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

Birol, İnanç; Raymond, Anthony; Jackman, Shaun D.; Pleasance, Stephen; Coope, Robin; Taylor, Greg; Yuen, Macaire Man Saint; Keeling, Christopher I.; Brand, Dana; Vandervalk, Benjamin P.; Kirk, Heather; Pandoh, Pawan; Moore, Richard A.; Zhao, Yongjun; Mungall, Andrew J.; Jaquish, Barry; Yanchuk, Alvin D.; Ritland, Carol; Boyle, Brian; Bousquet, Jean; Ritland, Kermit; Mackay, John; Bohlmann, Jörg; Jones, Steven J.M.

doi:10.1093/bioinformatics/btt178

Cited by 351 publications

(309 citation statements)

References 32 publications

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“…Seventeen of these have a corresponding partial or fulllength genomic DNA sequence (Online Resource 1) obtained by sequence capture of PG-29 (Sena et al 2014), the genotype used for the draft genome sequence (Birol et al 2013). Using the same criteria, 80 partial or full-length gene models were identified in the P. abies 1.0 assembly (Nystedt et al 2013).…”

Section: Resultsmentioning

confidence: 99%

“…In-depth functional studies of these chitinases are now underway to determine whether the in vitro and in vivo functions of these proteins are consistent with the functions predicted by in silico analysis. Availability of the draft white spruce genome sequence (Birol et al 2013) facilitates analysis of the regulation of these genes through promoter studies.…”

Section: Resultsmentioning

confidence: 99%

“…The Norway spruce results imply that the white spruce sequences identified in this study represent only a subset of the total number of chitinase genes in the white spruce genome. Mining of the v1.0 draft of the white spruce genome sequence (Birol et al 2013) yielded fewer putative genes than expressed sequences (J. Cooke and K. Muirhead, unpublished), but this will undoubtedly improve with future versions.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Diverse chitinases are invoked during the activity-dormancy transition in spruce

Galindo‐González

Kayal

Morris

et al. 2015

Tree Genetics & Genomes

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North temperate tree species such as white spruce (Picea glauca [Moench] Voss) have evolved strategies to protect themselves against abiotic and biotic stresses that trees encounter during the inclement winter months. Chitinases not only play well-documented roles in plant defense but also function during physiological and developmental preparations for overwintering, including growth cessation, cold and desiccation acclimation, and dormancy acquisition. Phylogenetic analysis of 31 white spruce and 52 Norway spruce chitinases identified genes falling into each of the five clusters, which sometimes-but not always-separated the different biochemical classes of chitinases. Digital expression profiling of white spruce and Norway spruce chitinases across multiple conditions revealed a range of spatiotemporal expression patterns. Transcript abundance profiling in buds, needles, stems, and roots by quantitative RT-PCR suggested roles for eight white spruce chitinases during the growth-to-dormancy transition. In silico analyses of these eight sequences suggested that two cluster 2/class I chitinases function as chitinolytic enzymes in the tree's constitutive defense arsenal during the winter months. A cluster 2/class I, cluster 2/class II, and cluster 1/ class IV chitinase each exhibit hallmarks of antifreeze proteins. Additionally, two cluster 2/class I chitinases and a cluster 1/ class IV chitinase may serve as vegetative storage proteins. One cluster 3/class II chitinase exhibited attributes suggesting that it is a chitinase-like gene functioning in cell wall synthesis. Taken together, our results imply that dormancy-associated chitinases act in concert to (1) confer protection against freezing injury, pests, and pathogens, (2) store nitrogen, and (3) promote cell maturation that precedes growth cessation.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Diverse chitinases are invoked during the activity-dormancy transition in spruce

Galindo‐González

Kayal

Morris

et al. 2015

Tree Genetics & Genomes

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“…To date, different conifer genome sequencing projects have been performed from diploid tissue and also from haploid megagametophytes, since they offer a major reduction in sequence complexity [2][3][4]. However, the reduced amount DNA that can be obtained from a single megagametophyte may be insufficient to sequence these large genomes [5].…”

Section: Introductionmentioning

confidence: 99%

Haploids in Conifer Species: Characterization and Chromosomal Integrity of a Maritime Pine Cell Line

Cabezas¹,

Morcillo

Vélez³

et al. 2016

Forests

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Abstract:Haploids are a valuable tool for genomic studies in higher plants, especially those with huge genome size and long juvenile periods, such as conifers. In these species, megagametophyte cultures have been widely used to obtain haploid callus and somatic embryogenic lines. One of the main problems associated with tissue culture is the potential genetic instability of the regenerants. Because of this, chromosomal stability of the callus and/or somatic embryos should also be assessed. To this end, chromosome counting, flow cytometry and genotyping using microsatellites have been reported. Here, we present an overview of the work done in conifers, with special emphasis on the production of a haploid cell line in maritime pine (Pinus pinaster L.) and the use of a set of molecular markers, which includes Single Nucleotide Polymorphisms (SNPs) and microsatellites or Single Sequence Repeats (SSRs), to validate chromosomal integrity confirming the presence of all chromosomic arms.

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“…The majority of those are constituted by fruit trees (peach, plum, pear, sweet orange, clementine, apple, coffee, papaya, and cocoa tree). The first forest tree genome published is Populus trichocarpa (Tuskan et al 2006) followed by Picea abies (Nystedt et al 2013), Hevea brasiliensis (Rahman et al 2013), Picea glauca (Birol et al 2013), Pinus taeda (Neale et al 2014), and Eucalyptus grandis (Myburg et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Structural and functional characterization of tree proteins involved in redox regulation: a new frontier in forest science

Jacquot

Couturier

Didierjean

et al. 2016

Annals of Forest Science

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& Key message This paper describes how the combination of genomics, genetic engineering, and 3D structural characterization has helped clarify the redox regulatory networks in poplar with consequences not only in system biology in plants but also in bacteria and mammalian systems. & Context Tree genomes are increasingly available with a large number of orphan genes coding for proteins, the function of which is still unknown.& Aims and methods Modern techniques of genome analysis coupled with recombinant protein technology and massive 3D structural determination of tree proteins should help elucidate the function of many of the proteins encoded by orphan genes. X-ray crystallography and NMR will be the methods of choice for protein structure determination. & Results In this review, we provide examples illustrating how the above-mentioned techniques improved our understanding of redox regulatory circuits in poplar, the first forest tree species sequenced. We showed that poplar peroxiredoxins use either thioredoxin or glutaredoxin as electron donors toHandling Editor: Jean-Michel Leban Executive summary This review describes the successful use of technologies to overproduce and purify recombinant enzymes from trees with the aim of solving their 3D structures and identifying their molecular interactions either with other proteins or with potential substrates. Currently only ca a dozen of tree genomes have been annotated and released including six forest species, but this will change rapidly with the oncoming release of the chestnut and oak genomes notably. The availability of additional genomes will open the way to identifying the function of a large number of orphan gene products, one of the ways to characterize these functions being to produce and analyze the corresponding protein products. reduce hydrogen peroxide. That glutaredoxin could be a reductant was unknown at the time of this discovery even in other biological organisms and was later confirmed notably by the observation that the two genes are fused in some bacteria and by the resolution of the structure of the bacterial hybrid protein. Similarly, genome analysis coupled to in vitro analysis of enzymatic properties led to the discovery that some plant methionine sulfoxide reductases can also use both thioredoxins and glutaredoxins as electron donors. Besides their disulfide reductase activity, it has been demonstrated that some poplar glutaredoxins are also involved in iron-sulfur center biogenesis and assembly. The original 3D structure determination has been made with poplar glutaredoxin C1 and then confirmed in a variety of other biological organisms including human. Our work also showed that in plants, socalled glutathione peroxidases use thioredoxins and not glutathione as electron donors. This is true for all nonselenocysteine-containing glutathione peroxidases. Finally, connections between the thioredoxin and glutaredoxin systems have been elucidated through the study of atypical poplar thioredoxins. & Conclusion Altogether, these data il...

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

Cited by 351 publications

References 32 publications

Diverse chitinases are invoked during the activity-dormancy transition in spruce

Diverse chitinases are invoked during the activity-dormancy transition in spruce

Haploids in Conifer Species: Characterization and Chromosomal Integrity of a Maritime Pine Cell Line

Structural and functional characterization of tree proteins involved in redox regulation: a new frontier in forest science

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