Novel microsatellites from the European plaice (Pleuronectes platessa)––identification by data mining and cross-species amplification in other flatfishes

The European plaice (Pleuronectes platessa; Pleuronectidae) is considered the most important flatfish for fisheries in Europe. Overall catches have been reduced drastically throughout the past decades, indicating a severe decline in the natural populations. However, a limited set of genetic tools are available to improve stock assessment and management for the species. Sequences of European plaice and its congener, the winter flounder (Pleuronectes americanus) deposited in the public database were searched for short tandem repeats. Out of 22 loci derived from database sequences, eight were amplified successfully and genotyping of 23 wild-caught individuals showed expected heterozygosities ranging from 0.18 to 0.84. The average allele number was 4.75 per locus (range 2–11). Successful cross-species amplification of the markers was demonstrated from two related flatfishes. All eight markers were successfully amplified from the European flounder (Platichthys flesus), a phylogenetically closely related species, whereas three of them worked in Achiroides melanorhynchus, an endemic species of Southeast Asia for which no microsatellites have been described to date.     

Genetic linkage map of olive flounder, Paralichthys olivaceus

Olive flounder, Paralichthys olivaceus, is an important fish species in Asia, both for fisheries and aquaculture. As the first step for better understanding the genomic structure and functional analysis, we constructed a genetic linkage map for olive flounder based on 180 microsatellites and 31 expressed sequence tag (EST)-derived markers. Twenty-four linkage groups were identified, consistent with the 24 chromosomes of this species. The total map distance was 1,001.3 cM based on Kosambi sex-average mapping, and the average inter-locus distance was 4.7 cM. Linkage between the loci was identified by an LOD score of ≥3. This linkage map may be used to map quantitative trait loci associated with important traits of the species and may assist in breeding programs.     

Female maturity,reproductive potential,relative distribution,and growth compared between arrowtooth flounder (Atheresthes stomias) and Kamchatka flounder (A. evermanni) indicating concerns for management

Arrowtooth flounder (Atheresthes stomias) and Kamchatka flounder (A. evermanni), major piscivorous predators in the eastern Bering Sea and Aleutian Islands, are morphologically similar. Consequently the two species have been managed together as a species complex using the length‐ and age‐at‐maturity derived from Gulf of Alaska arrowtooth flounder, which had been the only available maturity estimates. However, there could be serious management consequences if the two species matured at significantly different ages and fork lengths. Therefore, this study was conducted during 2007 and 2008 to determine if there were significant differences in maturation between the two species. Significant differences in size and age of female maturation and growth were found. The age and length of 50% maturity (A_50,L_50, respectively) for arrowtooth flounder females is 7.6 years of age and 480 mm in body length. In comparison, A_50,L₅₀ of Kamchatka flounder females is 10.1 years of age and 550 mm, meaning that Kamchatka flounder has a significantly lower reproductive potential than arrowtooth flounder. The large difference in reproductive potential indicates that managing the two species together as a species complex using the reproductive characteristics of arrowtooth flounder, was not conservative for Kamchatka flounder. This study also determined that arrowtooth flounder maturation was consistent between the Gulf of Alaska and eastern Bering Sea populations.     

Development of 81 new polymorphic EST-derived microsatellite markers for the olive flounder,Paralichthys olivaceus

Expressed sequence tags (ESTs) can be used to identify microsatellite markers. We developed 81 polymorphic microsatellite markers from 4,940 ESTs of the olive flounder, Paralichthys olivaceus. Out of 100 EST-derived microsatellites for which PCR primers were designed, 81 loci were polymorphic in 30 individuals from a single natural population with 2–28 (mean 10.6) alleles per locus. The observed and expected heterozygosities of these loci were 0.033–1.000 and 0.033–0.965, respectively. Segregation analysis within a mapping family revealed non-amplifying null alleles at five loci. These new EST-derived microsatellite markers should be useful for population genetic analyses, pedigree tracing and constructing a linkage map for olive flounder.     

Microsatellite markers for diverse Salix species

Forty‐six microsatellites were isolated from an enriched library of Salix burjatica and tested on 20 individuals (of nine species/hybrids) from the National Willows Collection (IACR‐Long Ashton Research Station, UK). Twenty‐nine were monomorphic, gave multilocus or unscorable patterns, or were duplicates. The remaining 17 microsatellites gave 2–22 alleles/locus. Three microsatellites successfully cross‐amplified in 31 additional Salix species. A further six were tested on panels comprising 6–25 individuals from the 31 species. Cross‐amplification was successful in all cases. These results suggest that the microsatellites isolated here should prove useful for population studies in a wide range of Salix species.     

Chloroplast microsatellites in Prunus,Rosaceae

Ten chloroplast microsatellite markers were developed from Japanese plum (Prunus salicina) based on nucleotide sequences of c. 4300 bp from six chloroplast regions. Out of 10 microsatellites, seven markers contained mononucleotide repeats. Almost all microsatellites displayed discrete amplified fragments for 17 species in Prunus. The microsatellites generated 46 different fragment types and differentiated all used species. Polymorphism was also observed within species for all microsatellites.     

A novel genome‐wide microsatellite resource for species of Eucalyptus with linkage‐to‐physical correspondence on the reference genome sequence

Keystone species in their native ranges, eucalypts, are ecologically and genetically very diverse, growing naturally along extensive latitudinal and altitudinal ranges and variable environments. Besides their ecological importance, eucalypts are also the most widely planted trees for sustainable forestry in the world. We report the development of a novel collection of 535 microsatellites for species of Eucalyptus, 494 designed from ESTs and 41 from genomic libraries. A selected subset of 223 was evaluated for individual identification, parentage testing, and ancestral information content in the two most extensively studied species, Eucalyptus grandis and Eucalyptus globulus. Microsatellites showed high transferability and overlapping allele size range, suggesting they have arisen still in their common ancestor and confirming the extensive genome conservation between these two species. A consensus linkage map with 437 microsatellites, the most comprehensive microsatellite‐only genetic map for Eucalyptus, was built by assembling segregation data from three mapping populations and anchored to the Eucalyptus genome. An overall colinearity between recombination‐based and physical positioning of 84% of the mapped microsatellites was observed, with some ordering discrepancies and sporadic locus duplications, consistent with the recently described whole genome duplication events in Eucalyptus. The linkage map covered 95.2% of the 605.8‐Mbp assembled genome sequence, placing one microsatellite every 1.55 Mbp on average, and an overall estimate of physical to recombination distance of 618 kbp/cM. The genetic parameters estimates together with linkage and physical position data for this large set of microsatellites should assist marker choice for genome‐wide population genetics and comparative mapping in Eucalyptus.     

Gill ventilation and O2 extraction during graded hypoxia in two ecologically distinct species of flatfish,the flounder (Platichthys flesus) and the plaice (Pleuronectes platessa)

Synopsis Gill ventilation, breathing frequency, breath volume, oxygen extraction from the ventilatory water current and oxygen uptake through the gills were measured in flounder, Platichthys flesus, and plaice, Pleuronectes platessa, at water O₂ tensions ranging from 35 to 155 mm Hg at 10° C. Ventilation volumes were similar in the two species at high water O₂ tension. Exposure to hypoxic water elicited a larger increase in ventilation in the flounder. The per cent extraction of O₂ from water decreased slightly in both species as water O₂ tension was lowered. At comparable levels of ventilation O₂ extraction was higher in flounder. At the higher levels of water O₂ tension, O₂ uptake across the gills of flounder was stable, the critical O₂ tension being between 60 and 100 mm Hg. The plaice behaved as an oxygen conformer over the entire range of O₂ tensions investigated. The superior ability of the flounder in maintaining OZ uptake across the gills during a reduction in water O₂ tension may in part explain why the species, unlike plaice, inhabits very shallow waters with large fluctuations in dissolved oxygen.     

Genetic diversity and differentiation of the Korean starry flounder (Platichthys stellatus) between and within cultured stocks and wild populations inferred from microsatellite DNA analysis

The Korean starry flounder, Platichthys stellatus, is economically valuable coastal resident fish species. However, the annual catch of this fish has fluctuated and suffered major declines in Korea. We examined the genetic diversity and population structure for four wild populations and three hatchery stocks of Korean starry flounder to protect its genetic integrity using nine microsatellites. A group of 339 genotypes belonging to seven populations were screened. High degrees of polymorphism at the microsatellite loci were observed within both the wild and hatchery populations. Compared to the wild populations, genetic changes, including reduced genetic diversity and highly significant differentiation, have occurred in cultured stocks. Significant population differentiation was also observed in wild starry flounder populations. Similar degrees of inbreeding and significant Hardy–Weinberg equilibrium deviations were detected in both the wild and the hatchery populations. The genetic connectivity pattern identified four distinct metapopulations of starry flounder in Korea by clustering in the phylogenetic tree, Bayesian analyses, molecular variance analysis, PCA and multidimensional scaling analysis. A pattern of isolation-by-distance was not significant. This genetic differentiation may be the result of the co-effects of various factors, such as historic dispersal, local environment or anthropogenic activities. These results provide useful information for the genetic monitoring of P. stellatus hatchery stocks, for the genetic improvement of this species by selective breeding and for designing suitable management guidelines for the conservation of this species.     

Evaluation of allelic diversity at chloroplast microsatellite loci among common wheat and its ancestral species

Twenty four chloroplast microsatellite loci having more than ten mononucleotide repeats were identified from the entire chloroplast DNA sequence of common wheat, Triticum aestivum cv Chinese Spring. For each microsatellite, a pair of primers were designed to produce specific PCR products in the range of 100– 200 bp. The allelic diversity at the microsatellite loci was evaluated using 43 accessions from 11 Triticum and Aegilops species involved in wheat polyploid evolution. Polymorphic banding patterns were obtained at 21 out of 24 chloroplast microsatellite loci. The three monomorphic microsatellites were found to be located in coding regions. For the polymorphic microsatellites, the number of alleles per microsatellite ranged from 2 to 7 with an average of 4.33, and the diversity values (H) ranged from 0.05 to 0.72 with an average of 0.47. Significant correlations (P<0.01) were observed between the number of repeats and the number of alleles, and between the number of repeats and diversity value, respectively. The genetic diversity explained by chloroplast microsatellites and nuclear RFLP markers were compared using 22 tetraploid accessions. Although the number of alleles for nuclear RFLP markers was found to be higher than that for chloroplast microsatellites, similar diversity values were observed for both types of markers. Among common wheat and its ancestral species, the percentages of common chloroplast microsatellite alleles were calculated to examine their phylogenetic relationships. As a result, Timopheevi wheat species were clearly distinguished from other species, and Emmer and common wheat species were divided into two main groups, each consisting of a series of wild and cultivated species from tetraploid to hexaploid. This indicates that the two types of chloroplast genomes of common wheat might have independently originated from the corresponding types of wild and cultivated Emmer wheat species. Received: 6 October 2000 / Accepted: 13 March 2001     

Isolation and characterization of microsatellites from a marine foodfish species ribbonfish Trichiurus haumela

The ribbonfish, Trichiurus haumela, is an important marine foodfish species. Supply of this fish relies on capture from the wild. No information about genetic diversity and population structure of wild stocks is available. Therefore, we developed the first set of 10 polymorphic microsatellites. The average allele number was 13.2 per locus ranging from six to 20. The expected heterozygosity was 0.84, whereas the observed heterozygosity was 0.71. This set of microsatellites provides a tool for assessing genetic diversity and population structure of this species.     

Characterization of microsatellites located within the genes of goldfish (Carassius auratus auratus)

The goldfish (Carassius auratus auratus; Cyprinidae) is not only an important ornamental fish species, but also a useful model for biological studies. The sequence of goldfish genes present in the public database was searched for short tandem repeats, and 11 polymorphic microsatellites were detected within eight important genes. Two microsatellites were located in coding regions of the c‐myc and GAP‐43 genes, respectively, whereas the others were mainly located in 5′ and 3′ untranscribed regions of other genes, such as gonadotropin and activin. The average allele number of these microsatellites was 5.5 per locus with a range between 3 and 9. These microsatellites will be useful for ecological and population genetic studies of this species, as well as for the ornamental fish industry.     

Characterization of microsatellite markers in the endangered Sinojackia xylocarpa (Styracaceae) and cross‐species amplification in closely related taxa

Twenty‐four polymorphic microsatellite loci were isolated and characterized from an AAG‐enriched genomic library of Sinojackia xylocarpa. The average allele number of these microsatellites was 3.3 per locus, ranging from two to seven. The observed and expected heterozygosities at population level were 0.10–0.83 and 0.10–1.00, respectively. In addition, successful cross‐species amplification of this set of microsatellites in three other species of Sinojackia and a closely related taxon, Changiostyrax dolichocarpa, suggested that this set of microsatellite markers should provide a useful tool for genetic and conservation studies of Sinojackia species and other closely related taxa in the Styracaceae.     

Novel microsatellites from the green swordtail (Xiphophorus hellerii) also display polymorphism in guppy (Poecilia reticulata)

The green swordtail (Xiphophorus hellerii; Poeciliidae) is a popular ornamental freshwater fish species. Fourteen microsatellites were isolated from a green swordtail genomic library enriched for CA‐repeats. Thirteen microsatellites were polymorphic in green swordtail; interestingly four of them were tetranucleotide‐type. Cross‐species amplification showed that 10 of the 14 microsatellites were polymorphic in guppy (Poecilia reticulata; Poeciliidae) as well. No significant directional difference of allele length was seen between the two species at any of the loci tested.     

Twelve novel polymorphic microsatellites in a marine fish species,yellow croaker Larimichthys polyactis

We isolated 12 polymorphic microsatellites from an important marine food fish Larimichthys polyactis and characterized them in 32 unrelated individuals. Among the 12 microsatellites, four were tetranucleotide repeats and eight were dinucleotide repeats. The allele number ranged from five to 25 with an average of 15.4/locus; average expected heterozygosity was 0.81, ranging from 0.57 to 0.95, whereas the observed heterozygosity ranged from 0.34 to 1.00 (average: 0.78). Nine of the 12 markers conformed to Hardy–Weinberg equilibrium and showed no sign of linkage. These microsatellites will be useful for population genetic studies and selective breeding programs of this species.     

New microsatellite markers in turbot (Scophthalmus maximus) derived from an enriched genomic library and sequence databases

Scophthalmus maximus is an important commercially aquaculture fish species. We tackle the search for new microsatellites using two different approaches: an enriched partial genomic library and a screening of all turbot DNA sequences deposited in GenBank. Out of 15 genomic library derived loci, five gave working primer pairs, with expected heterozygosities (H_E) ranging from 0.13 to 0.91. Out of seven loci derived from database sequences, two amplified successfully with an H_E ranging from 0.56 to 0.63. The average allele number of these microsatellites was 5.7 per locus with a range between two and 15.     

Characterization and cross-species amplification of microsatellites from the endangered Hawksbill turtle (Eretmochelys imbricate)

Twelve novel polymorphic microsatellites were isolated from the endangered Hawksbill turtle (Eretmochelys imbricate). Eight of 12 markers were used to study genetic diversity of two sea turtle species: E. imbricate and green sea turtle (C. mydas). In E. imbricate, the average allele number of the eight microsatellites was 6.25/locus with a range of 3–13. The average expected and observed heterozygosity was 0.66 and 0.63 respectively. In C. mydas, the average allele number of the eight markers was 11.63/locus. The observed heterozyosity (0.68) was lower than the expected heterozyosity (0.79). Most of 12 microsatellites amplified specific and polymorphic PCR products in other six turtle species. Hence, the developed microsatellites would facilitate studies on genetic diversity and population structure of E. imbricate and other marine turtle species.     

Zoogeographical classification of the macroparasite faunas of four flatfish species from the northeastern Atlantic

The macroparasite faunas of four righteye flounder species (flounder Platichthys flesus, witch flounder Glyptocephalus cynoglossus, American plaice Hippoglossoides platessoides and Atlantic halibut Hippoglossus hippoglossus) caught off the northern Norwegian coast at 70°N, were classified zoogeographically. The parasite faunas of all four host species were dominated by boreal parasites. This appears to be the situation with the entire area of distribution of these flatfish species. The relationship between the extension of the range of the host species towards the Arctic and the proportion of parasites belonging to the arctic group is indicated.     

Isolation and characterization of twelve novel microsatellites in yellow catfish, Pelteobagrus fulvidraco

The yellow catfish Pelteobagrus fulvidraco is a freshwater fish species. Due to overfishing and pollution of freshwater ecosystems, the wild stocks of this fish reduced substantially. We isolated and characterized 12 polymorphic microsatellites of this species. The number of alleles at the 12 microsatellite loci ranged from four to eight, with an average of 6.6/locus. The average observed heterozygosity was 0.72, whereas the expected heterozygosity ranged from 0.60 to 0.86 (average: 0.80). All 12 microsatellites conformed to Hardy–Weinberg Equilibrium and were in linkage equilibrium. These 12 novel microsatellites could facilitate studies of genetic diversity and population structure of the yellow catfish to supply necessary information of conservation of the yellow catfish.     

On the low viscosity blood of two cold water,marine sculpins

Summary The viscosities of blood from shorthorn sculpin (Myoxocephalus scorpius), longhorn sculpin (Myoxocephalus octodecemspinosus) and winter flounder (Pseudopleuronectes americanus) were compared using a cone-plate viscometer. Both species of sculpin were almost identical with respect to blood and plasma viscosity at the temperatures (0 and 15°C) and shear rates (2.3–90/s) examined. In contrast, the viscosities of winter flounder blood and plasma were considerably greater than those observed in the sculpins. This difference in blood viscosity between the shorthorn sculpin and the winter flounder persisted over the hematocrit range of 0 to 40% red blood cells. The viscosity of the plasma and the interactions between plasma proteins and red blood cells appeared to be the major reasons for the relatively high viscosity of the flounder blood. Although a proportion of the flounder blood viscosity was attributable to fibrinogen, other plasma proteins also appeared to play a significant role. The relatively low blood viscosity of the sculpin species may confer a circulatory advantage during periods of low water temperatures.