Genome because recent phylogenetic ZM241385MedChemExpress ZM241385 analysis based on the DNA sequence data and morphology comparison between Hexapoda (including insects) and Crustacea provided an unexpected finding that Branchiopoda (including the water flea Daphnia) is phylogenetically much closer to Hexapoda rather than Malacostraca [6-8]. Therefore, the crustacean genome, in particular the genetic differences between Branchiopoda and Hexapoda group and other sister groups need to be elucidated. The penaeid shrimp, which is classified into Decapoda in Malacostraca, has been the subject of intense research. Due to its commercial value, several papers on expressed sequence tag (EST) analysis and genetic linkage mapping has been published in the past few years. However, in depth information of their large genome, which is estimated to be about 70 of human genome in size and rich in AT and AAT sequences, is largely unknown [9-11]. As the first step towards understanding the shrimp genome organization, we constructed a BAC library (named MjBL2) from kuruma shrimp (Marsupenaeus japonicus) and performed BAC-end sequencing. The results clearly showed extreme redundancy of certain sequences in many BAC clones of the MjBL2 library. We chose one BAC clone (Mj024A04) for detailed analysis in terms of its entire sequence and redundancy in the shrimp genome and found numerous copies of DNA segments that contain the Mj024A04sequence. This indicates that hyper-expansion of such peculiar DNA segments occurred through segmental duplication events during evolution of the kuruma shrimp genome. ResultsBAC library construction and BAC-end sequencingmicrotiter plates and stored at -80 . The average insert size was estimated to be 135 kb by NotI digestion of 205 randomly selected BAC clones. BES analysis was further performed using 192 BAC clones randomly selected from MjBL2 and retrieved reads were assembled for contiguity [DDBJ: AG993477-AG993734]. Resulting BESs were classified into 29 singletons and 51 contiguous sequences consisting of 2 to 24 reads. Notably, the BLASTN and BLASTX analyses revealed that many of these BESs (20 reads in BLASTN, 55 reads in BLASTX) contained a sequence encoding a protein similar to “inhibitor of apoptosis protein (IAP)” reported in black tiger shrimp (Penaeus monodon) (see Additional file 1).DNA sequence of a representative BAC cloneOne of the BAC clones (Mj024A04) that possessed a sequence similar to “black tiger shrimp IAP” gene was randomly selected from MjBL2 for detailed analysis of its entire DNA sequence by employing shotgun sequencing method. The resulting genomic DNA sequence of 120 kb (Mj024A04-sequence) was analyzed by in silico annotation, revealing 27 putative genes that apparently seemed to be normal genomic region with exon-intron structure (Figure 1, see Additional file 2 and Additional file 3) [DDBJ: AP010878]. As shown in Figure 1, large GGTTA repeats were found in the PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26577270 middle of the sequence flanking gene 09, which encodes a protein similar to a reverse transcriptase of Takifugu rubripes [12]. Notably, of the other 26 genes, three genes (gene 01, 06, and 24) encode a protein homologous to IAP of three species, Xenopus laevis (african clawed frog), Drosophila melanogaster (fruit fly) and Rattus norvegicus (norway rat) and seven genes (gene 11, 13, 14, 15, 16, 17 and 18) were homologous to ORFs in “White Spot Syndrome Virus (WSSV)”, the major shrimp pathogenic dsDNA virus, which is highly virulent to penaeid shrimps as well as other cru.