Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis

Perera, Dinum; Magbanua, Zenaida V.; Thummasuwan, Supaphan; Mukherjee, Dipaloke; Arick, II, Mark; Chouvarine, Philippe; Nairn, Campbell J.; Schmutz, Jeremy; Grimwood, Jane; Dean, Jeffrey F. D.; Peterson, Daniel G.

doi:10.1016/j.gene.2018.04.024

Title: Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis

Journal Article · Sun Jul 01 00:00:00 EDT 2018 · Gene

DOI:https://doi.org/10.1016/j.gene.2018.04.024· OSTI ID:1631765

Perera, Dinum; Magbanua, Zenaida V.; Thummasuwan, Supaphan; Mukherjee, Dipaloke; Arick, II, Mark; Chouvarine, Philippe;

; Schmutz, Jeremy; Grimwood, Jane; Dean, Jeffrey F. D.; Peterson, Daniel G.

Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the “targeted” clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80% contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (α = 0.05) distributions in the targeted and random BAC clones (15.18 and 12.61 GM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08 GM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1631765

Alternate ID(s):: OSTI ID: 1543545; OSTI ID: 1616064

Journal Information:: Gene, Journal Name: Gene Vol. 663 Journal Issue: C; ISSN 0378-1119

Publisher:: ElsevierCopyright Statement

Country of Publication:: Netherlands

Language:: English

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Cited by: 5 works

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References (121)

Carbohydrate-related genes and cell wall biosynthesis in vascular tissues of loblolly pine (Pinus taeda) Nairn, C. J.; Lennon, D. M.; Wood-Jones, A. Tree Physiology, Vol. 28, Issue 7 https://doi.org/10.1093/treephys/28.7.1099	journal	July 2008
TILLING Mutants of Lotus japonicus Reveal That Nitrogen Assimilation and Fixation Can Occur in the Absence of Nodule-Enhanced Sucrose Synthase Horst, Irmtraud; Welham, Tracey; Kelly, Simon Plant Physiology, Vol. 144, Issue 2 https://doi.org/10.1104/pp.107.097063	journal	April 2007
CCoAOMT suppression modifies lignin composition in Pinus radiata Wagner, Armin; Tobimatsu, Yuki; Phillips, Lorelle The Plant Journal, Vol. 67, Issue 1, p. 119-129 https://doi.org/10.1111/j.1365-313X.2011.04580.x	journal	April 2011
In plants, highly expressed genes are the least compact Ren, X.; Vorst, O.; Fiers, M. Trends in Genetics, Vol. 22, Issue 10 https://doi.org/10.1016/j.tig.2006.08.008	journal	October 2006
[109] Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA Mandel, M.; Marmur, J. Nucleic Acids, Part B, Vol. 12, p. 195-206 https://doi.org/10.1016/0076-6879(67)12133-2	book	January 1968
Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences Wegrzyn, Jill L.; Lin, Brian Y.; Zieve, Jacob J. PLoS ONE, Vol. 8, Issue 9 https://doi.org/10.1371/journal.pone.0072439	journal	September 2013
Flow Cytometric Determination of Genome Size in the Taxodiaceae, Cupressaceae sensu stricto and Sciadopityaceae. Hizume, Masahiro; Kondo, Teiji; Shibata, Fukashi CYTOLOGIA, Vol. 66, Issue 3 https://doi.org/10.1508/cytologia.66.307	journal	January 2001
Automated generation of heuristics for biological sequence comparison Slater, Guy St C.; Birney, Ewan BMC Bioinformatics, Vol. 6, Issue 1 https://doi.org/10.1186/1471-2105-6-31	journal	February 2005
Adventures in the Enormous: A 1.8 Million Clone BAC Library for the 21.7 Gb Genome of Loblolly Pine Magbanua, Zenaida V.; Ozkan, Seval; Bartlett, Benjamin D. PLoS ONE, Vol. 6, Issue 1 https://doi.org/10.1371/journal.pone.0016214	journal	January 2011
The role of of laccase in lignification O'Malley, David M.; Whetten, Ross; Bao, Wuli The Plant Journal, Vol. 4, Issue 5 https://doi.org/10.1046/j.1365-313X.1993.04050751.x	journal	November 1993
Genetic evidence for the role of GDP-mannose in plant ascorbic acid (vitamin C) biosynthesis Conklin, P. L.; Norris, S. R.; Wheeler, G. L. Proceedings of the National Academy of Sciences, Vol. 96, Issue 7 https://doi.org/10.1073/pnas.96.7.4198	journal	March 1999
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies Neale, David B.; Wegrzyn, Jill L.; Stevens, Kristian A. Genome Biology, Vol. 15, Issue 3 https://doi.org/10.1186/gb-2014-15-3-r59	journal	January 2014
Regulation of sucrose and starch metabolism in potato tubers in response to short-term water deficit Geigenberger, Peter; Reimholz, Ralph; Geiger, Michael Planta, Vol. 201, Issue 4 https://doi.org/10.1007/s004250050095	journal	April 1997
Natural variation in expression of genes involved in xylem development in loblolly pine (Pinus taeda L.) Palle, Sreenath Reddy; Seeve, Candace M.; Eckert, Andrew J. Tree Genetics & Genomes, Vol. 7, Issue 1 https://doi.org/10.1007/s11295-010-0325-7	journal	August 2010
Up-regulation of sucrose synthase and UDP-glucose pyrophosphorylase impacts plant growth and metabolism Coleman, Heather D.; Ellis, Dave D.; Gilbert, Margarita Plant Biotechnology Journal, Vol. 4, Issue 1 https://doi.org/10.1111/j.1467-7652.2005.00160.x	journal	January 2006
Isolation and characterisation of laccase cDNAs from meristematic and stem tissues of ryegrass (Lolium perenne) Gavnholt, Britta; Larsen, Knud; Rasmussen, Søren K. Plant Science, Vol. 162, Issue 6 https://doi.org/10.1016/S0168-9452(02)00035-3	journal	June 2002
Comparative genomics and evolutionary analyses of the O-methyltransferase gene family in Populus Barakat, Abdelali; Choi, Alex; Yassin, Norzawani Buang M. Gene, Vol. 479, Issue 1-2 https://doi.org/10.1016/j.gene.2011.02.008	journal	June 2011
LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes Cossu, Rosa Maria; Casola, Claudio; Giacomello, Stefania Genome Biology and Evolution, Vol. 9, Issue 12 https://doi.org/10.1093/gbe/evx260	journal	December 2017
PtrKOR1 is required for secondary cell wall cellulose biosynthesis in Populus Yu, L.; Chen, H.; Sun, J. Tree Physiology, Vol. 34, Issue 11 https://doi.org/10.1093/treephys/tpu020	journal	April 2014
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations Campbell, Michael S.; Law, MeiYee; Holt, Carson Plant Physiology, Vol. 164, Issue 2 https://doi.org/10.1104/pp.113.230144	journal	December 2013
Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana Kirst, M.; Johnson, A. F.; Baucom, C. Proceedings of the National Academy of Sciences, Vol. 100, Issue 12 https://doi.org/10.1073/pnas.1132171100	journal	May 2003
The Cellulose Synthase Gene Superfamily and Biochemical Functions of Xylem-Specific Cellulose Synthase-Like Genes in Populus trichocarpa Suzuki, Shiro; Li, Laigeng; Sun, Ying-Hsuan Plant Physiology, Vol. 142, Issue 3 https://doi.org/10.1104/pp.106.086678	journal	September 2006
Structure and expression profile of the sucrose synthase multigene family in Arabidopsis Baud, S.; Vaultier, M. -N.; Rochat, C. Journal of Experimental Botany, Vol. 55, Issue 396 https://doi.org/10.1093/jxb/erh047	journal	January 2004
Characterization of the tomato ( Lycopersicon esculentum ) genome using in vitro and in situ DNA reassociation Peterson, Daniel G.; Pearson, William R.; Stack, Stephen M. Genome, Vol. 41, Issue 3 https://doi.org/10.1139/g98-025	journal	June 1998
Analyses of the sucrose synthase gene family in cotton: structure, phylogeny and expression patterns Chen, Aiqun; He, Shae; Li, Feifei BMC Plant Biology, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2229-12-85	journal	January 2012
Analysis of the giant genomes of F ritillaria ( L iliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size Kelly, Laura J.; Renny‐Byfield, Simon; Pellicer, Jaume New Phytologist, Vol. 208, Issue 2 https://doi.org/10.1111/nph.13471	journal	June 2015
Production of ethanol from carbohydrates from loblolly pine: A technical and economic assessment Frederick, W. J.; Lien, S. J.; Courchene, C. E. Bioresource Technology, Vol. 99, Issue 11 https://doi.org/10.1016/j.biortech.2007.08.086	journal	July 2008
Analysis of GDP-D-Mannose Pyrophosphorylase Gene Promoter from Acerola (Malpighia glabra) and Increase in Ascorbate Content of Transgenic Tobacco Expressing the Acerola Gene Badejo, A. A.; Tanaka, N.; Esaka, M. Plant and Cell Physiology, Vol. 49, Issue 1 https://doi.org/10.1093/pcp/pcm164	journal	January 2008
Cellulose synthesis in maize: isolation and expression analysis of the cellulose synthase (CesA) gene family Appenzeller, Laura; Doblin, Monika; Barreiro, Roberto Cellulose, Vol. 11, Issue 3/4 https://doi.org/10.1023/B:CELL.0000046417.84715.27	journal	September 2004
Genome size and base composition of five Pinus species from the Balkan region Bogunic, F.; Muratovic, E.; Brown, S. C. Plant Cell Reports, Vol. 22, Issue 1 https://doi.org/10.1007/s00299-003-0653-2	journal	August 2003
Characterisation of PtMYB1, an R2R3-MYB from pine xylem Patzlaff, Astrid; Newman, Lisa J.; Dubos, Christian Plant Molecular Biology, Vol. 53, Issue 4 https://doi.org/10.1023/B:PLAN.0000019066.07933.d6	journal	November 2003
The Norway spruce genome sequence and conifer genome evolution Nystedt, Björn; Street, Nathaniel R.; Wetterbom, Anna Nature, Vol. 497, Issue 7451 https://doi.org/10.1038/nature12211	journal	May 2013
Gene identification in novel eukaryotic genomes by self-training algorithm Lomsadze, A. Nucleic Acids Research, Vol. 33, Issue 20 https://doi.org/10.1093/nar/gki937	journal	November 2005
Consed: A Graphical Tool for Sequence Finishing Gordon, David; Abajian, Chris; Green, Phil Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.195	journal	March 1998
Characterization and varied expression of a membrane-bound endo-β-1,4-glucanase in hybrid poplar Maloney, Victoria J.; Mansfield, Shawn D. Plant Biotechnology Journal, Vol. 8, Issue 3 https://doi.org/10.1111/j.1467-7652.2009.00483.x	journal	April 2010
Microarray analysis of genes preferentially expressed in differentiating xylem of loblolly pine (Pinus taeda) Yang, Suk-Hwan; van Zyl, Leonel; No, Eun-Gyu Plant Science, Vol. 166, Issue 5 https://doi.org/10.1016/j.plantsci.2003.12.030	journal	May 2004
A beginner's guide to eukaryotic genome annotation Yandell, Mark; Ence, Daniel Nature Reviews Genetics, Vol. 13, Issue 5 https://doi.org/10.1038/nrg3174	journal	April 2012
Transcriptional networks for lignin biosynthesis: more complex than we thought? Zhao, Qiao; Dixon, Richard A. Trends in Plant Science, Vol. 16, Issue 4, p. 227-233 https://doi.org/10.1016/j.tplants.2010.12.005	journal	April 2011
Proteomic analysis of membrane preparations from developing Pinus radiata compression wood Mast, S.; Peng, L.; Jordan, T. W. Tree Physiology, Vol. 30, Issue 11 https://doi.org/10.1093/treephys/tpq084	journal	October 2010
How introns influence and enhance eukaryotic gene expression Le Hir, Hervé; Nott, Ajit; Moore, Melissa J. Trends in Biochemical Sciences, Vol. 28, Issue 4, p. 215-220 https://doi.org/10.1016/S0968-0004(03)00052-5	journal	April 2003
Cellulose Biosynthesis: Current Views and Evolving Concepts Saxena, Inder M.; Brown, R. Malcolm Annals of Botany, Vol. 96, Issue 1 https://doi.org/10.1093/aob/mci155	journal	May 2005
Unique Features of the Loblolly Pine ( Pinus taeda L.) Megagenome Revealed Through Sequence Annotation Wegrzyn, Jill L.; Liechty, John D.; Stevens, Kristian A. Genetics, Vol. 196, Issue 3 https://doi.org/10.1534/genetics.113.159996	journal	March 2014
Genomics of a phylum distant from flowering plants: conifers Ritland, Kermit Tree Genetics & Genomes, Vol. 8, Issue 3 https://doi.org/10.1007/s11295-012-0497-4	journal	March 2012
The irregular xylem 2 mutant is an allele of korrigan that affects the secondary cell wall of Arabidopsis thaliana Szyjanowicz, Pio M. J.; McKinnon, Iain; Taylor, Neil G. The Plant Journal, Vol. 37, Issue 5 https://doi.org/10.1111/j.1365-313X.2003.02000.x	journal	March 2004
An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing Zimin, Aleksey V.; Stevens, Kristian A.; Crepeau, Marc W. GigaScience, Vol. 6, Issue 1 https://doi.org/10.1093/gigascience/giw016	journal	January 2017
Three loblolly pine CesA genes expressed in developing xylem are orthologous to secondary cell wall CesA genes of angiosperms Nairn, C. Joseph; Haselkorn, Tamara New Phytologist, Vol. 166, Issue 3 https://doi.org/10.1111/j.1469-8137.2005.01372.x	journal	February 2005
Genetic evidence that the two isozymes of sucrose synthase present in developing maize endosperm are critical, one for cell wall integrity and the other for starch biosynthesis Chourey, P. S.; Taliercio, E. W.; Carlson, S. J. Molecular and General Genetics MGG, Vol. 259, Issue 1 https://doi.org/10.1007/s004380050792	journal	July 1998
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences Kovach, Allen; Wegrzyn, Jill L.; Parra, Genis BMC Genomics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2164-11-420	journal	January 2010
Six new cellulose synthase genes from Eucalyptus are associated with primary and secondary cell wall biosynthesis Ranik, M.; Myburg, A. A. Tree Physiology, Vol. 26, Issue 5 https://doi.org/10.1093/treephys/26.5.545	journal	May 2006
Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species Lorenz, W. Walter; Ayyampalayam, Savavanaraj; Bordeaux, John M. Tree Genetics & Genomes, Vol. 8, Issue 6 https://doi.org/10.1007/s11295-012-0547-y	journal	July 2012
Artemis: sequence visualization and annotation Rutherford, K.; Parkhill, J.; Crook, J. Bioinformatics, Vol. 16, Issue 10 https://doi.org/10.1093/bioinformatics/16.10.944	journal	October 2000
Sucrose Synthase Catalyzes the de novo Production of ADPglucose Linked to Starch Biosynthesis in Heterotrophic Tissues of Plants Baroja-Fernández, Edurne; Muñoz, Francisco José; Saikusa, Takayo Plant and Cell Physiology, Vol. 44, Issue 5 https://doi.org/10.1093/pcp/pcg062	journal	May 2003
Expressed Sequence Tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis Cairney, John; Zheng, Li; Cowels, Allison Plant Molecular Biology, Vol. 62, Issue 4-5 https://doi.org/10.1007/s11103-006-9035-9	journal	September 2006
Functional Genomic Analysis Supports Conservation of Function Among Cellulose Synthase-Like A Gene Family Members and Suggests Diverse Roles of Mannans in Plants Liepman, Aaron H.; Nairn, C. Joseph; Willats, William G. T. Plant Physiology, Vol. 143, Issue 4 https://doi.org/10.1104/pp.106.093989	journal	February 2007
Flow cytometric determination of genome size in Pinus O'Brien, Iona E. W.; Smith, Dale R.; Gardner, Richard C. Plant Science, Vol. 115, Issue 1 https://doi.org/10.1016/0168-9452(96)04356-7	journal	March 1996
Characterization and mapping of a putative laccase-like multicopper oxidase gene in the barley (Hordeum vulgare L.) Tomková, Lenka; Kučera, Ladislav; Vaculová, Kateřina Plant Science, Vol. 183 https://doi.org/10.1016/j.plantsci.2011.11.003	journal	February 2012
Phenylalanine Ammonia-Lyase from Loblolly Pine: Purification of the Enzyme and Isolation of Complementary DNA Clones Whetten, Ross W.; Sederoff, Ronald R. Plant Physiology, Vol. 98, Issue 1 https://doi.org/10.1104/pp.98.1.380	journal	January 1992
Lignin Biosynthesis Boerjan, Wout; Ralph, John; Baucher, Marie Annual Review of Plant Biology, Vol. 54, Issue 1, p. 519-546 https://doi.org/10.1146/annurev.arplant.54.031902.134938	journal	June 2003
Nuclear DNA Amounts in Angiosperms: Progress, Problems and Prospects Bennett, M. D. Annals of Botany, Vol. 95, Issue 1 https://doi.org/10.1093/aob/mci003	journal	January 2005
Improved repeat identification and masking in Dipterans Smith, Christopher D.; Edgar, Robert C.; Yandell, Mark D. Gene, Vol. 389, Issue 1 https://doi.org/10.1016/j.gene.2006.09.011	journal	March 2007
Transcriptional regulation of lignin biosynthesis Zhong, Ruiqin; Ye, Zheng-Hua Plant Signaling & Behavior, Vol. 4, Issue 11 https://doi.org/10.4161/psb.4.11.9875	journal	November 2009
Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries Lorenz, W. W.; Sun, F.; Liang, C. Tree Physiology, Vol. 26, Issue 1 https://doi.org/10.1093/treephys/26.1.1	journal	January 2006
The Biosynthesis of Cellulose Brown, R. Malcolm Journal of Macromolecular Science, Part A, Vol. 33, Issue 10 https://doi.org/10.1080/10601329608014912	journal	October 1996
Cell-wall carbohydrates and their modification as a resource for biofuels Pauly, Markus; Keegstra, Kenneth The Plant Journal, Vol. 54, Issue 4, p. 559-568 https://doi.org/10.1111/j.1365-313X.2008.03463.x	journal	May 2008
Hemicelluloses Scheller, Henrik Vibe; Ulvskov, Peter Annual Review of Plant Biology, Vol. 61, Issue 1 https://doi.org/10.1146/annurev-arplant-042809-112315	journal	June 2010
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects Holt, Carson; Yandell, Mark BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-491	journal	December 2011
Genomics of cellulose biosynthesis in poplars: Research review Joshi, Chandrashekhar P.; Bhandari, Suchita; Ranjan, Priya New Phytologist, Vol. 164, Issue 1 https://doi.org/10.1111/j.1469-8137.2004.01155.x	journal	August 2004
A Laccase Associated with Lignification in Loblolly Pine Xylem Bao, W.; O'Malley, D. M.; Whetten, R. Science, Vol. 260, Issue 5108 https://doi.org/10.1126/science.260.5108.672	journal	April 1993
Conifer R2R3-MYB transcription factors: sequence analyses and gene expression in wood-forming tissues of white spruce (Picea glauca) Bedon, Frank; Grima-Pettenati, Jacqueline; Mackay, John BMC Plant Biology, Vol. 7, Issue 1 https://doi.org/10.1186/1471-2229-7-17	journal	January 2007
Sucrose synthase affects carbon partitioning to increase cellulose production and altered cell wall ultrastructure Coleman, H. D.; Yan, J.; Mansfield, S. D. Proceedings of the National Academy of Sciences, Vol. 106, Issue 31 https://doi.org/10.1073/pnas.0900188106	journal	July 2009
Biosynthesis of plant cell wall polysaccharides — a complex process Lerouxel, Olivier; Cavalier, David M.; Liepman, Aaron H. Current Opinion in Plant Biology, Vol. 9, Issue 6 https://doi.org/10.1016/j.pbi.2006.09.009	journal	December 2006
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment Ewing, Brent; Hillier, LaDeana; Wendl, Michael C. Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.175	journal	March 1998
Characterization of EST-SSRs in loblolly pine and spruce Bérubé, Yanik; Zhuang, Jun; Rungis, Dainis Tree Genetics & Genomes, Vol. 3, Issue 3 https://doi.org/10.1007/s11295-006-0061-1	journal	October 2006
Towards decoding the conifer giga-genome Mackay, John; Dean, Jeffrey F. D.; Plomion, Christophe Plant Molecular Biology, Vol. 80, Issue 6 https://doi.org/10.1007/s11103-012-9961-7	journal	September 2012
The Amborella Genome and the Evolution of Flowering Plants Albert, V. A.; Barbazuk, W. B.; dePamphilis, C. W. Science, Vol. 342, Issue 6165 https://doi.org/10.1126/science.1241089	journal	December 2013
Genetic diversity associated with variation in silage corn digestibility for three O-methyltransferase genes involved in lignin biosynthesis Guillet-Claude, C.; Birolleau-Touchard, C.; Manicacci, D. Theoretical and Applied Genetics, Vol. 110, Issue 1 https://doi.org/10.1007/s00122-004-1808-4	journal	October 2004
Cellulose Synthase-Like Genes of Rice Hazen, Samuel P.; Scott-Craig, John S.; Walton, Jonathan D. Plant Physiology, Vol. 128, Issue 2 https://doi.org/10.1104/pp.010875	journal	February 2002
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data Birol, Inanc; Raymond, Anthony; Jackman, Shaun D. Bioinformatics, Vol. 29, Issue 12 https://doi.org/10.1093/bioinformatics/btt178	journal	May 2013
Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution El Baidouri, Moaine; Panaud, Olivier Genome Biology and Evolution, Vol. 5, Issue 5 https://doi.org/10.1093/gbe/evt025	journal	February 2013
Integration of Cot Analysis, DNA Cloning, and High-Throughput Sequencing Facilitates Genome Characterization and Gene Discovery Peterson, D. G. Genome Research, Vol. 12, Issue 5 https://doi.org/10.1101/gr.226102	journal	April 2002
Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase. Pear, J. R.; Kawagoe, Y.; Schreckengost, W. E. Proceedings of the National Academy of Sciences, Vol. 93, Issue 22 https://doi.org/10.1073/pnas.93.22.12637	journal	October 1996
Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing Seoane-Zonjic, Pedro; Cañas, Rafael A.; Bautista, Rocío BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2490-z	journal	February 2016
Overexpression of a Potato Sucrose Synthase Gene in Cotton Accelerates Leaf Expansion, Reduces Seed Abortion, and Enhances Fiber Production Xu, Shou-Min; Brill, Elizabeth; Llewellyn, Danny J. Molecular Plant, Vol. 5, Issue 2 https://doi.org/10.1093/mp/ssr090	journal	March 2012
Expression profiling and integrative analysis of the CESA/CSL superfamily in rice Wang, Lingqiang; Guo, Kai; Li, Yu BMC Plant Biology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2229-10-282	journal	January 2010
Identification and characterization of the Populus sucrose synthase gene family An, Xinmin; Chen, Zhong; Wang, Jingcheng Gene, Vol. 539, Issue 1 https://doi.org/10.1016/j.gene.2014.01.062	journal	April 2014
An expression analysis profile for the entire sucrose synthase gene family in rice Hirose, Tatsuro; Scofield, Graham N.; Terao, Tomio Plant Science, Vol. 174, Issue 5 https://doi.org/10.1016/j.plantsci.2008.02.009	journal	May 2008
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities Ewing, Brent; Green, Phil Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.186	journal	March 1998
Early genome duplications in conifers and other seed plants Li, Zheng; Baniaga, Anthony E.; Sessa, Emily B. Science Advances, Vol. 1, Issue 10 https://doi.org/10.1126/sciadv.1501084	journal	November 2015
A program for least squares analysis of reassociation and hybridization data Pearson, W. R.; Davidson, E. H.; Britten, R. J. Nucleic Acids Research, Vol. 4, Issue 6 https://doi.org/10.1093/nar/4.6.1727	journal	January 1977
Dna Reassociation Kinetics of four Conifers Rake, Adrian V.; Miksche, Jerome P.; Hall, Richard B. Canadian Journal of Genetics and Cytology, Vol. 22, Issue 1 https://doi.org/10.1139/g80-010	journal	March 1980
Characterization of the genome of bald cypress Liu, Wenxuan; Thummasuwan, Supaphan; Sehgal, Sunish K. BMC Genomics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2164-12-553	journal	November 2011
AUGUSTUS: a web server for gene finding in eukaryotes Stanke, M.; Steinkamp, R.; Waack, S. Nucleic Acids Research, Vol. 32, Issue Web Server https://doi.org/10.1093/nar/gkh379	journal	July 2004
A review of the production of ethanol from softwood Galbe, M.; Zacchi, G. Applied Microbiology and Biotechnology, Vol. 59, Issue 6 https://doi.org/10.1007/s00253-002-1058-9	journal	July 2002
Guar Seed -Mannan Synthase Is a Member of the Cellulose Synthase Super Gene Family Dhugga, K. S. Science, Vol. 303, Issue 5656 https://doi.org/10.1126/science.1090908	journal	January 2004
Involvement of Pinus taeda MYB1 and MYB8 in phenylpropanoid metabolism and secondary cell wall biogenesis: a comparative in planta analysis Bomal, Claude; Bedon, Frank; Caron, Sébastien Journal of Experimental Botany, Vol. 59, Issue 14 https://doi.org/10.1093/jxb/ern234	journal	September 2008
CotQuest: Improved algorithm and software for nonlinear regression analysis of DNA reassociation kinetics data Bunge, John; Chouvarine, Philippe; Peterson, Daniel G. Analytical Biochemistry, Vol. 388, Issue 2 https://doi.org/10.1016/j.ab.2009.03.007	journal	May 2009
Expression of a putative laccase gene, ZmLAC1, in maize primary roots under stress* Liang, Mingxiang; Haroldsen, Victor; Cai, Xiaoning Plant, Cell and Environment, Vol. 29, Issue 5 https://doi.org/10.1111/j.1365-3040.2005.01435.x	journal	May 2006
Cellulose Synthases and Synthesis in Arabidopsis Endler, Anne; Persson, Staffan Molecular Plant, Vol. 4, Issue 2 https://doi.org/10.1093/mp/ssq079	journal	March 2011
Draft genome of the living fossil Ginkgo biloba Guan, Rui; Zhao, Yunpeng; Zhang, He GigaScience, Vol. 5, Issue 1 https://doi.org/10.1186/s13742-016-0154-1	journal	November 2016
A High-Density Gene Map of Loblolly Pine ( Pinus taeda L.) Based on Exome Sequence Capture Genotyping Neves, Leandro Gomide; Davis, John M.; Barbazuk, William B. G3: Genes\|Genomes\|Genetics, Vol. 4, Issue 1 https://doi.org/10.1534/g3.113.008714	journal	November 2013
Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce Pavy, Nathalie; Pelgas, Betty; Beauseigle, Stéphanie BMC Genomics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2164-9-21	journal	January 2008
The cinnamate/monolignol pathway Umezawa, Toshiaki Phytochemistry Reviews, Vol. 9, Issue 1 https://doi.org/10.1007/s11101-009-9155-3	journal	November 2009
Evolution of Genome Size in Conifers Ahuja, M. Raj; Neale, David B. Silvae Genetica, Vol. 54, Issue 1-6 https://doi.org/10.1515/sg-2005-0020	journal	December 2005
Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size Stival Sena, Juliana; Giguère, Isabelle; Boyle, Brian BMC Plant Biology, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2229-14-95	journal	January 2014
A genome for gnetophytes and early evolution of seed plants Wan, Tao; Liu, Zhi-Ming; Li, Ling-Fei Nature Plants, Vol. 4, Issue 2 https://doi.org/10.1038/s41477-017-0097-2	journal	January 2018
Towards Understanding the Role of Membrane-bound Endo-β-1,4-glucanases in Cellulose Biosynthesis Mølhøj, Michael; Pagant, Silvère; Höfte, Herman Plant and Cell Physiology, Vol. 43, Issue 12 https://doi.org/10.1093/pcp/pcf163	journal	December 2002
Characterisation of a pine MYB that regulates lignification Patzlaff, Astrid; McInnis, Stephanie; Courtenay, Adrian The Plant Journal, Vol. 36, Issue 6 https://doi.org/10.1046/j.1365-313X.2003.01916.x	journal	December 2003
Isolation of milligram quantities of nuclear DNA from tomato (Lycopersicon esculentum), A plant containing high levels of polyphenolic compounds Peterson, Daniel G.; Boehm, Kevin S.; Stack, Stephen M. Plant Molecular Biology Reporter, Vol. 15, Issue 2 https://doi.org/10.1007/BF02812265	journal	June 1997
Synthesis, regulation and utilization of lignocellulosic biomass Harris, Darby; DeBolt, Seth Plant Biotechnology Journal, Vol. 8, Issue 3 https://doi.org/10.1111/j.1467-7652.2009.00481.x	journal	April 2010
Sequencing and Assembly of the 22-Gb Loblolly Pine Genome Zimin, Aleksey; Stevens, Kristian A.; Crepeau, Marc W. Genetics, Vol. 196, Issue 3 https://doi.org/10.1534/genetics.113.159715	journal	March 2014
Gene structure and molecular analysis of the laccase-like multicopper oxidase (LMCO) gene family in Arabidopsis thaliana McCaig, Bonnie C.; Meagher, Richard B.; Dean, Jeffrey F. D. Planta, Vol. 221, Issue 5 https://doi.org/10.1007/s00425-004-1472-6	journal	June 2005
Evolution of an Expanded Sex-Determining Locus in Volvox Ferris, P.; Olson, B. J. S. C.; De Hoff, P. L. Science, Vol. 328, Issue 5976 https://doi.org/10.1126/science.1186222	journal	April 2010
Molecular characterization of a phenylalanine ammonia-lyase gene (BoPAL1) from Bambusa oldhamii Hsieh, Lu-Sheng; Hsieh, Yi-Lin; Yeh, Chuan-Shan Molecular Biology Reports, Vol. 38, Issue 1 https://doi.org/10.1007/s11033-010-0106-2	journal	March 2010
The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes Djerbi, Soraya; Lindskog, Mats; Arvestad, Lars Planta, Vol. 221, Issue 5 https://doi.org/10.1007/s00425-005-1498-4	journal	June 2005
Sucrose Synthase in Legume Nodules Is Essential for Nitrogen Fixation Gordon, Anthony J.; Minchin, Frank R.; James, Caron L. Plant Physiology, Vol. 120, Issue 3 https://doi.org/10.1104/pp.120.3.867	journal	July 1999
The endo-1,4-β-glucanase Korrigan exhibits functional conservation between gymnosperms and angiosperms and is required for proper cell wall formation in gymnosperms Maloney, Victoria J.; Samuels, A. Lacey; Mansfield, Shawn D. New Phytologist, Vol. 193, Issue 4 https://doi.org/10.1111/j.1469-8137.2011.03998.x	journal	December 2011
Sucrose Synthase is an Integral Component of the Cellulose Synthesis Machinery Fujii, S.; Hayashi, T.; Mizuno, K. Plant and Cell Physiology, Vol. 51, Issue 2 https://doi.org/10.1093/pcp/pcp190	journal	January 2010
Evolution of Genome Size and Complexity in Pinus Morse, Alison M.; Peterson, Daniel G.; Islam-Faridi, M. Nurul PLoS ONE, Vol. 4, Issue 2 https://doi.org/10.1371/journal.pone.0004332	journal	February 2009
Genome Stability and Evolution: Attempting a Holistic View Schubert, Ingo; Vu, Giang T. H. Trends in Plant Science, Vol. 21, Issue 9 https://doi.org/10.1016/j.tplants.2016.06.003	journal	September 2016
What Do We Really Know about Cellulose Biosynthesis in Higher Plants? Guerriero, Gea; Fugelstad, Johanna; Bulone, Vincent Journal of Integrative Plant Biology, Vol. 52, Issue 2 https://doi.org/10.1111/j.1744-7909.2010.00935.x	journal	February 2010
Abnormal Lignin in a Loblolly Pine Mutant Ralph, J. Science, Vol. 277, Issue 5323 https://doi.org/10.1126/science.277.5323.235	journal	July 1997

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