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ABSTRACT: The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and sanger sequencing approaches. The complete genome DNA was 15, 824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNA(His) differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunits 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy.
Gene 02/2013; · 2.34 Impact Factor
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ABSTRACT: The mud crab (Scylla paramamosain) is a carnivorous portunid crab, mainly distributed along the southeastern coast of China. Mitochondrial DNA analysis in a previous study indicated a high level of genetic diversity and a low level of genetic differentiation. In this study, population genetic diversity and differentiation of S. paramamosain were investigated using nine microsatellite markers. In total, 397 wild specimens from 11 locations on the southeastern coast of China were sampled and genotyped. A high level of genetic diversity was observed, with the number of alleles, and the observed and expected heterozygosity per location in the range 7.8-9.6, 0.62-0.77 and 0.66-0.76, respectively. AMOVA analysis indicated a low level of genetic differentiation among the 11 locations, despite the fact that a statistically significant fixation index (F(ST)) value was found (F(ST)=0.0183, P<0.05). Out of 55 pairwise location comparisons, 39 showed significant F(ST) values (P<0.05), but all of them were lower than 0.05, except for one between Sanmen and Shantou locations. No significant deficiency of heterozygotes (inbreeding coefficient F(IS)=0.0007, P>0.05) was detected for all locations except Sanmen and Zhanjiang. Cluster analysis using UPGMA showed that all locations fell into one group except Sanmen. Significant association was found between genetic differentiation in terms of F(ST)/(1-F(ST)) and the natural logarithm of geographical distance (r(2)=0.1139, P=0.02), indicating that the genetic variation pattern closely resembled an isolation by distance model. This study supports the proposal of high genetic diversity and low genetic differentiation in S. paramamosain along the southeastern coast of China.
Journal of Experimental Biology 06/2012; 215(Pt 17):3120-5. · 3.00 Impact Factor
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ABSTRACT: Nibea albiflora is a commercially important fish species in China. Herein we report 16 novel polymorphic microsatellite markers in Nibea albiflora by using the 5′ anchored polymerase chain reaction (PCR) technique. The characteristics of these loci were estimated by using
a sample of 30 individuals. A total of 79 alleles were detected with an average of 4.9 alleles per locus. The number of alleles
per locus ranged from three to nine. The polymorphism information content (PIC) values for the 16 microsatellite loci ranged
from 0.3131 to 0.7910. The observed and expected heterozygosity per locus ranged from 0.2333 to 1.000 and from 0.3452 to 0.8421,
with an average of 0.7248 and 0.6592, respectively. Four loci significantly deviated from Hardy–Weinberg equilibrium after
Bonferroni correction (P<0.0031), and no significant linkage disequilibrium between pairs of loci was found. This study provides useful information
for studies on genetic diversity and structure, construction of genetic linkage maps of N.albiflora, and effective management of this fish resource.
Keywords
Nibea albiflora
–Microsatellite markers–Polymorphism–5′ Anchored PCR
Fisheries Science 05/2012; 77(5):707-711. · 0.94 Impact Factor
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ABSTRACT: Nineteen microsatellite DNA markers of Collichthys lucidus were developed. The number of alleles for each locus ranged from three to 11. A total of 104 alleles were identified in 30
individuals collected from Zhejiang, China. The observed and expected heterozygosity per locus ranged from 0.2857 to 1.000
and from 0.5539 to 0.8774, respectively. Significant deviation from Hardy–Weinberg equilibrium at four microsatellite loci
was detected after Bonferroni correction (P<0.0026). These novel loci will be helpful for understanding the background of C. lucidus at genetic level.
Keywords
Collichthys lucidus
–Genetic markers–Microsatellites–Polymorphism
Conservation Genetics Resources 04/2012; 3(3):503-506. · 0.49 Impact Factor
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ABSTRACT: Ferritin is an important protein for iron storage in cells. A hepatopancreas cDNA library from the mud crab Scylla paramamosain was constructed using the SMART technique. A complete cDNA sequence that showed high identity with the conserved sequence of the ferritin gene was cloned from the cDNA library and subjected to further investigation. The full-length ferritin gene of Scylla paramamosain (SpFer) consists of 767 bp and contains a complete open reading frame of 513 bp and a 26-bp iron-respective element in the 5′-untranslated region. The gene encodes a polypeptide of 170 amino acids, constituting a predicted molecular weight of 19.44 kDa and a theoretical isoelectric point of 5.24. The deduced protein shares 84% identity with the ferritin protein of the crab Eriocheir sinensis. Quantitative real-time PCR analyses revealed that the expression of ferritin was ubiquitous in different organs of S. paramamosain, including muscle, heart, ovary, testis, and hepatopancreas. The highest expression level was found in the heart, while testis tissue showed the lowest level. Ferritin mRNA expression in continuous developmental stages in zoeal phases, including Z1, Z2, Z3, Z4, and Z5, as well as megalopa and juvenile crab I stages, were also examined by quantitative real-time PCR. The expression level of ferritin was highest in the Z1 stage and lowest in the megalopa stage. This study provides useful information regarding the structure and function of ferritin and will play an important role in immunity and resistance research in S. paramamosain.
Journal of Crustacean Biology 03/2011; · 1.12 Impact Factor
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ABSTRACT: The mud crab Scylla paramamosain plays a significant role in fishery resources in China. In this study, we developed 18 polymorphic microsatellite markers in this important crab by 5' anchored PCR technique. A total of 125 alleles were detected in a single population of 32 individuals of S. paramamosain. The number of alleles per locus ranged from five to nine, with the allele size ranging from 166 to 316 bp. The polymorphism information content (PIC), observed and expected heterozygosity ranged from 0.39 to 0.88, from 0.33 to 0.92 and from 0.42 to 0.86, respectively. Three loci (Scypa13, Scypa14 and Scypa15) deviated significantly from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction (P < 0.0028), and no linkage disequilibrium was found between loci pairs. These polymorphic microsatellite markers will be useful for the study of population genetic structure, construction of genetic linkage maps and mapping of economically quantitative trait loci (QTL) in S. paramamosain.
Molecular Biology Reports 12/2010; 38(8):4999-5002. · 2.93 Impact Factor
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ABSTRACT: Scylla paramamosain is a commercially important crab species in China. Here we reported 12 novel polymorphic microsatellite markers isolated in S. paramamosain using PCR-based isolation of microsatellite arrays (PIMA). The analysis of genetic variability was performed in a sample of 29 individuals. A total of 82 alleles were detected with an average of 6.8 alleles per locus. The number of alleles, polymorphism information content (PIC), observed and expected heterozygosity per locus ranged from three to 12, from 0.42 to 0.88, from 0.38 to 1.00 and from 0.48 to 0.91, respectively. Three loci significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.0042) and no significant linkage disequilibrum between pairs of loci was found. Cross-species amplification of these markers was evaluated in three closely related crab species S. tranquebarica, S. olivacea, and S. serrata. This study will potentially be useful for stock management, constructing of a genetic linkage map, mapping economically important quantitative trait loci (QTL), and evaluating the population genetic diversity of S. paramamosain.
Journal of Crustacean Biology 06/2010; · 1.12 Impact Factor
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ABSTRACT: This research was conducted based on the bottom trawl surveys in Summer and Autumn. An analysis on the stock density and community structure of nekton in Taiwan Straits indicated that the average stock density was 8.50 kg x h(-1) in Summer and 6.94 kg x h(-1) in Autumn. The species number was 80 in Summer and 91 in Autumn, and the abundance, species diversity index, and evenness index were all higher in Autumn than in Summer. The average species diversity index was 2.0466 in Summer and 2.3964 in Autumn. The dominant species whose index of relatively importance (IRI) was > 200 were hairtail (Trichiurus japonicus), lanternbelly (Acropoma japonicum), red bigeye (Priacanthus macracanthus), large-scale lizardfish (Saurida undosquamis) and common Chinese squid (Loligo chinensis) in Summer, and hairtail (Trichiurus japonicus), skinnycheek lanternfish (Benthosema pterotum), wart perch (Psenopsis anomala), squid (Loligo chinensis), white-tipped mackerel scad (Decapterus maruaelsi) and deep pugnose ponyfish (Secuter ruconius) in Autumn. As a whole, the aggregated intensity of dominant species in Summer was higher than that in Autumn.
Ying yong sheng tai xue bao = The journal of applied ecology / Zhongguo sheng tai xue xue hui, Zhongguo ke xue yuan Shenyang ying yong sheng tai yan jiu suo zhu ban 11/2005; 16(10):1948-51.
