黑杨（毛果杨，Populus trichocarpa (Torr. & Gray)）的基因组。

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

作者信息

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, 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 J-C, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson D R, 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 C-J, 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

机构信息

Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.

出版信息

Science. 2006 Sep 15;313(5793):1596-604. doi: 10.1126/science.1128691.

DOI:10.1126/science.1128691

PMID:16973872

Abstract

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. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived 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 more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 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 lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

摘要

我们公布了毛果杨（Populus trichocarpa）的基因组草图。通过将鸟枪法序列组装与遗传图谱相结合，实现了基因组的染色体水平重建。鉴定出了超过45000个推定的蛋白质编码基因。对组装后的基因组分析发现了一次全基因组复制事件；该事件中约8000对重复基因在毛果杨基因组中得以保留。第二次更为古老的复制事件与毛果杨和拟南芥谱系的分化时间恰好重合，难以区分。核苷酸替换、串联基因重复和大规模染色体重排似乎在毛果杨中比在拟南芥中进行得要慢得多。毛果杨的蛋白质编码基因比拟南芥多，平均每个拟南芥基因有1.4到1.6个推定的毛果杨同源基因。然而，两个基因组中蛋白质结构域的相对频率相似。毛果杨中过度表达的例外情况包括与木质纤维素壁生物合成、分生组织发育、抗病性和代谢物运输相关的基因。