The complete mitochondrial genome of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae): genome characterization and phylogenetic considerations

The complete mitochondrial genome sequence of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae) was determined and phylogenetic analysis was conducted to elucidate the evolutionary relationship of the marbled rockfish with other Sebastinae species. This mitochondrial genome, consisting of 17301 bp, is highly similar to that of most other vertebrates, containing the same gene order and an identical number of genes or regions, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one putative control region. Most of the genes are encoded on the H-strand, while the ND6 and seven tRNA genes (for Gln, Ala, Asn, Tyr, Ser (UCA), Glu, and Pro) are encoded on the L-strand. The reading frame of two pairs of genes overlapped on the same strand (the ATPase 8 and 6 genes overlapped by ten nucleotides; ND4L and ND4 genes overlapped by seven nucleotides). The possibly nonfunctional light-strand replication origin folded into a typical stem-loop secondary structure and a conserved motif (5'-GCCGG-3') was found at the base of the stem within the tRNA(Cys) gene. An extent termination-associated sequence (ETAS) and conserved sequence blocks (CSB) were identified in the control region, except for CSB-1; unusual long tandem repeats were found at the 3' end of the control region. Phylogenetic analyses supported the view that Sebastinae comprises four genera (Sebates, Hozukius, Helicolenus, and Sebasticus).     

The complete mitochondrial genome of the marbled rockfish <Emphasis Type="Italic">Sebastiscus marmoratus</Emphasis> (Scorpaeniformes,Scorpaenidae): Genome characterization and phylogenetic considerations

The complete mitochondrial genome sequence of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae) was determined and phylogenetic analysis was conducted to elucidate the evolutionary relationship of the marbled rockfish with other Sebastinae species. This mitochondrial genome, consisting of 17301 bp, is highly similar to that of most other vertebrates, containing the same gene order and an identical number of genes or regions, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one putative control region. Most of the genes are encoded on the H-strand, while the ND6 and seven tRNA genes (for Gln, Ala, Asn, Tyr, Ser (UCA), Glu, and Pro) are encoded on the L-strand. The reading frame of two pairs of genes overlapped on the same strand (the ATPase 8 and 6 genes overlapped by ten nucleotides; ND4L and ND4 genes overlapped by seven nucleotides). The possibly nonfunctional light-strand replication origin folded into a typical stem-loop secondary structure and a conserved motif (5′-GCCGG-3′) was found at the base of the stem within the tRNA^Cys gene. An extent termination-associated sequence (ETAS) and conserved sequence blocks (CSB) were identified in the control region, except for CSB-1; unusual long tandem repeats were found at the 3′ end of the control region. Phylogenetic analyses supported the view that Sebastinae comprises four genera (Sebastes, Hozukius, Helicolenus, and Sebastiscus).     

The complete mitochondrial genome of the rockfish Sebastes schlegeli (Scorpaeniformes, Scorpaenidae)

We isolated rockfish Sebastes schlegeli mitochondrial DNA by long-polymerase chain reaction (Long-PCR) with conserved primers, and sequenced it by primer walking using flanking sequences as sequencing primers. S. schlegeli mitochondrial DNA consists of 16,526 bp and its structural organization is conserved in comparison with other fish. Using mitochondrial control region sequences, we compared related species from the genus Sebastes (Scorpaeniformes, Scorpaenidae), showing the similarity of S. schlegeli isolated from Korean and Japanese waters. In this paper, we report the basic characteristics of the S. schlegeli mitochondrial genome including structural organization, base composition of rRNAs and the tRNAs and protein-encoding genes, and characteristics of mitochondrial tRNAs. These findings are applicable to aquaculture and to molecular phylogenetics in the genus Sebastes.     

Cloning and characterization of 29 tetranucleotide and two dinucleotide polymorphic microsatellite loci from the endangered marbled murrelet (Brachyramphus marmoratus)

We developed 31 novel, polymorphic microsatellite loci in the marbled murrelet (Brachyramphus marmoratus), a critically endangered seabird. Variability was tested on 15 individuals from the Santa Cruz, California population, with each locus characterized by two to 12 alleles. Observed levels of heterozygosity ranged from 0.13 to 0.93. These loci provide a valuable means of assessing the population structure and demographic parameters of this species, which may be critical to its conservation across a fragmented habitat.     

Isolation and characterization of microsatellite markers for the Korean rockfish, Sebastes schlegeli

The Korean rockfish (Sebastes schlegeli) is an important commercial fish that is widely used in aquaculture. We isolated and characterized 18 polymorphic microsatellite loci from the Korean rockfish using a (GT)(13)-enriched genomic library. Polymorphism was assessed in 48 individuals from a single population collected from the northern coastal waters of the Yellow Sea. The observed and expected heterozygosities ranged from 0.0244 to 0.7660 (mean 0.4194) and 0.0244 to 0.8758 (mean 0.5002), respectively. Polymorphism at these loci indicated from two to 15 alleles (mean 5.7); 14 of 18 loci conformed to Hardy-Weinberg equilibrium. These markers should be useful for management and conservation studies of this species.     

Isolation and characterization of polymorphic microsatellite markers from Primula nutans (Primulaceae)

Seven polymorphic microsatellite loci were developed for a perennial seashore plant, Primula nutans. Degenerate oligonucleotide‐primed (DOP)–polymerase chain reaction (PCR)‐amplified DNA was ligated to TOPO TA vector and screened with radioactively labelled dinucleotide repeat probes. A sample of 378 individuals from Finland, Norway and Russia were used to characterize those loci, which exhibited two to four alleles per locus with observed heterozygosity of 0.003–0.229 and expected heterozygosity of 0.016–0.527. No linkage disequilibrium was found between these seven loci. These are the first microsatellite markers reported for P. nutans.     

Isolation and characterization of nine polymorphic microsatellite loci in the rock carp, Procypris rabaudi (Tchang)

Nine highly polymorphic microsatellite loci were isolated from AC- and GATA-repeat microsatellite enrichment DNA libraries in the rock carp, Procypris rabaudi (Tchang). The number of alleles for these loci ranged from eight to 18 in tested individuals. Polymorphism information content ranged from 0.712 to 0.908 with an average of 0.837. Average observed and expected heterozygosities were 0.719 and 0.870, respectively. These molecular markers will be useful for the assessment of genetic diversity and analysis of population structure in wild rock carp.     

Isolation and characterization of polymorphic microsatellite markers in the endangered Nothotsuga longibracteata (Pinaceae)

Twelve polymorphic microsatellite loci were isolated and characterized from an AC‐enriched genomic library of Nothotsuga longibracteata. The average allele number of these microsatellites was 8.3 per locus, ranging from two to 13. The ranges of observed and expected heterozygosities were 0.03–0.97 and 0.09–0.88, respectively. These polymorphic markers provide useful tools for the study of evolutionary history and conservation genetics of N. longibracteata.     

Isolation and characterization of polymorphic microsatellite markers for the brown-headed nuthatch (Sitta pusilla)

Populations of brown-headed nuthatches (Sitta pusilla) are declining throughout the species range. Here we characterize twelve polymorphic microsatellite loci for this species. Analysis of 32 presumably unrelated individuals from a single population revealed an average of 14.9 alleles per locus (range 4–25), an average observed heterozygosity of 0.74 (range 0.52–0.94) and an average polymorphic information content of 0.80 (range 0.57–0.95). We anticipate that these microsatellite markers will be useful for population genetic and behavioral studies on the brown-headed nuthatch and closely related species.     

Isolation and characterization of polymorphic microsatellite markers in Anthyllis vulneraria

To study the reproductive system of the putative autogamous species Anthyllis vulneraria in Belgian calcareous grasslands, eight polymorphic microsatellite loci were developed using the sequence‐tagged microsatellite profiling technique and 35 plants were typed for all loci. No linkage disequilibrium was found between any pair of loci. Over the loci, the number of alleles ranged from two to five. Observed and expected heterozygosities ranged from 0.053 to 0.688 and from 0.053 to 0.631, respectively. The estimated F_IS values (F_IS = 0.031 and 0.122) are not in accordance with a predominantly selfing reproductive system.     

Genetic and morphological identification of Sebastiscus tertius in the East China Sea (Scorpaeniformes: Scorpaenidae)

The allozymes and morphology of 110 specimens of three Sebastiscus species (S. marmoratus, S. tertius, and S. albofasciatus) in the East China Sea and near Japan were compared. Results of 20 allozyme loci studied showed that all three species were closely related (Nei's unbiased genetic distances, 0.057–0.133) but could be identified on the basis of informative loci with a few exceptions. Initial identification based on color patterns agreed with allozyme identification in more than 98% of Sebastiscus specimens and agreed completely in S. albofasciatus. One specimen that was initially identified as S. marmoratus because of the dark body color was actually S. tertius according to two informative allozyme loci. Number of pectoral fin rays differed between S. marmoratus (18 or fewer, 98%) and S. tertius (19 or more, 85%) in this study. The previously mentioned dark specimen had 19 pectoral fin rays, which are characteristic in S. tertius. Using seven morphological measurements, canonical discriminant analysis between S. marmoratus and S. tertius classified less than 90% of specimens into the original groups (species). Some specimens of S. tertius resembled S. marmoratus in body shape and vice versa. A combination of genetic characterization and morphological examination is necessary to identify S. marmoratus and S. tertius accurately. Distinction based on allozymes and color patterns with numbers of pectoral fin rays should provide satisfactory identification. Received: May 16, 2000 / Revised: December 19, 2000 / Accepted: January 24, 2001     

Isolation and characterization of nine polymorphic microsatellite loci from the desert locust,Schistocerca gregaria

Because of the scarcity of polymorphic genetic markers, only a few genetic studies on the population structure of the desert locust, Schistocerca gregaria, have been carried out. We isolated and characterized nine polymorphic dinucleotide microsatellite loci. These markers were evaluated using individuals from Niger and Senegal. Seven of these microsatellite markers are also applicable to the nongregarious subspecies Schistocerca gregaria flaviventris. Cross‐species applicability was limited to one of the loci in the sister species S. americana and in the locust Locusta migratoria.     

Isolation and characterization of 12 polymorphic microsatellite markers from ladyfish (Elops saurus Linnaeus)

Ladyfish (Elops saurus Linnaeus) is an economically important marine fish species. 76 microsatellite loci were isolated from an enriched genomic library of Elops saurus. Twelve of these markers were polymorphic in a test population with alleles per locus ranging from three to nine. The number of observed, expected heterozygosity and polymorphism information content (PIC) per locus in 20 individuals ranged from 0.2000 to 1.0000, 0.1897–0.8846, 0.1769–0.8476, respectively. One markers significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction analysis and there was no significant linkage disequilibrium found between pairs of markers. As a result, 12 microsatellite markers probably should provide sufficient level of genetic diversity to investigate the fine-scale population structure, stock management and enhancement, genetic linkage map construction and molecular marker-assisted breeding in Elops saurus Linnaeus.     

Isolation and characterization of polymorphic microsatellite DNA markers in the rock bream (Oplegnathus fasciatus)

From a (GT)₁₃-enriched genomic library of Oplegnathus fasciatus, 14 polymorphic microsatellite were isolated and characterized in a test population with alleles ranging from two to nine, the observed and expected heterozygosities from 0.0000 to 1.0000, and from 0.1726 to 0.8507, respectively. Five loci deviated from the Hardy–Weinberg equilibrium, and linkage disequilibrium between two loci was significant. Two loci were also polymorphic in Pagrosomus major assessed for cross-species amplification. These polymorphic microsatellites will be useful for genetic diversity analysis and molecule-assisted breeding for O. fasciatus. Changwei Shao contributed equally.     

Isolation and characterization of eleven polymorphic microsatellite markers of sand lance (Ammodytes personatus)

Eleven polymorphic microsatellite markers were developed to delineate population structure of Ammodytes personatus. These markers had between 8 and 27 alleles. Expected heterozygosity ranged from 0.818 to 0.965, whereas the observed heterozygosity ranged from 0.441 to 0.886. Five of the eleven markers conformed to Hardy–Weinberg equilibrium. We believe the markers will be useful for genetic diversity study of A. personatus.     

Isolation and characterization of eight polymorphic microsatellite markers from pink conch (Strombus gigas)

Many marine organisms have pelagic larvae, and these are often important agents of dispersal. The larval phase and the multiple paternity that occur in marine gastropods such as Strombus gigas are crucial for the success of this species throughout the Caribbean Sea. To analyse these factors, we developed eight microsatellite loci specific to S. gigas. On the same set of individuals, the microsatellite loci exhibited a greater level of polymorphism than previously studied allozyme markers and thus, will permit fine‐scale analysis and larval pool studies.     

Isolation and characterization of polymorphic microsatellite markers in the red snow crab (Chionoecetes japonicus)

A total of 12 polymorphic microsatellite DNA loci were isolated from the red snow crab, Chionoecetes japonicus (Brachyura: Majidae), one of important fisheries resources in the Far East. The number of alleles observed at each locus ranged from two to 19, with the observed and expected heterozygosities of 0.125-0.875 and 0.156-0.949, respectively, suggesting these loci to be a useful molecular marker for population analysis in this species. Of the 12 loci, seven also were available for genotyping of the snow crab, Chionoecetes opilio, implying these loci as a useful molecular marker in the genus Chionoecetes.