Identification of pigmentation genes in skin, muscle and tail of a Thai-flag variety of Siamese fighting fish Betta splendens

Pigmentation genes expressed in skin, body muscle and tail of Thai-flag compared with Blue, White and Red varieties of Siamese fighting fish Betta splendens were identified. In total, 22,919 new unigenes were found. Pearson correlation and PCA analysis revealed that expression profiles of genes in muscle, skin and tail across solid color variety were similar. In contrast, those in skin and red tail part of Thai-flag were closely related but they showed different expression profiles with the white tail part. Moreover, 21,347-64,965 SNPs were identified in exonic regions of identified genes. In total, 28,899 genes were differentially expressed between paired comparisons of libraries where 13,907 genes (48.12 %) were upregulated and 14,992 genes (51.88 %) were downregulated. DEGs between paired libraries were 106-5775 genes relative to the compared libraries (56-2982 and 50-2782 for upregulated and downregulated DEGs). Interestingly, 432 pigmentation genes of B. splendens were found. Of these, 297 DEGs showed differential expression between varieties. Many DEGs in melanogenesis (Bsmcr1r, Bsmcr5r, and Bsslc2a15b), tyrosine metabolism (Bstyr, Bstyrp1b and Bsdct), stripe repressor (BsAsip1 and BsAsip2b), pteridine (Bsgch2) and carotenoid (BsBco2) biosynthesis were downregulated in the Thai-flag compared with solid color varieties. Expression of Bsbco1l, Bsfrem2b, Bskcnj13, Bszic2a and Bspah in skin, muscle and tail of Thai-flag, Blue, Red and White varieties was analyzed by qRT-PCR and revealed differential expression between fish varieties and showed anatomical tissue-preferred expression patterns in the same fish variety. The information could be applied to assist genetic-based development of new B. splendens varieties in the future.

Assessing Genetic Diversity of Wild Populations and Different Color Varieties for Genetic Improvement of Siamese Fighting Fish Betta splendens in Thailand

To establish sustainable resources and founder populations for genetic improvement of the Siamese fighting fish Betta splendens, genetic diversity in wild and hatchery stocks was examined using mitochondrial (mt) DNA genes cytochrome b (cytb), 16S ribosomal DNA (16S rDNA), and cytochrome oxidase subunit I (COI), and eight microsatellite loci. Based on mtDNA sequences, restrictive levels of polymorphism (0, 3, and 1 substitutions) were observed in this study. For analysis of microsatellites, fluorescent multiplex PCR was developed, and subsequently identifying moderate levels of observed (H_o = 0.4488) and expected (H_e = 0.6627) heterozygosities and a high number of alleles per locus (15.125 alleles) for overall samples. Comparison of Siamese fighting fish from different sources revealed large genetic differences between pairs of farmed fish (eight groups) and between wild (three geographic locations) and farmed fish (P < 0.0031 following Bonferroni correction). This suggested limited exchanges of genetic resources between commercial farms. When different color varieties of B. splendens were compared, large genetic distances and significant F_ST estimates and genetic heterogeneity were found (P < 0.0031). Effective population sizes (N_e) were estimated and two farms (NP2-2BS and BK1-4BS) showed N_e greater than 10. Among color varieties, Multi-colors and Blue revealed reasonable N_e (large and 27.9), but lower N_e values (3.6-8.4) were found for the remaining color varieties. These results indicate an urgent need for the establishment of gene pool resources of B. splendens for effective genetic improvement of Siamese fighting fish in Thailand.

Transcriptome comparison for identification of pigmentation-related genes in different color varieties of Siamese fighting fish Betta splendens

Transcriptome comparison was performed to identify genes expressed in skin, muscle and tails of mono-color (Red, Blue, Black, White and Yellow), bi-color (Cambodian) and multi-color (Marble) varieties of Siamese fighting fish Betta splendens. In total, 163,140 unigenes covering 26.348 Gb were found. Of these, 93,899 (57.55 %) unigenes significantly matched at least one database. In total, 5039 differentially expressed genes (DEGs) were found where 2415 genes (47.93 %) showed higher expression and 2624 genes (52.07 %) showed lower expression for all pairwise comparisons. DEGs between paired color varieties were 133-443. Of these, 38-220 genes were more highly expressed while 37-280 genes were more lowly expressed relative to the compared varieties. A total of 897 sequences (148 genes) significantly matched pigmentation-related genes of Danio rerio (E-value < 1e-06). Of these, 19 DEGs were identified. Examples are tyrosinase-related protein 1a (BsTyrp1a), epidermal growth factor receptor (BsEgfr) and neurofibronin 1a (BsNf1a). Moreover, 711,123 SNPs were identified and 1365 of these were located in pigmentation-related genes. Interestingly, an A > C₄₇₄ SNP in the gene BsTrpm7 and an indel (position 3571) in the BsItgb1a gene were found only in Cambodian. A C > T₂₅₂₀ SNP in BsFzd4 and 10 of 11 SNPs in BsTyrp1a were found only in Black. Different expression levels (P < 0.05) were found for tyrosinase (BsTyr), BsTyrp1a, BsNf1a and BsEgf1 among skin, body muscle and tails of the same variety and among the same tissues of different varieties (Red, Green, Blue, Black, Cambodian and Multi-colors, N = 5 each).

A SNP of the hemocyanin gene (LvHc) is a marker for high growth and ammonia-tolerance in Pacific white shrimp Litopenaeus vannamei

Expression levels of hemocyanin (LvHc), activating transcription factor 4 (LvAtf4), glutathione S-transferase (LvGst), caspase 2 (LvCasp2) and anti-lipopolysaccharide factor (LvAlf) were examined in the hepatopancreas of Pacific white shrimp Litopenaeus vannamei juveniles exposed to a lethal concentration of ammonia-N (32.15 mg/l). The expression levels of all transcripts except LvAlf were significantly greater (P < 0.05) in tolerant shrimp (Lv-AT; N = 30) that survived up to 72 h post treatment (hpt) than in susceptible shrimp (Lv-AS24 and Lv-AS72; N = 45 and 15), that died within 24 h or between 24 and 72 hpt, respectively. Subsequently, effects of non-lethal concentrations of ammonia-N (control, 10 and 20 mg/l) on the expression of LvHc in juvenile shrimp were examined. Compared to the control, expression levels of LvHc transcripts in hemocytes and the hepatopancreas of tested shrimp changed after exposure to ammonia-N. One SNP (C > T₅₄₅) was found in the LvHc₃₂₂ gene segment. Real-time PCR amplification of specific alleles (real-time PASA) was developed for detection of C > T₅₄₅ genotypes. Juveniles in the lethal exposure test that carried a C/T₅₄₅ genotype showed a greater average body weight and total length (8.46 ± 0.36 g and 10.05 ± 0.16 cm) than those with a C/C₅₄₅ genotype (7.48 ± 0.31 g and 9.60 ± 0.13 cm) (P < 0.05). Similar results were found in the second generation (G2) of a growth-improved stock (3 and 4 families of BIOTEC-G2-L1 and BIOTEC-G2-L2) and in commercially farmed shrimp (2 groups). Accordingly, expression levels and SNP of LvHc can serve as markers for selection high growth performance in ammonia-tolerant L. vannamei.

Isolation and expression analysis of Bystin 1 transcript and protein during ovarian development of the giant tiger shrimp Penaeus monodon

The full-length cDNA of bystin isoform 1 (PmBys1) of the giant tiger shrimp Penaeus monodon was characterized. It was 1553 bp in length containing an ORF of 1365 bp corresponding to a polypeptide of 454 amino acids. The level of PmBys1 mRNA in ovaries was greater than that in other tissues of females and in testes of males in both juveniles and wild broodstock (P < .05). In non-ablated wild female broodstock, PmBys1 mRNA significantly and progressively increased in ovaries from stage I of development, peaking at stage IV (P < .05). Its level in stages I-IV of eyestalk-ablated broodstock was greater than that in non-ablated broodstock (P < .05). Injection of exogenous serotonin (50 μg/g body weight) into 18-month-old shrimp resulted in a significantly increase of ovarian PmBys1 mRNA at 6-48 h post injection (hpi) (P < .05). PmBys1 protein (52 kDa) was found in ovarian stages I-V of non-ablated wild broodstock and II-IV of ablated wild broodstock, respectively. Along with the 52 kDa band, immunoreactive bands of 50 and 43 kDa were also observed in ovarian stages II-IV of both non-ablated and ablated broodstock and in ovaries of post-spawning broodstock. The 43 KDa band was not observed in ovarian stage I of wild female broodstock or in premature juveniles. PmBys1 protein was localized in the ooplasm of previtellogenic oocytes, nucleo-cytoplasmic compartments of vitellogenic oocytes and cortical rods of mature oocytes in wild broodstock. The results implied a possible role for PmBys1 during ovarian development in P. monodon.

Characterization of transforming growth factor beta regulator 1-like and association between its expression levels and growth of the giant tiger shrimp Penaeus monodon

Molecular markers that allow selection of juveniles and broodstock with improved growth performances are useful for the shrimp industry. Here, the full-length cDNA of transforming growth factor beta regulator 1-like (PmTbrg1-l) in the giant tiger shrimp Penaeus monodon was determined. It was 1184 bp in length and contained an open reading frame (ORF) of 975 bp corresponding to a deduced polypeptide of 324 amino acids. Successful RNA interference (RNAi) carried out using juveniles injected with PmTbrg1-l dsRNA revealed reduced levels of PmTbrg1-l and myostatin (PmMstm) in hemocytes when compared to shrimp injected with saline solution and GFP dsRNA (P < .05). Associations between single-strand conformational polymorphism (SSCP) patterns or single nucleotide polymorphism (SNP) patterns and growth-related parameters (average body weight and total length) were examined. Juveniles with pattern III (corresponding to A/A₉₁₈; N = 37) showed a trend for greater average body weight and total length than those with patterns II (G/G₉₁₈; N = 42) and IV (A/G₉₁₈; N = 75). The expression level of PmTbrg1-l in the hepatopancreas of females was significantly higher than that in males (P < .05) in two sample sets of three-month-old domesticated juveniles (N = 59 and 50; P < .05). Moreover, its expression level in large-size juveniles was significantly higher than that in medium-size and small-size juveniles in both groups of samples (P < .05). Results indicated that PmTbrg1-l is functionally related with growth of P. monodon.

Bioinformatics characterization of a cathepsin B transcript from the giant river prawn, Macrobrachium rosenbergii: Homology modeling and expression analysis after Aeromonas hydrophila infection

Cathepsin B is a lysosomal proteolytic enzyme that has been suggested to play a role in pathological processes of immune system. In this study, the full-length cDNA sequence of cathepsin B transcript in the giant river prawn Macrobrachium rosenbergii (MrCTSB) was obtained from 454 pyrosequencing of cDNAs from hepatopancreas and muscle. It was 1158 bp in length, containing an open reading frame (ORF) of 987 bp corresponding to 328 amino acids. The predicted molecular mass and pI of MrCTSB protein was 36.04 kDa and 4.73. The major characteristics of MrCTSB protein consisted of a propeptide of C1 peptidase family at the N-terminus and a cysteine protease (Pept_C1) domain at the C-terminus. The 3-dimentional structure of MrCTSB was constructed by computer-assisted homology modeling. The folding of MrCTSB was highly conserved to human CTSB structure and the modeled MrCTSB displayed characteristics of cysteine proteinases superfamily. The docking study was performed to investigate binding interactions between known inhibitors against MrCTSB. Known inhibitors were oriented in the groove of catalytic site cleft. They bound to subsites from S2, S1, S1', and S2', respectively, with key residues in each subsite. Challenge of juvenile prawns with Aeromonas hydrophila revealed that the MrCTSB transcript in hepatopancreas significantly increased at 60-96 h post injection (hpi). This suggested that MrCTSB may play roles in innate immunity of M. rosenbergii. Our results provide useful information for a more comprehensive study in immune-related functions of MrCTSB.

Transcriptome-based discovery of pathways and genes related to reproduction of the black tiger shrimp (Penaeus monodon)

The black tiger shrimp (Penaeus monodon) is an aquatic animal with considerable economic importance. Poor reproductive maturation in captivity impedes sustainable aquaculture production of this species. This study aims to provide transcriptomic information on reproductive organs using 454 pyrosequencing technology. The transcriptome analysis of ovaries and testes revealed 41,136 transcripts with 20,192 contigs. We found novel sets of transcripts completing several important reproductive pathways such as gonadotropin-releasing hormone (GnRH) signaling and progesterone-mediated oocyte maturation. In addition, we found transcripts encoding for receptors crucial for initiation of the maturation process, such as GnRH receptor (GnRHR), voltage-dependent calcium channel L type alpha-1C (CACNA1C) and epidermal growth factor receptor (EGFR). Moreover, we found a putative novel vigillin encoding for an estrogen-induced polysome-associated protein, which has not been reported in penaeid shrimp. These results suggest that the regulatory mechanism of the pathways important to reproductive maturation might be similar to those in the vertebrate. The obtained data will consequently accelerate the study of reproductive biology of this important species to ensure a sustainable shrimp farming industry.

Differentially expressed transcripts in stomach of Penaeus monodon in response to AHPND infection

Acute Hepatopancreatic Necrosis Disease (AHPND) is an emerging disease in aquacultured shrimp caused by a pathogenic strain of Vibrio parahaemolyticus. As with several pathogenic bacteria, colonization of the stomach appeared to be the initial step of the infection for AHPND-causing Vibrio. To understand the immune responses in the stomach of black tiger shrimp (Penaeus monodon), differentially expressed transcripts (DETs) in the stomach during V. parahaemolyticus strain 3HP (VP3HP) infection was examined using Ion Torrent sequencing. From the total 42,998 contigs obtained, 1585 contigs representing 1513 unigenes were significantly differentially expressed with 1122 and 391 unigenes up- and down-regulated, respectively. Among the DETs, there were 141 immune-related unigenes in 10 functional categories: antimicrobial peptide, signal transduction pathway, proPO system, oxidative stress, proteinases/proteinase inhibitors, apoptotic tumor-related protein, pathogen recognition immune regulator, blood clotting system, adhesive protein and heat shock protein. Expression profiles of 20 of 22 genes inferred from RNA sequencing were confirmed with the results from qRT-PCR. Additionally, a novel isoform of anti-lipopolysaccharide factor, PmALF7 whose transcript was induced in the stomach after challenge with VP3HP was discovered. This study provided a fundamental information on the molecular response in the shrimp stomach during the AHPND infection that would be beneficial for future research.

Cloning, expression, and characterization of Aureobasidium melanogenum lipase in Pichia pastoris

cDNA of Aureobasidium melanogenum lipase comprises 1254 bp encoding 417 amino acids, whereas genomic DNA of lipase comprises 1311 bp with one intron (57 bp). The lipase gene contains a putative signal peptide encoding 26 amino acids. The A. melanogenum lipase gene was successfully expressed in Pichia pastoris. Recombinant lipase in an inducible expression system showed the highest lipase activity of 3.8 U/mL after six days of 2% v/v methanol induction. The molecular mass of purified recombinant lipase was estimated as 39 kDa using SDS-PAGE. Optimal lipase activity was observed at 35–37 °C and pH 7.0 using p-nitrophenyl laurate as the substrate. Lipase activity was enhanced by Mg2+, Mn2+, Li+, Ca2+, Ni2+, CHAPS, DTT, and EDTA and inhibited by Hg2+, Ag+, SDS, Tween 20, and Triton X-100. The addition of 10% v/v acetone, DMSO, p-xylene, and octanol increased lipase activity, whereas that of propanol and butanol strongly inhibited it.

Characterization and expression of cell division cycle 2 (Cdc2) mRNA and protein during ovarian development of the giant tiger shrimp Penaeus monodon

The meiotic maturation of oocytes is regulated by the maturation-promoting factor (MPF), a complex of Cdc2 (Cdk1) and Cyclin B. Here, the complete open reading frame (ORF) of Cdc2 in Penaeus monodon was characterized. PmCdc2 were 900bp in length corresponding to a polypeptide of 299 amino acids with the conserved Thr14, Tyr15 and Thr161 residues. Quantitative real-time PCR indicated that the expression level of PmCdc2 in wild intact broodstock was significantly increased in stages II (vitellogenic) and III (early cortical rod) ovaries relative to stage I (previtellogenic) ovaries and peaked in stage IV (mature) ovaries (P<0.05). The expression level of PmCdc2 in stages I-IV ovaries of eyestalk-ablated broodstock was greater than that of the same ovarian developmental stages in intact broodstock (P<0.05). Expression levels of PmCdc2 in ovaries of 18-month-old P. monodon upon 5-HT injection (50μg/g body weight) were significantly increased at 1hour post injection (hpi, P<0.05). Recombinant PmCdc2 protein and its polyclonal antibody were successfully produced. Western blot analysis revealed the expected 34kDa band (PmCdc2) along with a smaller band of 23kDa (ribosomal protein S3) in ovaries of juveniles and various ovarian stages of broodstock. Using phospho-Cdc2 (Thr161) polyclonal antibody, the positive signal of 34kDa was observed in all ovarian stages but the most intense signal was found in stage IV ovaries. Results in the present study indicated that PmCdc2 gene/protein plays an important role in the development and maturation of oocytes/ovaries in P. monodon.

Characterization, expression and localization of valosin-containing protein in ovaries of the giant tiger shrimp Penaeus monodon

Valosin-containing protein (VCP), a member of the ATPase-associated with diverse cellular activity (AAA) family, was identified from the giant tiger shrimp (Penaeus monodon). The full-length cDNA of the PmVCP mRNA consisted of 2,724 bp containing an ORF of 2,367 bp corresponding to a deduced polypeptide of 788 amino acids. The deduced PmVCP protein contained two putative Cdc48 domains (positions 17-103, E-value=2.00e-36 and 120-186, E-value=3.60e-11) and two putative AAA domains (positions 232-368, E-value=3.67e-24 and 505-644, E-value=3.73e-25). PmVCP mRNA expression in ovaries was greater than that in testes in both juveniles and broodstock. PmVCP was significantly up-regulated in stages II and IV ovaries in intact wild broodstock (P<0.05) but it was not differentially expressed during ovarian development in eyestalk-ablated broodstock (P>0.05). The expression level of PmVCP mRNA in ovaries of 14-month-old shrimp was not affected by progesterone injection (0.1μg/g body weight, P>0.05). In contrast, exogenous 5-HT administration (50μg/g body weight) resulted in an increase of PmVCP mRNA in ovaries of 18-month-old shrimp at 6 and 24h post-injection (hpi) (P<0.05). The rPmCdc48-VCP protein and its polyclonal antibody were successfully produced. Cellular localization revealed that PmVCP was localized in the ooplasm of previtellogenic oocytes. Subsequently, it was translocated into the germinal vesicle of vitellogenic oocytes. Interestingly, PmVCP was found in nucleo-cytoplasmic compartments, in the cytoskeletal architecture and in the plasma membrane of mature oocytes in both intact and eyestalk-ablated broodstock.

Identification of reproduction-related proteins and characterization of proteasome alpha 3 and proteasome beta 6 cDNAs in testes of the giant tiger shrimp Penaeus monodon

Cellular proteomic analysis was carried out to identify reproduction-related proteins in testes of wild and domesticated broodstock of Penaeus monodon. In total, 642 protein spots were characterized and 287 spots (44.70%) significantly matched protein sequences in the databases (P<0.05). To examine a role of the proteasome system in testicular development of P. monodon, the expression profiles of proteasome alpha 3 subunit (PmPsma3) and proteasome beta 6 (PmPsmb6) mRNA in different groups of domesticated shrimp and in wild broodstock were examined. The expression levels of these transcripts in testes of 18-month-old domesticated shrimp were significantly lower than those of wild broodstock (P<0.05). Interestingly, the expression levels of testicular PmPsma3 and PmPsmb6 in 18-month-old shrimp were significantly increased at 24 h following serotonin injection (50 μg/g body weight). Results suggested that reduced degrees of maturation in captive P. monodon males may be partially resolved by exogenous 5-HT administration.

Identification of reproduction-related proteins and characterization of the protein disulfide isomerase A6 cDNA in ovaries of the giant tiger shrimp Penaeus monodon

Proteomic analysis was carried out for identification of proteins functionally involved in ovarian development of the giant tiger shrimp (Penaeus monodon). A total of 335 protein spots including 183 spots from vitellogenic (stage II) and 152 spots from mature (stage IV) ovaries of intact P. monodon broodstock were examined. Of these, 75 (40.98%) and 59 (38.82%) spots significantly matched known proteins in the databases, respectively. In addition, 270 protein spots including 167 and 103 spots from respective ovarian stages of eyestalk-ablated broodstock were also characterized. A total of 95 (56.89%) and 62 (60.19%) spots matched known proteins, respectively. Among differentially expressed reproduction-related proteins, the full-length cDNA of protein disulfide isomerase A6 (PmPDIA6) was further characterized by RACE-PCR. PmPDIA6 was 1946bp in length containing an open reading frame (ORF) of 1293bp corresponding to a polypeptide of 430 amino acids. PmPDIA6 was up-regulated at stage III ovaries in intact shrimp (P<0.05). Interestingly, eyestalk ablation resulted in a lower expression level of PmPDIA6 in each stage of ovarian development compared to that of intact broodstock (P<0.05). Results in this study clearly indicated the potential of cellular proteomic studies and gene expression analysis for identification of proteins/genes differentially expressed during ovarian development of P. monodon.

Molecular cloning and expression analysis of the Mitogen-activating protein kinase 1 (MAPK1) gene and protein during ovarian development of the giant tiger shrimp Penaeus monodon

Isolation and characterization of genes and/or proteins differentially expressed in ovaries are necessary for understanding ovarian development in the giant tiger shrimp (Penaeus monodon). In this study, the full-length cDNA of P. monodon mitogen-activating protein kinase 1 (PmMAPK1) was characterized. PmMAPK1 was 1,398 bp in length containing an open reading frame of 1,098 bp that corresponded to a polypeptide of 365 amino acids. PmMAPK1 was more abundantly expressed in ovaries than in testes of P. monodon. Quantitative real-time PCR revealed differential expression levels of PmMAPK1 mRNA during ovarian development of intact broodstock, where it peaked in early cortical rod (stage III) ovaries (P < 0.05) and slightly decreased afterwards (P > 0.05). Likewise, the expression level of PmMAPK1 in early cortical rod and mature (IV) ovaries was significantly greater than that in previtellogenic (I) and vitellogenic (II) ovaries of eyestalk-ablated broodstock (P < 0.05). The PmMAPK1 transcript was localized in ooplasm of previtellogenic oocytes. In intact broodstock, the expression of the PmMAPK1 protein was clearly increased from previtellogenic ovaries in subsequent stages of ovarian development (P < 0.05). In contrast, the level of ovarian PmMAPK1 protein was comparable during oogenesis in eyestalk-ablated broodstock (P > 0.05). The PmMAPK1 protein was localized in ooplasm of previtellogenic and vitellogenic oocytes. It was also detected around the nuclear membrane of early cortical rod oocytes in both intact and eyestalk-ablated broodstock. Results indicated that PmMAPK1 gene products seem to play functional roles in the development and maturation of oocytes/ovaries in P. monodon.

A cDNA microarray, UniShrimpChip, for identification of genes relevant to testicular development in the black tiger shrimp (Penaeus monodon)

Background

Poor reproductive maturation in captive male broodstock of the black tiger shrimp (Penaeus monodon) is one of the serious problems to the farming industries. Without genome sequence, EST libraries of P. monodon were previously constructed to identify transcripts with important biological functions. In this study, a new version of cDNA microarray, UniShrimpChip, was constructed from the Peneaus monodon EST libraries of 12 tissues, containing 5,568 non-redundant cDNA clones from 10,536 unique cDNA in the P. monodon EST database. UniShrimpChip was used to study testicular development by comparing gene expression levels of wild brooders from the West and East coasts of Thailand and domesticated brooders with different ages (10-, 14-, 18-month-old).

Results

The overall gene expression patterns from the microarray experiments revealed distinct transcriptomic patterns between the wild and domesticated groups. Moreover, differentially expressed genes from the microarray comparisons were identified, and the expression patterns of eight selected transcripts were subsequently confirmed by reverse-transcriptase quantitative PCR (RT-qPCR). Among these, expression levels of six subunits (CSN2, 4, 5, 6, 7a, and 8) of the COP9 signalosome (CSN) gene family in wild and different ages of domesticated brooders were examined by RT-qPCR. Among the six subunits, CSN5 and CSN6 were most highly expressed in wild brooders and least expressed in the 18-month-old domesticated group; therefore, their full-length cDNA sequences were characterized.

Conclusions

This study is the first report to employ cDNA microarray to study testicular development in the black tiger shrimp. We show that there are obvious differences between the wild and domesticated shrimp at the transcriptomic level. Furthermore, our study is the first to investigate the feasibility that the CSN gene family might have involved in reproduction and development of this economically important species.

Genetic differentiation of the stingless bee Tetragonula pagdeni in Thailand using SSCP analysis of a large subunit of mitochondrial ribosomal DNA

Genetic diversity and population differentiation of the stingless bee Tetragonula pagdeni (Schwarz) was assessed using single-strand conformational polymorphism (SSCP) analysis of a large subunit of the ribosomal RNA gene (16S rRNA). High levels of genetic variation among individuals within each population (North, Northeast, Central, Prachuap Khiri Khan, Chumphon, and Peninsular Thailand) of T. pagdeni were observed. Analysis of molecular variance indicated significant genetic differentiation among the six geographic populations (Φ (PT) = 0.28, P < 0.001) and between samples collected from north and south of the Isthmus of Kra (Φ (PT) = 0.18, P < 0.001). In addition, Φ (PT) values between all pairwise comparisons were statistically significant (P < 0.01), indicating strong degrees of intraspecific population differentiation. Therefore, PCR-SSCP is a simple and cost-effective technique applicable for routine population genetic analyses in T. pagdeni and other stingless bees. The results also provide an important baseline for the conservation and management of this ecologically important species.

Isolation and characterization of genes functionally involved in ovarian development of the giant tiger shrimp Penaeus monodon by suppression subtractive hybridization (SSH)

Suppression subtractive hybridization (SSH) libraries between cDNA in stages I (previtellogenic) and III (cortical rod) ovaries of the giant tiger shrimp (Penaeus monodon) were established. In all, 452 ESTs were unidirectionally sequenced. Sequence assembly generated 28 contigs and 201 singletons, 109 of which (48.0%) corresponding to known sequences previously deposited in GenBank. Several reproduction-related transcripts were identified. The full-length cDNA of anaphase promoting complex subunit 11 (PmAPC11; 600 bp with an ORF of 255 bp corresponding to a polypeptide of 84 amino acids) and selenoprotein Mprecursor (PmSePM; 904 bp with an ORF of 396 bp corresponding to a polypeptide of 131 amino acids) were characterized and reported for the first time in penaeid shrimp. Semiquantitative RT-PCR revealed that the expression levels of PmSePM and keratinocyte-associated protein 2 significantly diminished throughout ovarian development, whereas Ser/Thrcheckpoint kinase 1 (Chk1), DNA replication licensing factor mcm2 and egalitarian were down-regulated in mature ovaries of wild P. monodon (p < 0.05). Accordingly, the expression profiles of PmSePM and keratinocyte-associated protein 2 could be used as biomarkers for evaluating the degree of reproductive maturation in domesticated P. monodon.

Genetic variation of Kaempferia (Zingiberaceae) in Thailand based on chloroplast DNA (psbA-trnH and petA-psbJ) sequences

Genetic variation and species authentication of 71 Kaempferia accessions (representing 15 recognized, six new, and four unidentified species) found indigenously in Thailand were examined by determining chloroplast psbA-trnH and partial petA-psbJ spacer sequences. Ten closely related species (Boesenbergia rotunda, Gagnepainia godefroyi, G. thoreliana, Globba substrigosa, Smithatris myanmarensis, S. supraneanae, Scaphochlamys biloba, S. minutiflora, S. rubescens, and Stahlianthus sp) were also included. After sequence alignments, 1010 and 865 bp in length were obtained for the respective chloroplast DNA sequences. Intraspecific sequence variation was not observed in Kaempferia candida, K. angustifolia, K. laotica, K. galanga, K. pardi sp nov., K. bambusetorum sp nov., K. albomaculata sp nov., K. minuta sp nov., Kaempferia sp nov. 1, and G. thoreliana, for which more than one specimen was available. In contrast, intraspecific sequence polymorphisms were observed in various populations of K. fallax, K. filifolia, K. elegans, K. pulchra, K. rotunda, K. marginata, K. parviflora, K. larsenii, K. roscoeana, K. siamensis, and G. godefroyi. A strict consensus tree based on combined psbA-trnH and partial petA-psbJ sequences revealed four major groups of Kaempferia species. We suggest that the genus Kaempferia is a polyphyletic group, as K. candida was distantly related and did not group with other Kaempferia species. Polymorphic sites and indels of psbA-trnH and petA-psbJ can be used as DNA barcodes for species diagnosis of most Kaempferia and outgroup species. Nuclear DNA polymorphism should be examined to determine if there has been interspecific hybridization and chloroplast DNA introgression in these taxa.

Expression and distribution of three heat shock protein genes under heat shock stress and under exposure to Vibrio harveyi in Penaeus monodon

A sudden increase in temperature results in heat shock stress of the cultured shrimp. To cope with the stress, shrimp has to overcome by triggering a response known as heat shock response. To understand the heat shock response in the black tiger shrimp (Penaeus monodon), we examined expression patterns and distribution of three heat shock protein (hsp) genes in P. monodon juveniles. The expression levels of hsp21, hsp70 and hsp90 were determined by quantitative real-time PCR in nine tissues (gill, heart, hepatopancreas, stomach, intestine, eyestalk, pleopod, thoracic ganglia and hemocyte) under untreated and heat shock conditions. Under untreated condition, all three hsp genes were differentially expressed in all examined tissues where the hsp70 transcript showed the highest basal level. Under heat shock condition, only hsp90 was inducible in all nine tissues when comparing to its untreated level. The time-course induction experiment in gill and hepatopancreas revealed that the transcriptional levels of hsp21, hsp70 and hsp90 were inducible under the heat shock condition and in time-dependent manner. To determine the response of the hsp genes upon bacterial exposure, we further determined transcript levels of the hsp genes in gill of P. monodon after Vibrio harveyi injection. The expression levels of hsp70 and hsp90 were significantly increased after a 3-h exposure to V. harveyi where the hsp21 transcript was induced later after a 24-h exposure. This evidence suggests for putative roles and involvement of the hsp genes as a part of immunity response against V. harveyi in P. monodon.

Molecular cloning and expression of progestin membrane receptor component 1 (Pgmrc1) of the giant tiger shrimp Penaeus monodon

Knowledge on molecular mechanisms of steroid hormonal induction on oocyte development may lead to the possible ways to effectively induce ovarian maturation in shrimp. In this study, progestin membrane receptor component 1 (Pgmrc1) of the giant tiger shrimp (Penaeus monodon) initially identified by EST analysis was further characterized. The full-length cDNA of Pgmrc1 was 2015bp in length containing an ORF of 573bp corresponding to a polypeptide of 190 amino acids. Northern blot analysis revealed a single form of Pgmrc1 in ovaries of P. monodon. Quantitative real-time PCR indicated that the expression level of Pgmrc1 mRNA in ovaries of both intact and eyestalk-ablated broodstock was greater than that of juveniles (P<0.05). Pgmrc1 was up-regulated in mature (stage IV) ovaries of intact broodstock (P<0.05). Unilateral eyestalk ablation resulted in an earlier up-regulation of Pgmrc1 since the vitellogenic (II) ovarian stage. Moreover, the expression level of Pgmrc1 in vitellogenic, early cortical rod and mature (II-IV) ovaries of eyestalk-ablated broodstock was greater than that of the same ovarian stages in intact broodstock (P<0.05). Pgmrc1 mRNA was clearly localized in the cytoplasm of follicular cells, previtellogenic and early vitellogenic oocytes. Immunohistochemistry revealed the positive signals of the Pgmrc1 protein in the follicular layers and cell membrane of follicular cells and various stages of oocytes. Taken the information together, Pgmrc1 gene products seem to play the important role on ovarian development and may be used as the bioindicator for monitoring progression of oocyte maturation of P. monodon.

Cloning and characterization of a melanization inhibition protein (PmMIP) of the black tiger shrimp, Penaeus monodon

Melanization is an important component of the innate immune responses in invertebrates and it is essential for defense against invading microorganism. Melanin formation, which is a result of activation of the so called prophenoloxidase activating system, needs to be controlled due to the dangerous effects of quinones and melanin which are produced during the process of melanization. Here, a cDNA for a melanization inhibition protein (MIP), named PmMIP, was identified from the black tiger shrimp, Penaeus monodon by RT-PCR using degenerated oligonucleotide primers and RACE-PCR. The complete sequence significantly matched MIP of the freshwater crayfish Pacifastacus leniusculus (PlMIP). PmMIP contains an N-terminal signal peptide and a fibrinogen related domain (FReD). RT-PCR was applied to examine the expression profiles of PmMIP in various tissues of juvenile P. monodon. PmMIP was expressed in all examined tissues except hemocytes and at very low levels in hepatopancreas and ovaries. The expression of this gene was very low during the larval stages and hardly present in egg and at the nauplius stage. A time-course expression analysis of PmMIP upon Vibrio harveyi challenge at protein levels in plasma was determined. The result shows that MIP protein in plasma was induced at 6 h and disappeared at 12 and 24 h and then the protein reappeared at 48 and 72 h post injection. These results suggest that upon bacterial infection the PmMIP protein is first released from tissues into hemolymph and then degraded to allow melanization to occur for fighting against bacteria.

Genetic population differentiation of the blue swimming crab Portunus pelagicus (Portunidae) in Thai waters revealed by RAPD analysis

Genetic diversity and population differentiation of the blue swimming crab, Portunus pelagicus, in Thailand were analyzed by RAPD analysis. One hundred and twelve RAPD fragments were generated from 109 individuals of P. pelagicus using OPA02, OPA14, OPB10, UBC122, and UBC158 primers. The percentage of polymorphic bands in each geographic sample and that of each primer across overall samples were 72.7-85.0 and 92.0-100%, respectively. Large numbers of polymorphic bands found in the RAPD analysis suggested high genetic diversity of Thai P. pelagicus. The mean genetic distance between samples across all primers was 0.0929-0.2471. Significant geographic heterogeneity was observed across samples overall and between all pairs of geographic samples (P < 0.01 for theta and P < 0.0001 for the exact test), indicating strong genetic differentiation of P. pelagicus in Thai waters, despite its high potential of dispersal. Limited gene flow levels (0.44-1.19 individuals per generation) of Thai P. pelagicus were also observed. A fine scale level of differentiation suggested that P. pelagicus from each geographic sample in Thai waters should be regarded as a separate genetic population and treated as a different exploited stock.

Identification of testis-relevant genes using in silico analysis from testis ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon)

Background

Poor reproductive maturation of the black tiger shrimp (Penaeus monodon) in captivity is one of the serious threats to sustainability of the shrimp farming industry. Understanding molecular mechanisms governing reproductive maturation processes requires the fundamental knowledge of integrated expression profiles in gonads of this economically important species. In P. monodon, a non-model species for which the genome sequence is not available, expressed sequence tag (EST) and cDNA microarray analyses can help reveal important transcripts relevant to reproduction and facilitate functional characterization of transcripts with important roles in male reproductive development and maturation.

Results

In this study, a conventional testis EST library was exploited to reveal novel transcripts. A total of 4,803 ESTs were unidirectionally sequenced and analyzed in silico using a customizable data analysis package, ESTplus. After sequence assembly, 2,702 unique sequences comprised of 424 contigs and 2,278 singletons were identified; of these, 1,133 sequences are homologous to genes with known functions. The sequences were further characterized according to gene ontology categories (41% biological process, 24% molecular function, 35% cellular component). Through comparison with EST libraries of other tissues of P. monodon, 1,579 transcripts found only in the testis cDNA library were identified. A total of 621 ESTs have not been identified in penaeid shrimp. Furthermore, cDNA microarray analysis revealed several ESTs homologous to testis-relevant genes were more preferentially expressed in testis than in ovary. Representatives of these transcripts, homologs of saposin (PmSap) and Dmc1 (PmDmc1), were further characterized by RACE-PCR. The more abundant expression levels in testis than ovary of PmSap and PmDmc1 were verified by quantitative real-time PCR in juveniles and wild broodstock of P. monodon.

Conclusions

Without a genome sequence, a combination of EST analysis and high-throughput cDNA microarray technology can be a useful integrated tool as an initial step towards the identification of transcripts with important biological functions. Identification and expression analysis of saposin and Dmc1 homologs demonstrate the power of these methods for characterizing functionally important genes in P. monodon.

Genetic diversity of wild and domesticated stocks of Thai abalone, Haliotis asinina (Haliotidae), analyzed by single-strand conformational polymorphism of AFLP-derived markers

Amplified fragment length polymorphism (AFLP) analysis was carried out on representative individuals of wild Haliotis asinina using 64 primer combinations. Nine polymorphic AFLPs were cloned and sequenced. Sequence-specific primers were designed from six AFLP-derived fragments. Three sequence-characterized amplified region (SCAR) markers (HaSCAR(320), HaSCAR(295), HaSCAR(327)) were selected for genotyping of 8-month-old domesticated stocks of H. asinina cultured separately at Sichang Marine Science Research and Training Station (N = 95) and at a hatchery in Trang province (N = 40) using single-strand conformational polymorphism analysis. Genotypes of wild abalone originating from Talibong Island (N = 25), Cambodia (N = 22), and the P(0) progeny established from Samet Island founders (N = 20) were also investigated. Significant genetic differentiation (P<0.0001 for the exact test and F(ST) = 0.8759-0.8919, P<0.001) between abalone from the Gulf of Thailand (Cambodia and Samet Island--east) and the Andaman Sea (Talibong Island--west) were observed. This demonstrated the strong biogeographic structure of H. asinina in Thai waters. Non-overlapping composite genotypes for wild abalone from different coastal regions allow us to determine founder contributions in domesticated abalone stocks. Almost all Sichang Marine Science Research and Training Station and the Trang province hatchery stocks exhibited the east coast genotypes (97% of the 135 samples). We suggest that abalone from the east coast population have better survival rates under cultivated conditions than those from the west coast population.

Expression of immune-related genes in the digestive organ of shrimp, Penaeus monodon, after an oral infection by Vibrio harveyi

In all previous studies, to study shrimp immune response, bacteria were directly injected into the shrimp body and as a consequence the initial step of a natural interaction was omitted. In this study we have instead used an immersion technique, which is a more natural way of establishing an infection, to study immune responses in black tiger shrimp (Penaeus monodon). Normally, Vibrio harveyi (Vh) is highly pathogenic to post-larval shrimp, but not to juveniles which usually resist an infection. In post-larvae, Vh causes a massive destruction of the digestive system, especially in the hepatopancreas and in the anterior gut. We have therefore investigated changes in transcription levels of fifteen immune-related genes and morphological changes in juvenile shrimp following an immersion of shrimp in Vh suspension. We found that a pathogenic bacterium, Vh, has the capacity to induce a local expression of some immune-related genes in shrimp after such a bacterial immersion. Our results show that in the juvenile gut small changes in expression of the antimicrobial peptide (AMP) genes such as antilipopolysaccharide factor isoform 3, crustin and penaeidin were observed. However some other genes were more strongly induced in their expression compared to the AMP genes. C-type lectin, Tachylectin 5a1 and mucin-like peritrophic membrane were increased in their expression and the C-type lectin was affected most in its expression. Several other examined genes did not change their expression levels. By performing histology studies it was found that Vh infection induced a strong perturbation of the midgut epithelium in some regions. As a consequence, the epithelial cells and basement membrane of the infected site were completely damaged and necrotic and massive hemocyte infiltration occurred underneath the affected tissue to combat the infection.

Suppression subtractive hybridization (SSH) for isolation and characterization of genes related to testicular development in the giant tiger shrimp Penaeus monodon

Suppression subtractive hybridization (SSH) cDNA libraries of the giant tiger shrimp, Penaeus monodon, were constructed. In total, 178 and 187 clones from the forward and reverse SSH libraries, respectively, of P. monodon were unidirectionally sequenced. From these, 37.1% and 53.5% Expressed Sequence Tags (ESTs) significantly matched known genes (E-value < 1e-04). Three isoforms of P. monodon progestin membrane receptor component 1: PM-PGMRC1-s (1980 bp), PM-PGMRC1-m (2848 bp), and PM-PGMRC1-l (2971 bp), with an identical ORF of 573 bp corresponding to a deduced polypeptide of 190 amino acids, were successfully identified by RACE-PCR. Interestingly, PMPGMRC1 showed a greater expression level in testes of juvenile than broodstock P. monodon (P < 0.05). Dopamine administration (10(-6) mol/shrimp) resulted in up-regulation of PMPGMRC1 in testes of juveniles at 3 hrs post treatment (P < 0.05), but had no effect on PM-Dmc1 (P > 0.05).

Molecular characterization and expression profiles of cyclin A and cyclin B during ovarian development of the giant tiger shrimp Penaeus monodon

The meiotic maturation of oocytes is regulated by maturation promoting factor (MPF), a complex of cdc2 (Cdk1) and cyclin B and other Cdk/cyclin complexes. To better understand molecular aspects governing reproductive maturation of the giant tiger shrimp (Penaeus monodon), the full length cDNAs and genomic organization of cyclins A and B (PMCyA and PMCyB) were characterized. A single form of PMCyA contained an open reading frame (ORF) of 1326 bp corresponding to a deduced protein of 441 amino acids. Its genomic sequence contained 5 exons, 4 introns and untranslated regions (UTRs) spanning 2586 bp in length. In contrast, PMCyB possessed three isoforms with an identical ORF of 1206 bp (401 amino acids) but three different 3' UTR lengths of 416, 543 and 1117 bp, respectively. Their respective genomic sequences were composed of 8 exons, 7 introns and UTRs covering 4181, 4307 and 4940 bp. Expression levels of both PMCyA and PMCyB in ovaries of broodstock were much greater than those of juveniles (P<0.05). During ovarian development and after spawning of normal shrimp broodstock, PMCyA was not differentially expressed (P>0.05) whereas the level of PMCyB in stage IV was greater than that of stage I ovaries (P<0.05). Unilateral eyestalk ablation, a technique commonly used to induce spawning in P. monodon female brooders, had no effects on transcription of PMCyB (P>0.05) but resulted in a lower expression of PMCyA at stage IV of ovarian development of this economically important species (P<0.05).

ReproArray(GTS): a cDNA microarray for identification of reproduction-related genes in the giant tiger shrimp Penaeus monodon and characterization of a novel nuclear autoantigenic sperm protein (NASP) gene

Expressed sequence tags (ESTs) were established from various tissues of the giant tiger shrimp (Penaeus monodon). To simultaneously examine expression patterns of a large number of transcripts in ovaries and testes of P. monodon, a cDNA microarray (ReproArray(GTS)) containing 4992 features amplified from cDNAs of ovary (1920) and testis (3072) EST libraries was constructed and subjected to high-throughput gene expression analysis in four different stages of ovarian development (previtellogenesis, vitellogenesis, early cortical rod and late cortical rod stages). Several transcripts were found to be differentially expressed during P. monodon ovarian development. Among many important reproduction-related genes with differential expression from microarray data, nuclear autoantigenic sperm protein (NASP) was further characterized by RACE-PCR. The full-length cDNA of P. monodon NASP (PmNASP) was 2126 bp in length containing an open reading frame (ORF) of 1812 bp corresponding to a deduced protein of 603 amino acids with 5? and 3?UTRs of 93 and 202 bp (excluding the poly A tail), respectively. Higher PmNASP transcript levels at later stages of ovarian development was consistently confirmed by quantitative real-time PCR. This study indicated that ReproArray(GTS) is effective for high-throughput screening of genes that play important roles in ovarian development of P. monodon.

Isolation and characterization of testis-specific DMRT1 in the tropical abalone (Haliotis asinina)

The Doublesex Male abnormal-3 Related Transcription factor-1 (DMRT1) gene encodes a protein containing the DNA-binding motif called the DM domain, involved in the sexual development of various species. To gain insight into its implications for gonadal differentiation in the tropical abalone (Haliotis asinina), a DMRT1 homolog was identified and characterized. The full length cDNA of HADMRT1 (1,740 bp with an ORF of 732 bp corresponding to a putative polypeptide of 243 amino acids) and its DM domain-less variant (HADMRT1-like, 1,430 bp with an ORF of 312 bp, 103 amino acids) were successfully isolated and reported for the first time in molluscs. HADMRT1 was specifically expressed in the testes of adult H. asinina (N = 16) but not in whole juveniles (2, 3, 5 months old, N = 6 for each group) and ovaries (N = 16), and pooled hemocytes (from 50 individuals) of adults. Tissue distribution analysis further revealed testis-specific expression of HADMRT1. Semiquantitative RT-PCR illustrated that the relative expression level of HADMRT1 in developed testes (stages II, III, and IV) was significantly greater than that in undeveloped testes (stage I) of abalone broodstock (P < 0.05).

Up-regulation of ribophorin I after yellow head virus (YHV) challenge in black tiger shrimp Penaeus monodon

This work constitutes the second report from a continuing investigation of shrimp genes that may be involved in apoptosis associated death resulting from yellow head virus (YHV) infection. Here, we describe from the black tiger shrimp Penaeus monodon, a ribophorin I-like gene that is probably a subunit of the oligosaccharyltransferase complex (OST), a key enzyme in N-linked glycosylation that occurs in the endoplasmic reticulum. The OST complex also contains DAD1 (defender against apoptotic death 1) that has been reported to control apoptosis and that we have previously reported from P. monodon. The full length ribophorin I of P. monodon comprised 2157 bp with the ORF of 1806 bp corresponding to 601 deduced amino acids and three putative N-linked glycosylation sites. Analysis revealed hydrophobic properties implying that it could be a membrane protein. Tissue distribution analysis using real-time RT-PCR with SYBR Green revealed that ribophorin I was endogenously expressed in all examined tissues of normal shrimp. However, unlike DAD1 that was down-regulated after YHV challenge, ribophorin I expression was up-regulated and remained high until the moribund stage.

Down-regulation of defender against apoptotic death (DAD1) after yellow head virus (YHV) challenge in black tiger shrimp Penaeus monodon

Here we describe the highly conserved gene, defender against apoptotic death (DAD1) identified from an EST library of the black tiger shrimp Penaeus monodon. The full-length cDNA of DAD1 of P. monodon comprised 638bp with an ORF of 345bp corresponding to 114 deduced amino acids. The deduced amino acid sequence was compared to known DAD1 sequences in the GenBank and in other databases. Phylogenetic analysis revealed that P. monodon DAD1 clustered with DAD1 from other invertebrates. Real-time RT-PCR with RNA extracts from normal P. monodon revealed DAD1 expression in several tissues including those of digestive and defense organs such as the hepatopancreas and hemocytes, respectively. If death from YHV infection was related to increased levels of apoptosis, we reasoned that the level of DAD1 should decrease as YHV infections progressed, especially in hemocytes (HC), one of its main targets. Real-time RT-PCR with RNA extracts from HC of P. monodon challenged with YHV revealed that the transcriptional level of DAD1 declined dramatically (approximately 50%) after YHV challenge. Although this suggests that DAD1 plays a role in mortality caused by YHV, control of apoptosis is complex and involves the interaction of many proteins, few of which have been characterized for shrimp. Thus, firm conclusions regarding the role of DAD1 must await the description and characterization of other proteins.

Expressed sequence tag analysis for identification and characterization of sex-related genes in the giant tiger shrimp Penaeus monodon

Sex-related genes expressed in vitellogenic ovaries of the giant tiger shrimp, Penaeus monodon, were identified by an EST approach. A total of 1051 clones were unidirectionally sequenced from the 5 terminus. Nucleotide sequences of 743 EST (70.7%) significantly matched known genes previously deposited in the GenBank (E-value <10(-4)) whereas 308 ESTs (29.3%) were regarded as newly unidentified transcripts (E-value >10(-4)). A total of 559 transcripts (87 contigs and 472 singletons) were obtained. Thrombospondin (TSP) and peritrophin (79 and 87 clones accounting for 7.5 and 8.3% of clones sequenced, respectively) predominated among characterized transcripts. Several full length transcripts (e.g. cyclophilin, profillin and thioredoxin peroxidase) were also isolated. A gene homologue encoding chromobox protein (PMCBX, ORF of 567 nucleotides encoding a protein of 188 amino acids) which is recognized as a new member of the HP1 family was identified. Expression patterns of 14 of 25 sex-related gene homologues in ovaries and testes of P. monodon broodstock were examined by RT-PCR. Female sterile and ovarian lipoprotein receptor homologues were only expressed in ovaries whereas the remaining transcripts except disulfide isomerase related P5 precursor and adenine nucleotide translocator 2 were higher expressed in ovaries than testes of P. monodon broodstock. A homologue of ubiquitin specific proteinase 9, X chromosome (Usp9X) revealed a preferential expression level in ovaries than testes of broodstock-sized P. monodon (N = 13 and 11, P <0.05) but was only expressed in ovaries of 4-month-old shrimp (N = 5 for each sex).

Genetic heterogeneity of the blue swimming crab (Portunus pelagicus) in Thailand determined by AFLP analysis

Genetic diversity and population differentiation of the blue swimming crab (Portunus pelagicus) in Thailand, originating from Ranong and Krabi located in the Andaman Sea (west) and Chanthaburi, Prachuap Khiri Khan, and Suratthani located in the Gulf of Thailand (east), were examined by AFLP analysis. High genetic diversity of P. pelagicus in Thai waters was found (N=72). The four primer combinations generated 227 AFLP fragments, and the percentage of polymorphic bands in each geographic sample was 66.19-94.38%. The mean genetic distance between pairs of samples was 0.1151-0.2440. Geographic heterogeneity analyses using the exact test and FST-based statistics between all pairwise comparisons were statistically significant (P<0.01), indicating a fine-scale level of intraspecific population differentiation of Thai P. pelagicus. The estimated number of migrants per generation (Nem) was 0.26-0.76, suggesting restricted gene flow levels of P. pelagicus in Thai waters.

Genetic Differentiation of the Giant Honey Bee (Apis dorsata) in Thailand Analyzed by Mitochondrial Genes and Microsatellites

Genetic diversity and population differentiation of the giant honey bee (Apis dorsata) in Thailand were examined. Six PCR-RFLP mitotypes were generated from digestion of the COI-COII, Cytb-tRNA(ser), ATPase6-8, and lrRNA genes with Dra I and Hin fI. Low genetic diversity (h=0.074, pi=0.032%) and a lack of genetic population differentiation between A. dorsata originating from geographically different regions were observed from mtDNA polymorphisms (P > 0.05). In contrast, microsatellite (A14, A24, and A88) polymorphisms revealed a relatively high level of genetic diversity in A. dorsata (H (o)=0.68-0.74, average number of alleles per locus=6.0-9.0). Both A24 and A88 indicated significant population differentiation between bees from the north-to-central region (north, northeast, and central regions), peninsular Thailand, and Samui Island.

Genetic diversity of the giant tiger shrimp (Penaeus monodon) in Thailand revealed by PCR-SSCP of polymorphic EST-derived markers

A total of 90 ESTs from normal and 157 from subtractive ovarian cDNA libraries of the giant tiger shrimp (Penaeus monodon) were sequenced. SSCP analysis of disulfide isomerase (DSl), zinc finger protein (ZFP), PMO920, and PMT1700 was carried out for population genetic studies of P. monodon in Thai waters. The number of codominant alleles per locus for overall samples was 6 for PMO920, 5 for PMT1700, and 12 for ZFP, and there were 19 dominant alleles for DSI. The observed heterozygosity of each geographic sample was 0.3043-0.5128 for PMO920, 0.3462-0.4643 for PMT1700, and 0.5000-0.8108 for ZFP. Linkage disequilibrium analysis indicated that genotypes of these loci segregate randomly (P > 0.05). Low genetic distance was found between pairs of geographic samples (0.0077-0.0178). The neighbor-joining tree constructed from the average genetic distance of overall loci allocated the Andaman samples (Satun, Trang, and Phangnga) into one cluster, and Chumphon and Trat into other clusters. Geographic differentiation between Satun-Trat and Satun-Phangnga was found only at the ZFP locus (P < 0.05), suggesting low degrees of genetic subdivision of Thai P. monodon.

Mitochondrial DNA diversity and genetic differentiation of the honeybee (Apis cerana) in Thailand

Genetic diversity of the honeybee (Apis cerana) in Thailand collected from north, northeast, the central region, peninsular Thailand, and Samui Island (n = 181) was examined by PCR-RFLP of ATPase6-ATPase8. Interestingly, 78 individuals (43.09%) of the southern-latitude bees exhibited length heteroplasmy of the PCR product. The gel-eluted ATPase6-ATPase8 (825 bp) of each bee was restricted with TaqI, SspI, and VspI, respectively. Eight mitotypes were generated and revealed biogeographic differentiation between conspecific samples of A. cerana. AAA, ACA, AAD, BAA, ADA, and ABA were found only in the north-to-central samples (north, northeast, and central region); BBB and BBC were found in the southern-latitude bees; and BBC was restrictively found in the Samui sample. Large genetic distances were observed between each of the north-to-central samples and peninsular Thailand and Samui samples, but lower levels of genetic distance were found within each region. Geographic heterogeneity and phylogenetic analyses indicated that Thai A. cerana could be genetically differentiated into northern Thailand, peninsular Thailand, and Samui Island populations.

Development of polymorphic expressed sequence tag-derived microsatellites for the extension of the genetic linkage map of the black tiger shrimp (Penaeus monodon)

In this study, microsatellite markers were developed for the genetic linkage mapping and breeding program of the black tiger shrimp Penaeus monodon. A total of 997 unique microsatellite-containing expressed sequence tags (ESTs) were identified from 10 100 EST sequences in the P. monodon EST database. AT-rich microsatellite types were predominant in the EST sequences. Homology searching by the blastn and blastx programs revealed that these 997 ESTs represented 8.6% known gene products, 27.8% hypothetical proteins and 63.6% unknown gene products. Characterization of 50 markers on a panel of 35-48 unrelated shrimp indicated an average number of alleles of 12.6 and an average polymorphic information content of 0.723. These EST microsatellite markers along with 208 other markers (185 amplified fragment length polymorphisms, one exon-primed intron-crossing, six single strand conformation polymorphisms, one single nucleotide polymorphism, 13 non-EST-associated microsatellites and two EST-associated microsatellites) were analysed across the international P. monodon mapping family. A total of 144 new markers were added to the P. monodon maps, including 36 of the microsatellite-containing ESTs. The current P. monodon male and female linkage maps have 47 and 36 linkage groups respectively with coverage across half the P. monodon genome.

Genetic variation and species identification of Thai Boesenbergia (Zingiberaceae) analyzed by chloroplast DNA polymorphism

Genetic variation and molecular phylogeny of 22 taxa representing 14 extant species and 3 unidentified taxa of Boesenbergia in Thailand and four outgroup species (Cornukaempferia aurantiflora, Hedychium biflorum, Kaempferia parviflora, and Scaphochlamys rubescens) were examined by sequencing of 3 chloroplast (cp) DNA regions (matK, psbA-trnH and petA-psbJ). Low interspecific genetic divergence (0.25-1.74%) were observed in these investigated taxa. The 50% majority-rule consensus tree constructed from combined chloroplast DNA sequences allocated Boesenbergia in this study into 3 different groups. Using psbA-1F/psbA-3R primers, an insertion of 491 bp was observed in B. petiolata. Restriction analysis of the amplicon (380-410 bp) from the remaining species with Rsa I further differentiated Boesenbergia to 2 groupings; I (B. basispicata, B. longiflora, B. longipes, B. plicata, B.pulcherrima, B. tenuispicata, B. thorelii, B. xiphostachya, Boesenbergia sp.1 and Boesenbergia sp.3; phylogenetic clade A) that possesses a Rsa I restriction site and II (B.curtisii, B. regalis, B. rotunda and Boesenbergia sp.2; phylogenetic clade B and B. siamensis; phylogenetic clade C) that lacks a restriction site of Rsa I. Single nucleotide polymorphism (SNP) and indels found can be unambiguously applied to authenticate specie-origin of all investigated samples and revealed that Boesenbergia sp.1, Boesenbergia sp.2 and B. pulcherrima (Mahidol University, Kanchanaburi), B. cf. pulcherrima1 (Prachuap Khiri Khan) and B. cf. pulcherrima2 (Thong Pha Phum, Kanchanaburi) are B. plicata, B. rotunda and B. pulcherrima, respectively. In addition, molecular data also suggested that Boesenbergia sp.3 should be further differentiated from B. longiflora and regarded as a newly unidentified Boesenbergia species.

Penaeus monodon gene discovery project: the generation of an EST collection and establishment of a database

A large-scale expressed sequence tag (EST) sequencing project was undertaken for the purpose of gene discovery in the black tiger shrimp Penaeus monodon. Initially, 15 cDNA libraries were constructed from different tissues (eyestalk, hepatopancrease, haematopoietic tissue, haemocyte, lymphoid organ, and ovary) of shrimp, reared under normal or stress conditions, to identify tissue-specific genes and genes responding to infection and heat stress. A total of 10,100 clones were analyzed by single-pass sequencing from the 5' end. Clustering and assembling of these ESTs resulted in a total of 4845 unique sequences with 917 overlapping contigs and 3928 singletons. The redundancy of each cDNA library ranged from 13.4% to 61.3% with an overall redundancy of 61.1%. About half of these ESTs (2365 clones, 48.8%) showed significant homology (BLASTX, e-values <10(-4)) to known genes. A high proportion of P. monodon ESTs was most similar to the predicted protein sequences from various organisms, e.g. Homo sapiens (9%), Mus musculus (7%), Drosophila (6%), Gallus sp.(6%), and Anopheles (5%). Only 6% showed the highest similarity to other known genes from shrimp due to the limited sequence entries of the species in the public database. Several tissue-specific transcripts were identified as well as the candidate genes that may be implicated in the immune response. In addition, bioinformatic mining of microsatellites from the P. monodon ESTs identified 997 unique microsatellite containing ESTs in which 74 loci resided within the genes of known functions. Consequently, the P. monodon EST database was established. The EST sequence data and the BLAST results were stored and made available through a web-accessible database (). This EST database provides a useful resource for gene identification and functional genomic studies of shrimp.

Identification of sex-specific expression markers in the giant tiger shrimp (Penaeus monodon)

Bulked segregant analysis (BSA) and AFLP were used for isolation of genomic sex determination markers in Penaeus monodon. A total of 256 primer combinations were tested against 6-10 bulked genomic DNA of P. monodon. Five and one candidate female- and male-specific AFLP fragments were identified. Female-specific fragments were cloned and further characterized. SCAR markers derived from FE10M9520, FE10M10725.1, FE10M10725.2 and FE14M16340 provided the positive amplification product in both male and female P. monodon. Further analysis of these markers using SSCP and genome walk analysis indicated that they were not sex-linked. In addition, sex-specific (or differential) expression markers in ovaries and testes of P. monodon were analyzed by RAP-PCR (150 primer combinations). Twenty-one and fourteen RAP-PCR fragments specifically/differentially expressed in ovaries and testes of P. monodon were successfully cloned and sequenced. Expression patterns of 25 transcripts were tested against the first stranded cDNA of ovaries and testes of 3-month-old and broodstock-sized P. monodon (N=5 and N=7-10 for females and N=4 and N=5-7 for males, respectively). Five (FI-4, FI-44, FIII-4, FIII-39 and FIII-58) and two (M457-A01 and MII-51) derived RAP-PCR markers revealed female- and male-specific expression patterns in P. monodon. Surprisingly, MII-5 originally found in testes showed a higher expression level in ovaries than did testes of juvenile shrimps but a temporal female-specific pattern in P. monodon adults.