Limited microsynteny between the genomes of Pristionchus pacificus and Caenorhabditis elegans
Limited microsynteny between the genomes of Pristionchus pacificus and Caenorhabditis elegans
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DOI：
10.1093/nar/gkg359
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发表时间：
2003-05-15
影响因子：
14.9
通讯作者：
Sommer, RJ
中科院分区：
文献类型：
--
作者：
Lee, KZ;Eizinger, A;Sommer, RJ
线虫是研究发育过程进化的一类有吸引力的生物。太平洋刺线虫（Pristionchus pacificus）被确立为一种辅助生物，用于比较其外阴发育及其他过程与秀丽隐杆线虫（Caenorhabditis elegans）的异同。太平洋刺线虫遗传连锁图谱的绘制为了解该物种基因组的结构和组织提供了初步见解。太平洋刺线虫和秀丽隐杆线虫彼此分离超过1亿年，因此这两种线虫的基因组结构可能存在很大差异。为了评估这两个基因组之间的同线性程度，我们获得了太平洋刺线虫126kb的连续基因组序列，该序列位于发育模式基因pal - 1的侧翼。在这个区间内预测的20个开放阅读框中，有11个在秀丽隐杆线虫中有直系同源基因。这11个直系同源基因中的10个位于秀丽隐杆线虫的第三号染色体上，这表明存在同线性。然而，这些基因中的大多数分布在秀丽隐杆线虫基因组的12Mb区间内，并且只有三对基因显示微同线性。因此，染色体内重排在线虫中频繁发生，这限制了基于两个基因组内的位置信息来鉴定太平洋刺线虫和秀丽隐杆线虫直系同源基因的可能性。
Nematodes are an attractive group of organisms for studying the evolution of developmental processes. Pristionchus pacificus was established as a satellite organism for comparing vulva development and other processes to Caenorhabditis elegans. The generation of a genetic linkage map of P.pacificus has provided a first insight into the structure and organization of the genome of this species. Pristionchus pacificus and C.elegans are separated from one another by >100 000 000 years such that the structure of the genomes of these two nematodes might differ substantially. To evaluate the amount of synteny between the two genomes, we have obtained 126 kb of continuous genomic sequence of P.pacificus, flanking the developmental patterning gene pal-1. Of the 20 predicted open reading frames in this interval, 11 have C.elegans orthologs. Ten of these 11 orthologs are located on C.elegans chromosome III, indicating the existence of synteny. However, most of these genes are distributed over a 12 Mb interval of the C.elegans genome and only three pairs of genes show microsynteny. Thus, intrachromosomal rearrange ments occur frequently in nematodes, limiting the likelihood of identifying orthologous genes of P.pacificus and C.elegans based on positional information within the two genomes.