Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA.
Genome Biol. 2011;12(5):R48. doi: 10.1186/gb-2011-12-5-r48. Epub 2011 May 27.
Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.
Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.
When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.
最近的系统发育分析将新喀里多尼亚森林中特有的林下树种 Amborella trichopoda 确定为与包括所有其他已知开花植物物种的一个分支的姐妹群。Amborella 基因组是了解被子植物基因组进化的独特参考，因为它可以作为外群来进行比较分析。物理图谱、BAC 末端序列和样本鸟枪法序列提供了对 8.7 亿碱基对的 Amborella 基因组的初步看法。
对来自每个连续体的 Amborella BAC 末端进行分析表明，长末端重复逆转录转座子的密度与蛋白质编码基因的密度呈负相关。在 Amborella BAC 连续体与已测序的拟南芥、杨树、葡萄和水稻基因组的比较中，鉴定出了同基因、可能是祖先的基因块。同线性丧失的简约映射证实了先前的分析，表明导致拟南芥和水稻的谱系的结构变化速度比导致杨树和葡萄的谱系更快。在拟南芥、杨树和葡萄基因组中鉴定出的γ古六倍体事件表明，它发生在所有其他已知的被子植物从 Amborella 分支分化之后。
当将 BAC 末端序列置于物理图谱的背景下时，仅代表 Amborella 基因组的 5.4%的序列就有助于重建在所有开花植物的最后共同祖先中存在的基因块。Amborella 基因组是推断祖先被子植物和随后的基因组进化的宝贵参考。
