Jung Sook, Jiwan Derick, Cho Ilhyung, Lee Taein, Abbott Albert, Sosinski Bryon, Main Dorrie
Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA.
BMC Genomics. 2009 Feb 10;10:76. doi: 10.1186/1471-2164-10-76.
Fragmentary conservation of synteny has been reported between map-anchored Prunus sequences and Arabidopsis. With the availability of genome sequence for fellow rosid I members Populus and Medicago, we analyzed the synteny between Prunus and the three model genomes. Eight Prunus BAC sequences and map-anchored Prunus sequences were used in the comparison.
We found a well conserved synteny across the Prunus species -- peach, plum, and apricot -- and Populus using a set of homologous Prunus BACs. Conversely, we could not detect any synteny with Arabidopsis in this region. Other peach BACs also showed extensive synteny with Populus. The syntenic regions detected were up to 477 kb in Populus. Two syntenic regions between Arabidopsis and these BACs were much shorter, around 10 kb. We also found syntenic regions that are conserved between the Prunus BACs and Medicago. The array of synteny corresponded with the proposed whole genome duplication events in Populus and Medicago. Using map-anchored Prunus sequences, we detected many syntenic blocks with several gene pairs between Prunus and Populus or Arabidopsis. We observed a more complex network of synteny between Prunus-Arabidopsis, indicative of multiple genome duplication and subsequence gene loss in Arabidopsis.
Our result shows the striking microsynteny between the Prunus BACs and the genome of Populus and Medicago. In macrosynteny analysis, more distinct Prunus regions were syntenic to Populus than to Arabidopsis.
已有报道称，在图谱定位的李属序列与拟南芥之间存在部分共线性保守情况。随着蔷薇I类成员杨树和苜蓿基因组序列的可得，我们分析了李属与这三个模式基因组之间的共线性。比较中使用了8个李属BAC序列和图谱定位的李属序列。
利用一组同源的李属BAC，我们发现桃、李和杏等李属物种与杨树之间存在高度保守的共线性。相反，在该区域我们未检测到与拟南芥的任何共线性。其他桃BAC也与杨树显示出广泛的共线性。在杨树中检测到的共线性区域长达477 kb。拟南芥与这些BAC之间的两个共线性区域要短得多，约为10 kb。我们还发现了李属BAC与苜蓿之间保守的共线性区域。共线性阵列与杨树和苜蓿中推测的全基因组复制事件相对应。利用图谱定位的李属序列，我们在李属与杨树或拟南芥之间检测到许多具有多个基因对的共线性块。我们观察到李属 - 拟南芥之间的共线性网络更为复杂，这表明拟南芥中存在多次基因组复制和随后的基因丢失。
我们的结果表明李属BAC与杨树和苜蓿基因组之间存在显著的微共线性。在宏观共线性分析中，与杨树共线性的李属区域比与拟南芥共线性的区域更明显。
