allow also to obtain important whole genome sequence data and develop highly polymorphic and informative genetic markers, such as microsatellites and single nucleotide polymorphisms  ...  Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data // Bioinformatics. 2013. V. 29. N. 12. P. 1492-1497. Chhatre V., Byram T., Neale D. B. et al.  ... 
doaj:09488a209ebc4f46bbbf6a7f00473bcf fatcat:yuv3q4q2t5akpg3id6fgcdvmu4

Towards decoding the conifer giga-genome

John Mackay, Jeffrey F. D. Dean, Christophe Plomion, Daniel G. Peterson, Francisco M. Cánovas, Nathalie Pavy, Pär K. Ingvarsson, Outi Savolainen, M. Ángeles Guevara, Silvia Fluch, Barbara Vinceti, Dolores Abarca (+2 others)
2012 Plant Molecular Biology  
Exploratory sequencing in pines and spruces have pointed out some of the unique properties of these giga-genomes and suggested strategies that may be needed to extract value from their sequencing.  ...  Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions  ...  The authors are very grateful to Susana Ferrándiz for helping with the preparation of the manuscript.  ... 
doi:10.1007/s11103-012-9961-7 pmid:22960864 fatcat:nqkhg3vvnbby5a4nrfwkx6hx54

Kollector: transcript-informed, targeted de novo assembly of gene loci

Erdi Kucuk, Justin Chu, Benjamin P Vandervalk, S Austin Hammond, René L Warren, Inanc Birol
2017 Bioinformatics  
transcript targets in their corresponding genomic space using whole genome shotgun sequencing reads.  ...  Motivation: Despite considerable advancements in sequencing and computing technologies, de novo assembly of whole eukaryotic genomes is still a time-consuming task that requires a significant amount of  ...  Acknowledgements We would like to thank Golnaz Jahesh from Canada's Michael Smith Genome Research Centre for her contributions to packaging, testing and releasing of the Kollector software.  ... 
doi:10.1093/bioinformatics/btx405 pmid:28903539 pmcid:PMC5860073 fatcat:avr6ys2npvfszi44pg23my5d4y

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

David B Neale, Jill L Wegrzyn, Kristian A Stevens, Aleksey V Zimin, Daniela Puiu, Marc W Crepeau, Charis Cardeno, Maxim Koriabine, Ann E Holtz-Morris, John D Liechty, Pedro J Martínez-García, Hans A Vasquez-Gross (+25 others)
2014 Genome Biology  
We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial  ...  The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly.  ...  We also wish to thank the management and staff of the DNA Technologies core facility at the UC Davis Genome Center for providing expert and timely HiSeq sequencing services to this project.  ... 
doi:10.1186/gb-2014-15-3-r59 pmid:24647006 pmcid:PMC4053751 fatcat:nxvjetmno5estnc5ieu5qebgo4

The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants

Alexis R Sullivan, Yrin Eldfjell, Bastian Schiffthaler, Nicolas Delhomme, Torben Asp, Kim H Hebelstrup, Olivier Keech, Lisa Öberg, Ian Max Møller, Lars Arvestad, Nathaniel R Street, Xiao-Ru Wang (+1 others)
2019 Genome Biology and Evolution  
To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies  ...  Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered  ...  Acknowledgments The authors acknowledge support from the National Genomics Infrastructure in Uppsala funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation and the Swedish Research  ... 
doi:10.1093/gbe/evz263 pmid:31774499 pmcid:PMC6944214 fatcat:kndy5a4dt5f3xpq4m73sgpi3i4

Preliminary Results of De Novo Whole Genome Sequencing of the Siberian Larch (Larix sibirica Ledeb.) and the Siberian Stone Pine (Pinus sibirica Du Tour)

K. V. Krutovsky, N. V. Oreshkova, Yu. A. Putintseva, A. A. Ibe, K. O. Deych, E. A. Shilkina
2014 Sibirskij Lesnoj Žurnal  
These data are not enough to assemble and annotate whole genomes, but the obtained nucleotide sequences have allowed us to discover and develop effective highly polymorphic molecular genetic markers, such  ...  Sequence data can be used also to discover single nucleotide polymorphisms (SNPs).  ...  Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data // Bioinformatics. 2013. V. 29. N. 12. P. 1492-1497. Burrows M., Wheeler D.  ... 
doaj:24160dc34b78469ca0244b50b6f545db fatcat:iqww6lfj4ndurkytoww3drwk4q

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

Allen Kovach, Jill L Wegrzyn, Genis Parra, Carson Holt, George E Bruening, Carol A Loopstra, James Hartigan, Mark Yandell, Charles H Langley, Ian Korf, David B Neale
2010 BMC Genomics  
Results: We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS) sequences representing 7.5% of the genome.  ...  The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24).  ...  Cook and Jinliang Gao for assistance with BAC library screening, Charles Nicolet for technical support in WGS sequencing and Michela Troggio for sharing the unpublished apple genome.  ... 
doi:10.1186/1471-2164-11-420 pmid:20609256 pmcid:PMC2996948 fatcat:ur7hmgf3rzd5pi3xf2x2nlhjve

The Transcriptomics of Secondary Growth and Wood Formation in Conifers

Ana Carvalho, Jorge Paiva, José Louzada, José Lima-Brito
2013 Molecular Biology International  
Due to the gradual improvement of the NGS technologies and inherent bioinformatics tools, two draft assemblies of the whole genomes sequence of Picea abies and Picea glauca arose in the current year.  ...  Until very recently, no whole genome sequencing of a conifer genome was available.  ...  Later, the assembly of the 20.8-Gb Picea glauca (white spruce) genome from whole-genome shotgun sequencing data was reported [89] .  ... 
doi:10.1155/2013/974324 pmid:24288610 pmcid:PMC3830773 fatcat:ayfzju4au5dbzegsa7et2xtynm

Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

J. L. Wegrzyn, J. D. Liechty, K. A. Stevens, L.-S. Wu, C. A. Loopstra, H. A. Vasquez-Gross, W. M. Dougherty, B. Y. Lin, J. J. Zieve, P. J. Martinez-Garcia, C. Holt, M. Yandell (+10 others)
2014 Genetics  
In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine (Pinus taeda L.), which comprises 20.1 Gb of sequence.  ...  The size and complexity of their genomes (∼20-40 Gb, 2n = 24) have delayed the arrival of a well-annotated reference sequence.  ...  The whole-genome shotgun sequencing and assembly ) produced two reference sequences.  ... 
doi:10.1534/genetics.113.159996 pmid:24653211 pmcid:PMC3948814 fatcat:pyc3ph7gzvgyvmsikanpufwwsm

ntCard: a streaming algorithm for cardinality estimation in genomics data

Hamid Mohamadi, Hamza Khan, Inanc Birol
2017 Bioinformatics  
We used three datasets of 480 GB, 500 GB and 2.4 TB in size, where the first two representing whole genome shotgun sequencing experiments on the human genome and the last one on the white spruce genome  ...  However, calculating a k-mer histogram from large volumes of sequencing data is a challenging task.  ...  Acknowledgements We thank the Sequencing Lab and the Bioinformatics Technology Lab (BTL) at Genome Sciences Centre, British Columbia Cancer Agency for their assistance with this project.  ... 
doi:10.1093/bioinformatics/btw832 pmid:28453674 pmcid:PMC5408799 fatcat:yjiuglhcjrgktf6zrhiqonxcwe
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