Frank Ronald L, Kandoth Cyriac, Ercal Fikret
Biological Sciences Department, Missouri S&T, Rolla, MO 65409, USA.
BMC Bioinformatics. 2008 Aug 12;9 Suppl 9(Suppl 9):S2. doi: 10.1186/1471-2105-9-S9-S2.
Gene family identification from ESTs can be a valuable resource for analysis of genome evolution but presents unique challenges in organisms for which the entire genome is not yet sequenced. We have developed a novel gene family identification method based on negative selection patterns (NSP) between family members to screen EST-generated contigs. This strategy was tested on five known gene families in Arabidopsis to see if individual paralogs could be identified with accuracy from EST data alone when compared to the actual gene sequences in this fully sequenced genome.
The NSP method uniquely identified family members in all the gene families tested. Two members of the FtsH gene family, three members each of the PAL, RF1, and ribosomal L6 gene families, and four members of the CAD gene family were correctly identified. Additionally all ESTs from the representative contigs when checked against MapViewer data successfully identify the gene locus predicted.
We demonstrate the effectiveness of the NSP strategy in identifying specific gene family members in Arabidopsis using only EST data and we describe how this strategy can be used to identify many gene families in agronomically important crop species where they are as yet undiscovered.
从ESTs中识别基因家族对于基因组进化分析而言可能是一种宝贵资源，但对于尚未进行全基因组测序的生物体来说，这带来了独特的挑战。我们开发了一种基于家族成员间负选择模式（NSP）的新型基因家族识别方法，用于筛选由EST生成的重叠群。该策略在拟南芥的五个已知基因家族上进行了测试，以确定仅根据EST数据与这个已完成全基因组测序的实际基因序列相比，能否准确识别各个旁系同源基因。
NSP方法在所有测试的基因家族中都能独特地识别家族成员。FtsH基因家族的两个成员、PAL基因家族、RF1基因家族和核糖体L6基因家族的各三个成员，以及CAD基因家族的四个成员都被正确识别。此外，当根据MapViewer数据检查代表性重叠群的所有EST时，成功识别出了预测的基因位点。
我们证明了NSP策略仅使用EST数据在拟南芥中识别特定基因家族成员的有效性，并且描述了该策略如何用于识别在重要农艺作物物种中尚未被发现的许多基因家族。
