Open Access Research article

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

Takashi Koyama1, Shuichi Asakawa2, Takayuki Katagiri1, Atsushi Shimizu3, Fernand F Fagutao1, Rapeepat Mavichak1, Mudjekeewis D Santos1, Kanako Fuji1, Takashi Sakamoto1, Toshihide Kitakado1, Hidehiro Kondo1, Nobuyoshi Shimizu4, Takashi Aoki1 and Ikuo Hirono1*

Author Affiliations

1 Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan

2 Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, the University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan

3 Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan

4 Advanced Research Center for Genome Super Power, Keio University, 2 Okubo, Tsukuba, Ibaraki, 300-2611, Japan

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BMC Genomics 2010, 11:141  doi:10.1186/1471-2164-11-141

Published: 26 February 2010

Additional files

Additional file 1:

BAC-ends anchored gene homologues identified by BLAST search. The significant matches (E-value < 0.1) of BAC-End-Sequences against public databases are shown in the list.

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Additional file 2:

27 putative genes with nearest homologues in the BAC clone Mj024A04. The BLASTP top hits and the E-values are shown.

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Additional file 3:

Exon-intron architecture of putative genes in BAC clone Mj024A04. Exon-intron architectures predicted by GENSCAN are shown.

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Additional file 4:

Primers used in this study. The orientation (forward or reverse) of all primers is indicated by 'f' or 'r' in the end of each primer name. Primers whose name is 'Gene--f or r' were used for PCR detection of each putative gene fragment from BAC clones. Primers for quantitative PCR of 4 putative genes (gene 01, 09, 16 and 27) in the BAC clone Mj024A04 and TGase for internal control are indicated by 'qt' at the beginning of each primer name. Primers for three microsatellite markers are indicated by 'MS' at the beginning of each primer name. Three microsatellites repeat regions (02, 33 and 64) were determined by RepeatMasker program [41]. Forward primers (f) were labeled by 6-FAM and reverse primers (r) were designed with tailed primer (Applied Biosystems).

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Additional file 5:

Schematic representation and frequency of BAC clones that hybridized with probe F, M and R. Number and percentage of positive clones in each group are shown. Data were based on the hybridization results for 381 clones in MjBL2 Plate 24. Location of each probes used in this study is indicated by red boxes.

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Additional file 6:

DNA fingerprints of kuruma shrimp BAC clones. 3 BAC clones from each hybridization positive groups (represented by positive probes at the top of each figures) and negative (neg) group were randomly selected. BAC DNA of all clones and Mj024A04 (B) were digested with EcoRI and HindIII.

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Additional file 7:

BAC genotyping using three microsatellite markers (MS02, 33 and 64) in Mj024A04. Genotypes representing the same size as the three microsatellite markers were taken as the same group. One base difference was regarded as experimental error.

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Additional file 8:

Calculation of the number of genotypes in shrimp genomes. Possible numbers of total genotypes were calculated using recursive formula for the marginal distribution and observed number of different genotypes. X-axis indicates the number of genotypes (θ). Y-axis indicates log-likelihood function of each given number of genotype. 90% and 95% confidence intervals (CI) are indicated above.

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Additional file 9:

Phylogenetic tree of BIR domains of BIRPs. BIR domains in the putative IAP genes found in Mj024A04 were compared with BIR domains from several organisms. Amino acid sequences of putative IAP gene 01, 06 and 24 were predicted by GENSCAN [42]. Each BIR domains was identified using InterProScan (version 22.0) [44]. Multiple sequence alignment and the phylogenetic tree of BIR domains were constructed using ClustalW after excluding all gap positions and assigning confidence of 1000 bootstrap samples. If multiple BIR domains were observed in a single gene, they are labelled alphabetically at the end of the gene's name. The GenBank identifier (GI) numbers for BIRP amino acid sequences and regions of BIR domains used in the analysis are as follows: bir-1_CAEEL (17564820; 15-88), bir-2_CAEEL (17557418; 22-99 and 165-242), Bir1p_SACCE (6322548; 20-117 and 153-241), bruce_DROME (45550729; 246-322), Bruce_HOMSA (153792694; 284-360), cIAP-1_HOMSA (14770185; 44-115, 182-252 and 267-338), cIAP-2_HOMSA (13639695; 27-98, 167-237 and 253-324), deterin_DROME (21355525; 26-102), gp019_BMNPV (9630835; 27-98 and 129-201), gp041_OPMNV (9629979; 22-93 and 124-195), gp242_MSEV (9631408; 15-77), IAP_GVCP (1170470; 5-75 and 106-177), IAP_PENMO (133754273; 12-83, 103-173 and 253-324), Iap2B_DROME (28573797; 7-78, 111-181 and 210-281), ML-IAP_HOMSA (11545910; 85-156), NAIP_HOMSA (119393878; 58-129, 157-229 and 276-347), OpIAP_ORGPSMNPV (9629973; 16-86 and 109-180), sfIAP_SPOFR (7021325; 98-168 and 208-279), Survivin_HOMSA (59859878; 13-89), survivin_SCHPO (162312092; 20_100 and 115-195), threadB_DROME (24664971; 42-112 and 224-295), VF193_IIV6 (33302608; 35-110), XIAP_HOMSA (12643387; 24-95, 161-232 and 263-332). GeneIDs in which Daphnia plex BIRPs were retrieved from wFleaBase [18] and regions of the BIR domains used in the analysis are as follows: Bruce_DAPPL (NCBI_GNO_248214; 320-396), Deterin_DAPPL (NCBI_GNO_774064; 21-105), IAP2_DAPPL (NCBI_GNO_324854; 9-75 and 158-229), thread_DAPPL (NCBI_GNO_284524; 52-122 and 158-229). BIR domains of putative gene 01, 06 and 24 used in the analysis are as follows: Gene 01 (18-95, 124-194 and 244-315), Gene 06 (36-106, 124-199, 268-339, 659-730 and 787-858), Gene 24 (9-80, 100-170 and 248-319).

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Additional file 10:

Southern blot hybridization of putative genes for detection of CpG-methylation. Kuruma shrimp genomic DNA (20 μg) was digested completely, electrophoresed and blotted. Hybridization and washing were performed under low stringency condition at 42°C. The restriction enzymes that were used are indicated by their initials (M; MspI, H; HpaII). The putative gene that was used for probe synthesis is indicated at the bottom. Left lane is λ/HindIII marker as size standard.

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