Comparative Analysis of the Genomes of Three Field Isolates of the Rice Blast Fungus <i>Magnaporthe oryzae</i>from Southern China

Rice blast caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among different isolates of M. oryzae in the nature field, we re-sequenced and analyzed the genomes of three field isolates, QJ08-2006, QJ10-10, and QJ10-3001, which showed distinct pathogenicity on Xin-Yin-Zhan, an elite variety in South China. Genome annotation indicated that these three isolates assemblies have similar genome sizes with 38.4 Mb, 38.3 Mb, and 38.4 Mb, respectively. The QJ08-2006 assembly has 2082 contigs with an N50 of 127.4 kb, the QJ10-10 assembly has 2239 contigs with an N50 of 105.13 kb, the QJ10-3001 assembly has 2025 contigs with an N50 of 133.16 kb. A total of 10,432 genes including 1408 putative secreted protein genes were identified from the annotated isolate QJ08-2006 genome, 10,418 genes including 1410 putative secreted protein genes were identified in QJ10-10, and 10,401 genes including 1420 putative secreted protein genes were identified in QJ10-3001. There are as many as 11,076 identical genes in these three isolates and contained only a few unique genes among three isolates, of which 277 unique genes in QJ08-2006 and 264 unique genes in QJ10-10, and 213 unique genes in QJ10-3001. Most of the predicted secreted protein genes had been identified, and the three re-sequenced strains contained 371, 369, and 387 small Indel, respectively. Avr genes were analyzed in several sequenced Magnaporthe strains, the results revealed that Avr-Pi9 and Avr-Piz-t were present in all the sequenced isolates. The isolates QJ08-2006 contained AvrPib, QJ10-10, and QJ10-3001 had an insertion of a Pot3 element in the promoter of the AvrPib gene. Our results showed that, the rapid dominancy of virulence mutant isolates via clonal propagation displayed in the field after the release of the elite variety Xin-Yin-Zhan.

草鱼含信号肽分泌蛋白的预测分析

采用组合的信号肽分析软件SignalP 3.0,TMHMM 2.0,big-PI,TargetP 1.1和Lipop 1.0对已公布的522个草鱼ORF编码蛋白的N端氨基酸序列进行信号肽分析,同时系统分析了信号肽的类型及结构。结果表明,522个草鱼氨基酸序列中分泌蛋白有61个,占其基因组编码蛋白的11.7%。编码这些蛋白的可读框(ORF)最小值为127 bp,最大值为5032 bp,平均910 bp,引导它们的信号肽长度介于15～32个氨基酸之间,平均为21个氨基酸。通过对草鱼分泌蛋白切割位点信号肽类型分析发现具Ⅰ型信号肽的分泌蛋白有17个,Ⅱ型的有4个。草鱼分泌蛋白中,42个具可预测功能,19个为未知功能蛋白。已知功能的分泌蛋白主要集中于细胞代谢,细胞调控及转运,细胞膜结构,细胞的免疫等领域。

水稻基因组中分泌蛋白的初步分析

本文利用SignalP3.0两种算法NN(neural network)和HMM(hidden markov model)对水稻基因组中59712个ORF进行了初步的筛选,其中有4433个ORF编码的蛋白具有分泌特性,占整个基因组的7.3%。4433个具有分泌特性的蛋白,在染色体的分布是不均一的。在1号染色体的所占的比例最多,为8.8%;而12号染色体上所占的比例最少,为5.0%。其中在具有分泌特性的蛋白中,酶类、非酶类和推测蛋白分别占具有分泌型信号肽蛋白的24.9%、45.7%和29.5%。