Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus

Abstract

BackgroundHigher 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.ResultsMj024A04 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.ConclusionsOur 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.

Suitability of the clonal marbled crayfish for biogerontological research: a review and perspective, with remarks on some further crustaceans

“…This species is a short-lived monitor organism in ecotoxicology and has occasionally been used for ageing research as well (Dudycha 2003). A genome sequencing project for the first decapod crustacean, the commercially most valuable Pacific white shrimp Litopenaeus vannamei, is on the way and the necessary EST databases, linkage maps or BAC libraries are rapidly increasing (Stillman et al 2008;Koyama et al 2010). Moreover, techniques for the identification of genes and their products are more and more adopted for shrimp and crayfish (Shechter et al 2007;Robalino et al 2009).…”

Shrimp Viral Diseases, Import Risk Assessment and International Trade

“…No outbreaks of WSSV have ever been reported from shrimp in Australia and this data suggests that WSSV-shrimp association has been very ancient and has been existing globally. The Japanese investigators have constructed a bacterial artificial chromosome library that has about 3X coverage of the 2,000 Mbp kuruma shrimp (Marsupenaeus japonicus) genome and detected seven ORFs that show homology with predicted proteins of WSSV [9]. This further suggests that Japanese shrimp also have long history of association with WSSV with the viral gene segments inserted into the host chromosome.…”

BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

“…However, research into the shrimp genome remains limited and fragmented, and is far from adequate to provide basic support for functional genes studies and genetic breeding projects. Indeed, besides the large genome size (~2.45 Gb, C value=2.50 pg) (Seinen Chow, 1990) and the presence of abundant repetitive sequences (Koyama et al, 2010;Huang et al, 2011), little is known about the shrimp genome structure. There is no physical map for the shrimp genome, though this was fi rst proposed more than a decade ago (Alcivar-Warren et al, 1997), and there are few Large-insert genomic libraries, such as bacterial artifi cial chromosome (BAC) or fosmid libraries, are important resources for genomic research (Ren et al, 2003).…”

“…Currently, there are two BAC libraries for shrimp, a 101 kb-insert BAC library for pacifi c white shrimp ( Litopenaeus vannamei ) ) and a 135 kb-insert BAC library for Kuruma shrimp ( Marsupenaeus japonicas ) (Koyama et al, 2010). In addition, two fosmid libraries for L .…”