Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus
© Koyama et al; licensee BioMed Central Ltd. 2010
Received: 30 September 2009
Accepted: 26 February 2010
Published: 26 February 2010
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.
The genomes of crustaceans are extremely diverse in their size, with the smallest one having a C-value of 0.14 pg and the largest one weighing 64.62 pg, differing by a factor of 460 [1, 2]. Despite their economic importance and production in huge biomass, little is known about the genome organization of crustaceans, especially Malacostraca (including shrimps and crabs) except for the presence of numerous repetitive sequences [3–5]. Recently, although the genomic DNA sequence of a crustacean, water flea Daphnia pulex, has been determined, it seems improper to make any conclusion on the crustacean genome because recent phylogenetic 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 Mj024A04-sequence. This indicates that hyper-expansion of such peculiar DNA segments occurred through segmental duplication events during evolution of the kuruma shrimp genome.
BAC library construction and BAC-end sequencing
To provide an overview of the composition and organization of the kuruma shrimp nuclear genome, we constructed BAC library (MjBL2) using kuruma shrimp genomic DNA prepared from hemocytes of 13 shrimps and analyzed the BAC-end sequence (BES). MjBL2 consists of 49,152 BAC clones, which were arrayed in 128 microtiter plates and stored at -80°C. The average insert size was estimated to be 135 kb by Not I 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 clone
Redundancy of Mj024A04-sequence homologues in the kuruma shrimp BAC library
Detection of Mj024A04-sequence and its copy number in the kuruma shrimp genome
BAC genotyping and PCR detection of putative genes in Mj024A04-sequence
Kuruma shrimp Mj024A04-sequence has unique characteristic among arthropod genomes
We performed micro-synteny comparisons of Mj024A04-sequence with genome sequences of other 2 arthropods Drosophila melanogaster (version FB2008_02)  and Daphnia pulex (release 1, 2007/07/07)  using TBLASTN algorithm. However, we could not find any micro-synteny relation between Mj024A04 and Drosophilla or Daphnia genome (data not shown), suggesting the uniqueness of Mj024A04-sequence within known arthropod genomes.
BAC library construction and BAC-end sequencing for a first characterization of the kuruma shrimp genome
The amount of kuruma shrimp nuclear DNA has been reported to be 2.83 pg indicating that kuruma shrimp genome size is almost the same as other penaeid shrimps such as Litopenaeus vannamei and Penaeus monodon whose genome size are reported to be approximately 2,000 Mbp . In this study, we first constructed BAC library from the kuruma shrimp. Average insert size of MjBL2 BAC clones were estimated to be 135 kb and total MjBL2 insert size could be calculated as approximately 6,600 Mbp, showing that MjBL2 represented 3.3 times coverage of kuruma shrimp genome. Although MjBL2 is not suitable for physical mapping and genome sequencing because it was constructed from 13 shrimps, MjBL2 is useful as the first step for characterizing the kuruma shrimp genome. We performed BES analysis to acquire the first glimpse into the sequence composition of the unsequenced kuruma shrimp genome. The results of BES analysis were very surprising because even with only 192 clones analyzed, we detected 51 contigs and each contigs contained multiple reads varying from 2 to 24. This suggested that following the typical BAC construction method , we obtained multiple copies of the same DNA fragments in the kuruma shrimp genome. However, putative genes such as black tiger shrimp IAP gene homologue that we annotated by BLAST does not seem to be the gene that has potential duplication activity like the transposable elements. To further ascertain the abnormality of the kuruma shrimp genome, we further analyzed these DNA segment in the kuruma shrimp genome.
Gene contents of a representative BAC clone Mj024A04
Mj024A04 BAC clone randomly selected from BAC clones that possessed black tiger shrimp IAP sequences was fully sequenced and 27 genes were predicted in silico. Of the 27 predicted genes, we found three genes homologous to IAP. It is known that apoptosis is a genetically programmed pathway of controlled cell suicide that has critical roles in several processes such as development, tissue homeostasis, DNA damage responses and pathological processes . IAPs have been shown to block apoptosis by inhibition of the proteolytic activity of caspases, the central components of the apoptotic machinery, through direct binding of Baculoviral IAP Repeat (BIR) domains present in the IAPs . Cellular homologues called the BIR-domain-containing protein (BIRPs) are characterized by the presence of a variable number of BIR domains. These homologues have been identified in yeasts, nematodes, flies and higher vertebrates [21–23]. In Drosophila, four kinds of IAP homologues (Thread or IAP1, IAP2, Bruce and Deterin or CG12265) have been found . We analyzed the phylogenetic relationships of putative gene 01, 06 and 24 with other BIR domains in several organisms (see Additional file 9). The BIR domains in the putative gene 24 were clustered together with the BIR domains found in black tiger shrimp IAP gene, suggesting the putative gene 24 may have the same function as black tiger shrimp IAP . Particularly of interest, putative gene 06 contains five BIR domains and this is the first report on BIRPs containing more than three BIR domains. BIR domains are known to play important roles in protein-protein interactions and it has been shown that the presence of multiple BIR domains in a single protein molecule increases the affinity of BIRPs to a target protein. In addition, the range of target molecules in which BIRPs can interact also increases with the number of BIR domains . Hence, putative gene 06 that has five BIR domains may be a novel BIRP that has a different function.
Furthermore, of the other 24 genes, we found seven genes homologous to ORFs in WSSV. It is known that certain mammalian dsDNA viruses, such as herpesvirus and poxvirus, mimic structure and function of host genes to evade detection and destruction by the host immune system . Similarly, "potential horizontal gene transfers" has been found in baculoviruses, infectious pathogens of insects [27, 28], hence such viral genome structure can be regarded as repositories of important information about host immune processes . The presence of multiple WSSV-like genes in kuruma shrimp genome strongly suggests similar mimicking mechanisms or horizontal gene transfers can also be seen in this virus group. Moreover, with the absence of homologous proteins in the current database, this information will provide a good starting point for understanding unknown WSSV-host interactions.
The first identification of multiple duplications of large DNA segments in the shrimp genome
As high-resolution whole genome sequences are not yet available for Malacostraca or Decapoda species, it is difficult to make any conclusion if multiple copies of peculiar large DNA segments (Mj024A04-sequence) found in kuruma shrimp are also present in other species. However, micro-synteny analysis revealed that Mj024A04-sequence is not found in two other arthropod genomes, Drosophila and Daphnia, suggesting that the duplicated large DNA fragments have occurred after establishment of Malacostraca in the Crustacea.
It is also unclear whether the redundancy is the result of polyploidization or segmental duplication. Previous studies revealed a wide range of chromosome numbers and variation of genomic DNA content in several species in Decapoda, suggesting the possibility of polyploidization. However, re-association kinetics of genomic DNA and electrophoretic analysis of enzyme polymorphism have suggested that polyploidization is considered to be a rare event [30, 31]. Thus, we assumed that highly redundant large DNA segments in the kuruma shrimp may have arose from segmental duplication events.
Segmental duplications (SDs) are duplicated blocks of genomic DNA, typically ranging in size from 1 kb to 200 kb . SDs are composed of apparently normal genomic DNA containing high-copy repeats and gene sequences with intron-exon architecture, hence it is difficult to detect a priori without having well-assigned genome information . In this regard, the human genome is the most studied genome about SDs. Human reference genome contains an abundance of large DNA segments with various copy numbers (from 2 to 18), representing ≥ 5% of the genome, that have been accumulated through evolution over 40 million years . These duplications are shown to be clustered up to 10-fold enrichment within pericentromeric and subtelomeric regions of human chromosomes .
SDs are also reported in Drosophila melanogaster. In fly, SDs account for ~1.4% of the genome (1.66 Mbp/118.35 Mbp), ranging from 346 bp to 81.1 kb in length. The Drosophila genome appears to be significantly poor in large (>10 kb) duplicated blocks with only 7.21% as compared to human genome. The chromosome 4 that appears to be enriched in heterochromatic domains and the pericentromeric regions of the chromosomes X, 2 and 3 in Drosophila have also high SD density.
It is reported that subtelomeres are notably rich in degenerate telomeric repeats relative to adjacent single-copy sequences or other genomic regions (~10- and ~100-fold, respectively) in the human genome . We analyzed the number of kuruma shrimp BAC clones harboring GGTTA repeats based on colony hybridization . Results showed that the rate of GGTTA-positive BAC clone are found to be 3 times higher in the BAC clones positive for F, M or R probes than GGTTA-positive rate in all BAC clones tested (45.4% and 17.1%, respectively), suggesting that Mj024A04-sequence and its duplicates are located predominantly in subtelomeric regions and perhaps in pericentromeric regions.
The absence of transcripts of putative genes in Mj024A04 in several tissues of an adult shrimp
We attempted to detect RNA transcripts for some putative genes analyzed in several tissues of kuruma shrimp but gene expression was so weak despite their high copy number. Together with subtelomeric localization, we considered that this low level of gene expression might be caused by epigenetic control mechanisms, such as CpG-methylation, histone-hypoacetylation and histone-methylation. Although we have attempted to detect CpG-methylation in Mj024A04 segments by genomic Sourthern blot analysis with CpG-methylation insensitive restriction enzyme Msp I and its sensitive isoschizomer Hpa II, we could not detect any CpG-methylation indicating that transcription level of Mj024A04 is strictly suppressed by other factors (see Additional file 10).
Genome rearrangements are common phenomena in the eukaryotes, which facilitate not only species diversification but also genetic variation within species. Studies based on the whole genome sequence in primates suggest that significant proportion of the lineage-specific duplication results in different gene expression pattern and mechanistic consequence of changes in the chromosome structure . Furthermore, in a study on Plasmodium falciparum, a causative agent of severe human malaria, the authors revealed that eight SDs, which are located on seven different chromosomes, have copy number polymorphism among different strains. The expression levels of the genes found within the SDs are also correlated in part with the gene copy number . These studies strongly suggest that SDs are widely distributed and play significant roles in making biological differences among closely related species. Biological significance of SDs in kuruma shrimp Marsupenaeus japonicus is still obscure due to lack of the entire genome sequence information of Decapoda species. Nonetheless, it is interesting how SDs and numerous putative genes such as WSSV homologues act in this species. Furthermore, such hyper-expansion of DNA segments should be taken into serious consideration in whole-genome sequencing and effective construction of genetic linkage maps of this economically important species.
BAC library construction and sequencing of BAC ends
Kuruma shrimp BAC library (MjBL2) was constructed according to the protocol as described previously, with minor modification . Briefly, hemocytes from 13 kuruma shrimps were embedded in 1% low melting agarose plugs and digested in the presence of proteinaseK. Those high molecular weight DNA were partially digested with Hin dIII and size fractionated by electrophoresis on CHEF DR-II apparatus (BioRad). Over 150 kb genomic DNA was extracted with NaI and GELase (EPICENTRE), ligated into pBAC-lac vector and used for transformation of E. coli DH10B T1 phage resistant cells (Invitrogen). A total of 49,152 BAC clones were picked and arrayed on 128 microtiter plates each with 384 wells by Q-Pix (Genetix). High Density Replica (HDR) filters were made using Bio Grid (Bio Robotics). BAC-end sequencing was performed in Dragon Genomics Center (Takara Bio, Shiga, Japan) and retrieved AB1 files were processed for clustering using Phred, Phrap and Consed [38–40]. To identify significant matches to the deposited sequences in the public database, BLASTN and BLASTX algorithms were employed after masking repeat elements with RepeatMasker (version 3.2.8)  using cross-match as a search engine.
Shotgun sequencing, data assembly and analysis
Shotgun library was made from purified DNA of Mj024A04 BAC clone using shotgun library construction kit (Invitrogen). Colony PCR conditions were; an initial denaturation step for 5 min at 95°C, followed by 35 cycles of denaturation step at 95°C for 30 sec, annealing at 55°C for 30 sec and extension step at 72°C for 2 min, and a final extension step at 72°C for 5 min to complete the reaction. M13 forward and reverse primers and rTaq DNA polymerase (Bioneer) mixed in a total volume of 15 μ l was used for the colony PCR. Excess primers and dNTPs were removed by ExoSAP-IT (GE Healthcare), following manufacturing instruction. Sequence reactions were performed with SP6 and T7 primers using BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) following manufacturing instruction and electrophoresed with ABI 3130xl Genetic Analyzer (Applied Biosystems). Retrieved AB1 files were base-called and assembled by Phred, Phrap and Consed [38–40]. The sequence gaps were closed using a combination of re-sequencing of shotgun clones and BAC direct sequencing. Presumative genes were predicted by GENSCAN . Amino acid sequences of presumed genes were annotated using BLASTP algorithm. Micro-synteny analysis was performed by applying TBLASTN algorithm onto two databases FlyBase (version FB2008_02)  and wFleaBase (first release, 2007/07/07) .
Southern blot hybridization analysis
Kuruma shrimp genomic DNA (20 μ g) was digested completely with Bam HI, Eco RI, Hin dIII, Bam HI and Eco RI, Bam HI and Hin dIII, Eco RI and Hin dIII, Bgl II and Dra I, respectively and separated using 0.7% agarose gel. After hydrolysis in 0.25 N HCl and denaturation in 1.5 M NaOH and 0.5 M NaCl, the gel was then blotted onto positive charged nylon membranes (Pall Gelman Laboratory) in 0.4 N NaOH. Hybridization was performed with the probe labelled with [α-32P]dCTP using Random Primer DNA Labeling Kit Ver. 2 (Takara) at 42°C in PerfectHyb hybridization solution (TOYOBO) for 4 hrs and washing were carried out 3 times with 2× SSC/0.1% SDS at 50°C for 30 min. The autoradiogram was developed with a STARION FLA-9000 Reader (Fujifilm).
Chromosomal localization of Mj024A04-sequence
Mj024A04 BAC DNA was fluorescent labeled as a FISH probe by nick translation method using the FISH Tag DNA Multicolor kit (Invitrogen) according to manufacture's instructions. The specimens were prepared from the testis cells according to the previous report . After the final heat denaturation of labeled probe and heat denaturation and dehydration of the specimens, hybridization was performed in 2× SSC/65% formamide hybridization buffer at 37°C for 24 hrs. Washings were performed three times with 2× SSC/50% formamide, 1× SSC and 4× SSC/0.1% Tween 20, respectively at 45°C for 5 min. Finally, the specimens were counterstained with Hoechst 33258 (Invitrogen) and examined under a Nikon Eclipse E600 epifluorescence microscope (Nikon). Photographs were taken with a MicroMax Cooled-CCD and IPLab software (Nippon Roper).
Copy number estimation of Mj024A04 genes
Primer pairs for quantitative PCR were designed for 4 predicted genes (gene 01, 09, 16 and 27) and the putative single copy gene, transglutaminase (TGase; DQ436474), using Primer Express Software Version 3.0 (Applied Biosystems) (primers were shown in Additional file 4). 0.1 ng of the kuruma shrimp genomic DNA were prepared from the brain, hemocytes, heart, testis, muscle, swimleg, intestine and 3 larvae were used as template in a 20 μ l reaction mixture containing 10 μ l of SYBR Green PCR Master Mix reagent (Applied Biosystems), 1 μ l of genomic DNA template or plasmid containing target DNA sequences as standard, 8.2 μ l of deionized water and 0.4 μ l of 10 μ M forward and reverse primer. PCR reactions were performed and quantified by the 7300 Real-Time PCR System (Applied Biosystems). All of PCR reactions were performed as follows: 50°C for 2 min and 95°C for 10 min, followed by 40 cycles of 95°C for 15 sec and 60°C for 1 min, with a dissociation stage at 95°C for 15 sec, 60°C for 30 sec and 95°C for 15 sec. The PCR reaction was repeated three times for each template. The copy number of each putative gene was estimated by absolute quantification method and Ct values of the amplified target genomic DNA fragments in each sample were computed by the SDS program, using default parameters.
BAC genotyping using microsatellites
once the outcome of K N by the random sampling of size N is observed, a likelihood function of θ (say L(θ)) can be obtain through its probability distribution, which is calculated by the recursive formula above. The parameter θ is then estimated by maximizing L(θ). The 100(1-α)% confidence interval is also derived by the likelihood profile as , where is the maximum likelihood estimated of θ and χ2(1-α) is the upper 100 α-percent of the χ2 distribution with the degree of freedom 1.
1. Vertebrate Section, National Fisheries Research and Development Institute, 940 Quezon Ave., Quezon City, 1103, Philippines
2. Biology Department, Ateneo de Manila University, Katipunan Ave., Loyola Heights, Quezon City, 1108 Philippines
RM: Charoen Pokphand Food Public Company Limited, Shrimp Culture Research Center, 82/2 M 4, Rama II Rd., Bangtorat, Amphor Muang, Samutsakorn City, 74000 Thailand
This work was supported by the Sasakawa Scientific Research Grant from The Japan Science Society and Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
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