Scholl Elizabeth H, Thorne Jeffrey L, McCarter James P, Bird David Mck
Center for the Biology of Nematode Parasitism, Box 7253, North Carolina State University, Raleigh, NC 27695, USA.
Genome Biol. 2003;4(6):R39. doi: 10.1186/gb-2003-4-6-r39. Epub 2003 May 19.
Published accounts of horizontally acquired genes in plant-parasitic nematodes have not been the result of a specific search for gene transfer per se, but rather have emerged from characterization of individual genes. We present a method for a high-throughput genome screen for horizontally acquired genes, illustrated using expressed sequence tag (EST) data from three species of root-knot nematode, Meloidogyne species.
Our approach identified the previously postulated horizontally transferred genes and revealed six new candidates. Screening was partially dependent on sequence quality, with more candidates identified from clustered sequences than from raw EST data. Computational and experimental methods verified the horizontal gene transfer candidates as bona fide nematode genes. Phylogenetic analysis implicated rhizobial ancestors as donors of horizontally acquired genes in Meloidogyne.
High-throughput genomic screening is an effective way to identify horizontal gene transfer candidates. Transferred genes that have undergone amelioration of nucleotide composition and codon bias have been identified using this approach. Analysis of these horizontally transferred gene candidates suggests a link between horizontally transferred genes in Meloidogyne and parasitism.
已发表的关于植物寄生线虫中水平获得基因的报道并非专门针对基因转移本身进行搜索的结果，而是源于对单个基因的表征。我们提出了一种用于高通量基因组筛选水平获得基因的方法，并以三种根结线虫（南方根结线虫属）的表达序列标签（EST）数据为例进行说明。
我们的方法鉴定出了先前假定的水平转移基因，并揭示了六个新的候选基因。筛选部分取决于序列质量，从聚类序列中鉴定出的候选基因比从原始EST数据中鉴定出的更多。计算和实验方法验证了水平基因转移候选基因是真正的线虫基因。系统发育分析表明根瘤菌祖先可能是南方根结线虫中水平获得基因的供体。
高通量基因组筛选是鉴定水平基因转移候选基因的有效方法。使用这种方法已经鉴定出了核苷酸组成和密码子偏好发生改善的转移基因。对这些水平转移基因候选基因的分析表明，南方根结线虫中的水平转移基因与寄生作用之间存在联系。
