The genome of black cottonwood, Populus trichocarpa (Torr.&Gray)

Journal Article · Fri Sep 01 04:00:00 EDT 2006 · Science

DOI:https://doi.org/10.1126/science.1128691· OSTI ID:901819

Tuskan, G A; 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, R R; Bhalerao, R P; Blaudez, D; Boerjan, W; Brun, A; Brunner, A; Busov, V ; Campbell, M; Carlson, J; Chalot, M; Chapman, J; Chen, G -L; Cooper, D; Coutinho, P M; Couturier, J; Covert, S; Cronk, Q; Cunningham, R; Davis, J; Degroeve, S; Dejardin, A; dePamphillis, C; Detter, J; Dirks, B; Dubchak, I; Duplessis, S; Ehiting, 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, J -C; Locascio, P; Lou, Y; Lucas, S; Martin, F; Montanini, B; Napoli, C; Nelson, D R; Nelson, D; Nieminen, K; Nilsson, O; 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, C; Uberbacher, E; Unneberg, P; Vahala, J; Wall, K; Wessler, S; Yang, G; Yin, T; Douglas, C; Marra, M; Sandberg, G; Van der Peer, Y; Rokhsar, D

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. Over 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event, with approximately 8,000 pairs of duplicated genes from that event surviving in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication and gross chromosomal rearrangement appear to proceed substantially slower in Populus relative to Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average between 1.4-1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with disease resistance, meristem development, metabolite transport and lignocellulosic wall biosynthesis.

• Research Organization: Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE; National Science Foundation; Genome Canada, SwedishAgricultural University, International Populus GenomeConsortium
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 901819
• Report Number(s): LBNL--59968; BnR: YN0100000
• Journal Information: Science, Journal Name: Science Journal Issue: 5793 Vol. 313; ISSN 0193-4511; ISSN SCEHDK
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
ARABIDOPSIS
BIOSYNTHESIS
COTTONWOODS
DISEASE RESISTANCE
GENES
GENETIC MAPPING
MERISTEMS
METABOLITES
NUCLEOTIDES
PROTEINS
TRANSPORT