Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul 133-791, South Korea.
Gene. 2012 Aug 15;505(1):108-13. doi: 10.1016/j.gene.2012.05.032. Epub 2012 Jun 4.
Information of genome structure with its size variation may provide important clues for evolutionary processes at lower taxon level in eukaryotes. Here, we analyzed the compact genome structure of the monogonont rotifer, Brachionus koreanus in the light of transphyletic genome comparison and economic genome usage. To confirm the genome compactness of B. koreanus, we compared the genomic structure of several selected genes with those of human and pufferfish. For example, one of the large genes, DNA-dependent protein kinase (DNA-PK) with dimeric protein Ku70 and Ku80, showed high similarity, even though genomic DNA lengths were quite different. The replication protein As (RPAs) as a heterotrimeric protein also showed a compact genomic structure including all the essential domains and motifs in B. koreanus. Regarding transmembrane protein-containing genes, the B. koreanus P-glycoprotein (P-gp) showed exactly the same topology of the TM domain compared to those of human and pufferfish, even though it had a compact genome structure. In addition, the gene structure of an inducible repair enzyme O(6)-methylguanine DNA methyltransferase (O(6)-MGMT) of B. koreanus showed the highest compactness among the genes tested. The objective of this report is to evaluate the potential for whole genome sequencing and functional genomic research using the monogonont rotifer B. koreanus as a non-model organism that plays important roles in aquatic food-webs. Subsequently, we discussed possible reasons for compact genome structures as well as small and fewer introns from several perspectives. We conclude that the small size genome of B. koreanus would make this species potentially useful for comparative genome structure analysis of non-model species through whole genome sequencing and genetic mapping.
基因组结构及其大小变异的信息可能为真核生物较低分类群水平的进化过程提供重要线索。在这里，我们分析了单巢轮虫秀丽隐杆线虫的紧凑基因组结构，从跨生物基因组比较和经济基因组利用的角度来看。为了证实秀丽隐杆线虫基因组的紧凑性，我们比较了几种选定基因的基因组结构与人类和河豚的基因组结构。例如，一种大基因，具有二聚体蛋白 Ku70 和 Ku80 的 DNA 依赖性蛋白激酶 (DNA-PK)，尽管基因组 DNA 长度差异很大，但显示出高度相似性。作为异源三聚体蛋白的复制蛋白 A (RPAs) 也显示出包括秀丽隐杆线虫所有必需结构域和基序的紧凑基因组结构。关于包含跨膜蛋白的基因，秀丽隐杆线虫的 P-糖蛋白 (P-gp) 与人类和河豚的 P-gp 相比，TM 结构域的拓扑结构完全相同，尽管它具有紧凑的基因组结构。此外，秀丽隐杆线虫诱导修复酶 O(6)-甲基鸟嘌呤 DNA 甲基转移酶 (O(6)-MGMT) 的基因结构在测试的基因中显示出最高的紧凑性。本报告的目的是评估使用单巢轮虫秀丽隐杆线虫作为非模式生物进行全基因组测序和功能基因组研究的潜力，因为它在水生食物网中发挥着重要作用。随后，我们从几个角度讨论了紧凑基因组结构以及较小和较少内含子的可能原因。我们得出的结论是，秀丽隐杆线虫的小基因组大小使得该物种有可能通过全基因组测序和遗传图谱对非模式物种进行比较基因组结构分析。
