Populus trichocarpa

Information about Poplar Genome

Populus trichocarpa (poplar), native to western North America, is a deciduous broadleaf tree species. The poplar has important economic roles, not only for timber, but also for the processing industry materials. It has become an important raw material for plywood, fibreboard, papermaking match, sanitary chopsticks and packaging industry. The rapid growth and compact genome size (~500 Mbp) has promote it as an ideal model organism in plant biology.
The full genome sequence was finished in 2006[1], and the latest genome assembly (v3, http://plants.ensembl.org/Populus_trichocarpa/Info/Annotation/) was integrated to construct 19 chromosomes. It has the following information:

　　● Genome Size: 423Mb
　　● Number of Chromosomes: 19
　　● Number of Unplaced Scaffolds: 3663
　　● Number of Protein-coding Genes: 42950
　　● Number of transcripts: 63498

Genome Re-sequencing Projects and Variation Identification

Recently, thousands of popular accessions have been re-sequenced [2-5]. We gathered these data, and identified variations using our standard computational pipeline.

References

[1] Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313(5793):1596-1604. [PMID=16973872]

[2] Faivre-Rampant P, Zaina G, Jorge V, Giacomello S, Segura V, Scalabrin S, Guerin V, De Paoli E, Aluome C, Viger M, Cattonaro F, Payne A, PaulStephenRaj P, Le Paslier MC, Berard A, Allwright MR, Villar M, Taylor G, Bastien C, Morgante M: New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array. Mol Ecol Resour, 16(4):1023-1036. [PMID=26929265]

[3] Mousavi M, Tong C, Liu F, Tao S, Wu J, Li H, Shi J: De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies. BMC Genomics, 17:656. [PMID=27538483]

[4] Fahrenkrog AM, Neves LG, Resende MF, Jr., Vazquez AI, de Los Campos G, Dervinis C, Sykes R, Davis M, Davenport R, Barbazuk WB, Kirst M: Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides. New Phytol, 213(2):799-811. [PMID=27596807]

[5] Tong C, Li H, Wang Y, Li X, Ou J, Wang D, Xu H, Ma C, Lang X, Liu G, Zhang B, Shi J: Construction of High-Density Linkage Maps of Populus deltoides x P. simonii Using Restriction-Site Associated DNA Sequencing. PloS one, 11(3):e0150692. [PMID=26964097]