Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus.
Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus.
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DOI：
10.1186/1471-2164-11-141
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发表时间：
2010-02-26
期刊：
影响因子：
4.4
通讯作者：
Hirono I
中科院分区：
文献类型：
--
作者：
Koyama T;Asakawa S;Katagiri T;Shimizu A;Fagutao FF;Mavichak R;Santos MD;Fuji K;Sakamoto T;Kitakado T;Kondo H;Shimizu N;Aoki T;Hirono I
高等甲壳类动物（Malacostraca纲）是种类最丰富、形态最多样的非昆虫节肢动物，其许多成员具有重要的商业价值。尽管甲壳类动物的DNA序列信息呈指数级增长，但人们对马拉斯卡虫的基因组结构知之甚少。本文构建了一个细菌人工染色体文库，并对养殖最广泛的甲壳类动物之一黑虾（Marsupenaeus japonicus）进行了BAC末端测序，以提供其基因组信息，结果发现该文库中存在一个冗余序列。我们检查了包含冗余序列的BAC克隆，以进一步分析其长度，拷贝数和在库鲁马虾基因组中的位置。Mj024A04 BAC克隆包含一个冗余序列，包含27个假定基因，似乎显示出正常的基因组DNA结构。值得注意的是，在推测的基因中，3个基因编码凋亡抑制蛋白的同源蛋白，7个基因编码白斑综合征病毒的同源蛋白，白斑综合征病毒是一种已知影响甲壳类动物的剧毒病原体。对381个BAC克隆的集落杂交和PCR分析表明，几乎一半的BAC克隆保持了与代表BAC克隆Mj024A04同源的DNA片段。Mj024A04部分序列在黑虾核基因组中被多次检测到，计算拷贝数至少为100。基于微卫星的BAC基因分型清楚地显示，Mj024A04同源序列至少从48个不同的染色体位点中克隆出来。与水蚤和果蝇基因组序列缺乏微同步关系表明，这些片段在目前节肢动物基因组序列中具有独特性。我们的研究结果表明，在黑虾基因组中发生了大DNA片段的超扩增。虽然我们只分析了一部分重复的DNA片段，但我们的结果表明，按照正常的分析方法很难分析虾基因组。因此，在研究虾基因组的其他独特结构时，有必要避免重复序列（如片段重复）。
Higher crustaceans (class Malacostraca) represent the most species-rich and morphologically diverse group of non-insect arthropods and many of its members are commercially important. Although the crustacean DNA sequence information is growing exponentially, little is known about the genome organization of Malacostraca. Here, we constructed a bacterial artificial chromosome (BAC) library and performed BAC-end sequencing to provide genomic information for kuruma shrimp (Marsupenaeus japonicus), one of the most widely cultured species among crustaceans, and found the presence of a redundant sequence in the BAC library. We examined the BAC clone that includes the redundant sequence to further analyze its length, copy number and location in the kuruma shrimp genome. Mj024A04 BAC clone, which includes one redundant sequence, contained 27 putative genes and seemed to display a normal genomic DNA structure. Notably, of the putative genes, 3 genes encode homologous proteins to the inhibitor of apoptosis protein and 7 genes encode homologous proteins to white spot syndrome virus, a virulent pathogen known to affect crustaceans. Colony hybridization and PCR analysis of 381 BAC clones showed that almost half of the BAC clones maintain DNA segments whose sequences are homologous to the representative BAC clone Mj024A04. The Mj024A04 partial sequence was detected multiple times in the kuruma shrimp nuclear genome with a calculated copy number of at least 100. Microsatellites based BAC genotyping clearly showed that Mj024A04 homologous sequences were cloned from at least 48 different chromosomal loci. The absence of micro-syntenic relationships with the available genomic sequences of Daphnia and Drosophila suggests the uniqueness of these fragments in kuruma shrimp from current arthropod genome sequences. Our results demonstrate that hyper-expansion of large DNA segments took place in the kuruma shrimp genome. Although we analyzed only a part of the duplicated DNA segments, our result suggested that it is difficult to analyze the shrimp genome following normal analytical methodology. Hence, it is necessary to avoid repetitive sequence (such as segmental duplications) when studying the other unique structures in the shrimp genome.
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