Twelve novel polymorphic microsatellite loci for the Yellow grouper (Epinephelus awoara) and cross-species amplifications

Yellow grouper (Epinephelus awoara) is a commercially important marine fish species. A dinucleotide-enriched genomic library of E. awoara was constructed using the method of FIASCO. Twelve loci were polymorphic in a test population with alleles per locus ranging from two to eight, and observed and expected heterozygosities per locus from 0.13 to 1.00 and from 0.20 to 0.86, respectively. Five loci significantly deviated from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was found between pairs of loci. Cross-species amplification of these polymorphic microsatellite loci was performed in additional two related species. These polymorphic microsatellite loci would be useful for investigating genetic diversity of E. awoara and related species. L. Zhao and C. Shao have contributed equally to this work.     

Ten polymorphic microsatellite loci in the giant scallop (Mizuhopecten yessoensis)

Ten novel microsatellite loci were isolated from giant scallop Mizuhopecten yessoensis, and the polymorphisms were examined to estimate genetic variability. The genetic variabilities varied depending on the locus. The number of alleles ranged from two to 17, and the observed and expected heterozygosities ranged from 0.17 to 0.99 and 0.33 to 0.90, respectively. Six loci showed significant Hardy–Weinberg disequilibrium. The high variabilities revealed in this study suggest that microsatellites should prove useful for various genetic investigations.     

Isolation and characterization of polymorphic microsatellite loci from a dinucleotide-enriched genomic library of seven-band grouper (Epinephelus septemfasciatus) and cross-species amplification

Seven-band grouper (Epinephelus septemfasciatus) is a commercially important fishery species. Sixty-six microsatellite loci were isolated from a dinucleotide-enriched genomic library of E. septemfasciatus. Twelve of these loci were polymorphic in a test population with alleles per locus ranging from two to five, and observed and expected heterozygosities per locus from 0.04 to 1.00 and from 0.28 to 0.76, respectively. Three loci significantly deviated from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was found between pairs of loci after Bonferroni correction. Cross-species amplification of these polymorphic microsatellite loci was performed in additional two related species. These polymorphic microsatellite loci would be useful for investigating genetic resource of E. septemfasciatus and other related species. Lili Zhao and Changwei Shao have contributed equally.     

Development and characterization of 32 microsatellite loci in the giant grouper Epinephelus lanceolatus (Serranidae)

An economically important marine fish species, the giant grouper Epinephelus lanceolatus (Serranidae) is widely cultured in Taiwan and costal areas of China. We isolated and characterized 32 polymorphic microsatellite loci from a CA-enriched genomic library of giant grouper. The number of alleles per locus ranged from 3 to 7, with a mean of 4.69. Observed and expected heterozygosities per locus varied from 0.387 to 1.000 and from 0.377 to 0.843, respectively. Six loci significantly deviated from Hardy-Weinberg equilibrium. After sequential Bonferroni's correction, only two loci showed deviation from Hardy-Weinberg equilibrium, and no linkage disequilibrium was found between any pair of loci. These microsatellites can be useful tools for the study of population genetics in the giant grouper.     

Cryopreservation of giant grouper Epinephelus lanceolatus (Bloch, 1790) sperm

The grouper, Epinephelus lanceolatus, is a vulnerable species of high economic value. An effective protocol was developed for the cryopreservation of E. lanceolatus by comparing different extenders produced by mixing various cryoprotectants (dimethyl sulfoxide, methanol and glycerol) and diluents (MPRS, TS‐2, TS‐19, Cortland and Hank's). Using computer‐assisted sperm analysis (CASA) and morphological analysis, the sperm motility and fertilization rates from post‐thaw sperm were comparable to untreated controls. The results revealed that MPRS (containing 12% DMSO) or TS‐19 (containing 12% DMSO), were the optimum extenders for protecting the sperm from cryo‐damage in liquid nitrogen. The post‐thaw sperm maintained high motility (90.61 ± 3.03%) and a fertilization rate (92.27 ± 2.43%) similar (P > 0.05) to fresh sperm (94.34 ± 4% and 94.10 ± 1.87%). This study is the first to report on the successful sperm cryopreservation of E. lanceolatus and provides an important tool for repopulating this species through aquaculture.     

A chromosome‐level genome assembly of the giant grouper (Epinephelus lanceolatus) provides insights into its innate immunity and rapid growth

The giant grouper (Epinephelus lanceolatus) is the largest coral reef teleost, with a native range that spans temperate and tropical waters in the Pacific and the Indian Oceans. It is cultured artificially and used as a breeding species in aquaculture due to its rapid growth rate. Here we report a giant grouper genome assembled at the chromosome scale from sequences generated using Illumina and high‐throughput chromatin conformation capture (Hi‐C) technology. The assembly comprised 1.086 Gb, with 98.4% of the scaffold sequences anchored into 24 chromosomes. The contig and scaffold N50 values were 119.9 kb and 46.2 Mb, respectively. The assembly is of high integrity, including 96.4% universal single‐copy orthologues based on BUSCO analysis. Through chromosome‐scale evolution analysis, we identified alignments of six giant grouper chromosomes to three stickleback chromosomes and some of the genes located within the breakpoints of reshuffling events may related to development and growth. From the 24,718 protein‐coding genes, we found that several gene families related to innate immunity and glycan biosynthesis were significantly expanded in the giant grouper genome compared to other teleost genomes. In addition, we identified several genes related to the hormone signalling pathway and innate immunity that have experienced positive selection or accelerated evolution, implicating their roles in immune defence and fast growth of the species. The high‐quality genome assembly will provide a valuable genomic resource for further biological and evolutionary studies, and useful genomic tools for breeding of the giant grouper.     

Characterization of polymorphic microsatellite loci from black grouper,Mycteroperca bonaci (Teleostei: Serranidae)

Many groupers in the western Atlantic are vulnerable to overfishing, and appropriate management requires knowledge of the population structure of these fish. To this end microsatellite markers were developed from black grouper, Mycteroperca bonaci, using an enrichment procedure. Five loci with levels of polymorphism ranging from 0.5 to 0.9 were selected. These markers also proved to be useful in scamp, M. phenax; red grouper, Epinephelus morio; and goliath grouper, E. itajara. Conformation to Hardy–Weinberg equilibrium was observed except for heterozygote deficiencies noted for E. morio at two of the loci used for this species.     

A set of 16 consensus primer pairs amplifying the complete mitochondrial genomes of orange-spotted grouper (Epinephelus coioides) and Hong Kong grouper (Epinephelus akaara)

Groupers are of considerable economic value; however, their classification and evolutionary relationships have long been hindered by the overwhelming number of species and lack of morphological specializations. Mitochondrial genome is a source of original markers that are potentially useful in the study of phylogeny and population genetics of groupers. We describe a set of 16 new primer pairs that allow PCR amplification of the entire mitochondrial genomes of orange-spotted grouper and Hong Kong grouper. This primer set has been defined for consensus over eight other grouper species, facilitating further studies on the molecular evolution and population genetics of groupers.     

Allozyme and microsatellite loci provide discordant estimates of population differentiation in the endangered dusky grouper (Epinephelus marginatus) within the Mediterranean Sea

The dusky grouper, Epinephelus marginatus, inhabits coastal reefs in the Mediterranean Sea and Atlantic Ocean. A decline in the abundance of this long-lived protogynous hermaphrodite has led to its listing as an endangered species in the Mediterranean, and heightened management concerns regarding its genetic variability and population substructure. To address these concerns, we analysed genetic variation at seven microsatellite and 28 allozyme loci in dusky groupers sampled from seven areas (for microsatellites) and three areas (for allozymes) in the west-central Mediterranean. Levels of genetic variability were higher for microsatellites than for allozymes (mean H(E) = 0.78 and 0.07, respectively), but similar to those observed in other marine fishes with comparable markers. Both microsatellites and allozymes revealed significant genetic differentiation among all areas analysed with each class of marker, but the magnitude of differentiation revealed by allozymes over three locales (F(ST) = 0.214) was greater than that detected with microsatellites over seven areas, or over the three areas shared with the allozyme analysis (F(ST) = 0.018 and approximately 0, respectively). A large proportion of the allozyme differentiation was due to a single locus (ADA*) possibly influenced by selection, but allozyme differentiation over the three areas was still highly significant (F(ST) = 0.06, P < 0.0001), and the 95% confidence intervals for allozyme and microsatellite F(ST) did not overlap when this locus was excluded. There was no evidence of isolation by distance with either class of markers. Our results lead us to conclude that dusky groupers are not panmictic in the Mediterranean Sea and suggest that they should be managed on a local basis. However, more work is needed to elucidate genetic relationships among populations.     

斜带石斑鱼淋巴器官个体发育的组织学

本文应用连续组织切片技术和组织学观察,对出膜后1～60天的斜带石斑鱼(Epinephelus coioides)各期仔鱼、稚鱼和幼鱼的淋巴器官组织进行了研究,描述了淋巴器官的个体发育过程和组织学结构特征。研究表明：实验水温为22．0～27．8℃时,孵化后第10天出现头肾原基。头肾原基由未分化的造血干细胞组成。随着鱼体的生长,头肾原基的造血干细胞很快分化成不同类型的细胞;头肾主要由网状内皮系统支持下的淋巴造血组织构成。第11天出现脾脏原基。脾脏原基由造血细胞组成,淋巴化速度相对较慢。脾脏在整个发育过程中,红细胞和类红细胞占优势,没有红髓和白髓之分。第13天出现胸腺原基。胸腺发育速度较快,是明显的淋巴器官。胸腺主要由胸腺细胞(淋巴细胞)和上皮细胞组成,外区和内区没有明显的界限,但很容易区分。胸腺外被单层的上皮细胞层与咽腔相隔,保持浅表的位置,并且在整个发育过程中,胸腺与头肾是独立分开的。免疫器官原基出现顺序是头肾、脾脏和胸腺;而免疫器官淋巴化的顺序是胸腺,头肾和脾脏。和其它硬骨鱼类一样,斜带石斑鱼在早期发育阶段,淋巴器官的发育较迟,出现相对滞后的现象[动物学报49(6)：819～828,2003]。     

Highly polymorphic microsatellite loci from the giant mottled eel (Anguilla marmorata)

Eighteen polymorphic microsatellite loci from the giant mottled eel (Anguilla marmorata) were identified and their characteristics were described. These markers were tested in two wild populations from China (n = 20) and Australia (n = 20) respectively. The number of alleles ranged from 9 to 14 with an average of 11.28 per locus. The mean expected heterozygosity (H_E) was 0.8696 in the population from China, 0.8823 in the population from Australia. No locus deviates significantly from Hardy–Weinberg proportions (P < 0.05).     

Characterization of polymorphic microsatellite loci for the invasive monk parakeet (Myiopsitta monachus)

Microsatellite loci were characterized for the monk parakeet (Myiopsitta monachus) from a GT_n‐enriched genomic library. Twelve of 14 microsatellite loci were polymorphic, averaging 6.7 alleles per locus across the 20 individuals genotyped. Mean expected heterozygosity was 0.72, with locus‐specific values ranging from 0.53 to 0.90. An equally high multilocus probability of identity (2.48 × 10^?12) was revealed for this set of loci. In addition, all 12 loci were demonstrated to cross‐amplify to varying extents within three additional parrot genera suggesting their potential utility for population‐level studies in a broad range of Neotropical psittacines.     

Characterization of eight microsatellite loci in Steller sea lions (Eumetopias jubatus)

Steller sea lions (Eumetopias jubatus) are listed as an endangered species in western Alaska and have exhibited a significant population decline throughout their range. Eight microsatellite loci were isolated from genomic DNA libraries. In addition, all these markers were found to be variable in nine individuals of the California sea lion (Zalophus californicus). This panel of markers was developed to analyse population structure in Steller sea lions throughout their range.     

Development and characterization of eight polymorphic microsatellite loci from Pistacia lentiscus L. (Anacardiaceae)

We have developed a set of eight polymorphic nuclear microsatellite markers for the Mediterranean shrub Pistacia lentiscus by means of an enriched library method. Characterization for the eight loci was carried out on 42 individuals from two populations sampled in southern Spain. The overall number of alleles detected was 59, ranging from three to 13 per locus. Expected heterozygosity per locus and population ranged from 0.139 to 0.895. Two loci albeit only in one population (Seville) departed significantly from Hardy-Weinberg equilibrium expectations and no linkage disequilibrium between pairs of loci was detected. These markers will be used in studies of gene flow across a fragmented landscape.     

Characterization of polymorphic microsatellite loci for the polychaete tubeworm Hobsonia florida

Eight dinucleotide microsatellite loci were isolated and characterized from Hobsonia florida, a tube‐dwelling ampharetid polychaete. The identified loci were highly polymorphic, with allelic diversity ranging from six to 11 alleles. Levels of expected heterozygosity were 0.52 or greater in all cases, averaging 0.78 across the complete set of loci. Cross‐species amplification was successful in three of the eight loci for one or both of the other species (Melinna cristata and Ampharete acutifrons) tested. Although these novel loci were designed for immediate utility in H. florida population‐level research, these results indicate they may prove useful in studies of other related taxa.     

Isolation and description of eight polymorphic microsatellite loci for the winged-kelp Alaria nana

Here I report on the isolation of eight microsatellites from the winged-kelp, Alaria nana, using an enrichment protocol. Using 55 individuals from Tatoosh, WA and complete data at all loci, loci displayed 6-11 alleles with observed and expected heterozygosities of 0.396-0.754, and 0.769-0.872 respectively. Using an isolated, randomly breeding subset, six of the eight loci were determined to be in Hardy-Weinberg equilibrium. These markers will be useful in assessing population structure in the intertidal and inferring patterns of dispersal.     

Characterization of 10 novel microsatellite loci for the brown marbled grouper, Epinephelus fuscoguttatus (Serranidae)

Epinephelus fuscoguttatus is a commercially important marine fish species in southeast Asia. Due to overfishing and water pollution, this species has been declared as near-threatened. Thus, to provide information to help maintain and preserve the species, microsatellites were developed, using an enriched genomic library method. Thirty individuals were collected from the hatchery of the Fishery Research Institute, Terengganu, Malaysia. These individuals, from four to six years old, originated from Sabah and are maintained in captive culture as broodstock. Genomic DNA was extracted from the fins of selected individuals that weighed 3-8 kg. Ten microsatellite loci were found to be polymorphic in this population, with 5 to 21 alleles per locus. Observed and expected heterozygosities ranged from 0.53 to 0.97 and 0.59 to 0.95, respectively. Only one locus deviated significantly from Hardy-Weinberg equilibrium and no significant linkage disequilibrium was found among the pairs of loci. These polymorphic microsatellite loci will be used by the Malaysian Fishery Research Institute for investigating genetic diversity and for developing breeding strategies.     

Characterization of 12 polymorphic microsatellite loci for the whitespotted bamboo shark (Chiloscyllium plagiosum Bennett)

Twelve polymorphic microsatellite loci without linkage disequilibrium were isolated and characterized from a microsatellite DNA-enriched DNA library for the whitespotted bamboo shark (Chiloscyllium plagiosum Bennett, 1830). These loci show polymorphism information content ranging from 0.384 to 0.885, allele number ranging from 4 to 12, effective allele number ranging from 1.686 to 9.438, and observed and expected heterozygosities from 0.229 to 1.000 and from 0.407 to 0.894 respectively. Four loci show strong Hardy-Weinberg deviations. We expect that these markers would be useful for population genetic and breeding studies of the whitespotted bamboo shark.     

Isolation and characterization of eight polymorphic microsatellite loci in the rainforest canopy tree,Syzygium sayeri (Myrtaceae)

Eight polymorphic microsatellite loci were isolated from the rainforest canopy tree, Syzygium sayeri, in order to study parentage and subsequently pollen dispersal among individuals in wild populations. Screening of one natural population (n = 64) mapped in a 500 × 500 m area at Cape Tribulation, north Queensland, Australia, yielded two to 11 alleles per locus with observed levels of heterozygosity ranging from 0.07 to 0.70. One locus was significantly out of Hardy–Weinberg equilibrium after Bonferroni correction for multiple tests. These loci should provide a useful tool in further understanding the dispersal patterns of this species.     

Characterization of eight polymorphic microsatellite DNA markers for the greenside darter,Etheostoma blennioides (Percidae)

The greenside darter, Etheostoma blennioides is a small benthic fish found in fast‐flowing streams in eastern North America. In Canada, this species is native to three, and introduced into one, Great Lakes tributaries in southwestern Ontario. It is currently listed as a species of Special Concern. To characterize population genetic structure and diversity in the Canadian populations of greenside darter, eight polymorphic microsatellite markers were developed for the species. The polymerase chain reaction primers were tested between 32 and 60 individuals from the Sydenham River and yielded a high number of alleles (four to 42 per locus), and observed heterozygosities ranging from 0.14 to 0.82.