Summary
Publication
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, Déjardin 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, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé 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, Rouzé 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 (New York, N.Y.). 2006 Sep 15; 313 5793 1596-604
Name
Populus trichocarpa - Reference Genome
Resource Type
Genome Assembly
Organism
Details
Program, Pipeline, Workflow or Method Name
Arachne
Program Version
Arachne-v20071016HA
Date Performed
Friday, November 10, 2017 - 10:20
Data Source
Description and Download
Copied from JGI Phytozome Populus trichocarpa was sequenced ten times over to attain the highest quality standards and to produce a relatively contiguous, high quality plant genome. Poplar was chosen as the first tree DNA to be sequenced because of its relatively compact genetic complement, some 50 times smaller than the genome of pine, making the poplar an ideal model system for trees. The poplar genome, divided into 19 chromosomes, is four times larger than the genome of the first sequenced plant, Arabidopsis thaliana . Analysis of the assembled genome reveals a whole-genome duplication event; about 8,000 pairs of duplicated genes from that event survived in the Poplar genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages (from JGI - The Joint Genome Insitute and Tuskan, et.al.). This is the second improved version of poplar (v3 assembly) and includes 81 Mb of finished clone sequence combined with a new, high density poplar map. This genome release represents 6 years of genome improvement, advances in genome assembly, and poplar experimental work funded by the DOE. Genome
  • The main genome assembly is approximately 422.9 Mb arranged in 1,446 scaffolds
  • Approximately 422.9 Mb arranged in 8,313 scaffolds (~2.585 gap)
  • Scaffold N50 (L50) = 19.5 Mb (8)
  • Contig N50 (L50) = 552.8 Kb (206)
  • 181 scaffolds are > 50kb in size, representing approximately 97.3% of the genome
Loci
  • 42,950 loci containing protein-coding transcripts
Transcripts
  • 63,498 protein-coding transcripts

Downloads

Genomic scaffolds
All Gene Models CDS (fasta format)
All Gene Models Protein (fasta format)
All Gene Models GFF (Fasta format)
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