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).     

Genetic structure in the marbled rockfish (Sebastiscus marmoratus) across most of the distribution in the northwestern Pacific

The marbled rockfish (Sebastiscus marmoratus) is an important species that is widely distributed across the marginal seas of the northwestern Pacific. Several kinds of DNA markers, such as amplified fragment length polymorphisms (AFLP), mitochondrial DNA (mtDNA) and single nucleotide polymorphisms (SNPs), have been used to assess the population genetic characteristics of this species in previous studies. However, there have been no genetic profiling studies to cover the entire distribution. Here, six highly polymorphic microsatellite markers were applied to 18 populations across a spatially large area (from the Sea of Japan in the north to the South China Sea in the south). The results showed that the whole population exhibits high, stable genetic diversity, low relatedness and large effective population size. There was very weak genetic differentiation overall and no isolation by distance occurred among the populations, which may be attributed to significant contemporary gene flow, each generation. The above results may lead us to infer that the recent S. marmoratus population structure could be considered as one large integrated population. The present study will be beneficial to population conservation and fisheries management of S. marmoratus and will lead to better insights into the genetic characteristics of other species that belong to the Sebastidae family.     

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 36 polymorphic microsatellite markers in Schima superba (Theaceae)

? Premise of the study: Our objective was to develop microsatellite markers to investigate the level of genetic diversity within and among populations in a dominant evergreen broad-leaved tree, Schima superba, in southern China. ? Methods and Results: Thirty-six microsatellite markers were developed and showed polymorphism in three populations. The number of alleles per locus ranged from six to 34, with an average of 19. The observed and expected heterozygosities ranged from 0.242 to 1.000 and from 0.504 to 0.945, respectively. ? Conclusions: The developed microsatellites will be useful for studying genetic diversity and population structure in S. superba.     

Isolation and characterization of polymorphic microsatellite markers for peacock wrasse (Symphodus tinca)

Eight polymorphic microsatellite loci were isolated and characterized for the peacock wrasse (Symphodus tinca), a labrid fish inhabiting the Mediterranean and Black seas. Characterization of 35 individuals from the western Mediterranean indicated a relatively high allelic diversity (mean = 12.4, range 9–17), and observed heterozygosity ranging from 0.65 to 0.91. We found no evidence of linkage disequilibrium between pairs of loci. Two loci showed significant departure from Hardy–Weinberg equilibrium. These polymorphic markers can be useful in most basic population genetic applications.     

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.     

基于454测序技术的青藏高原黄绿蜜环菌微卫星引物的开发

【目的】本研究利用454焦磷酸测序技术,对青藏高原黄绿蜜环菌(Armillaria luteo-virens)转录组进行测序,从获得的Expressed sequence tags(EST)序列中开发EST-SSR引物。【方法】利用高通量测序获得的EST序列设计微卫星引物,通过PCR扩增、琼脂糖凝胶电泳和毛细管电泳检测筛选出合格的微卫星引物。【结果】共得到了1997121条reads,总数据量超过80Mb,序列平均长度为449bp。对于所获得的reads进行拼接后得到了22236条非冗余的EST序列,其中含有2024条contigs(平均读长974bp)和20212条singletons(平均读长404bp)。在所有序列中共找到321条符合条件的含有SSR的序列,从中随机选择98对,成功开发出27对具有多态性条带的微卫星引物。利用采集自3个不同居群的66个个体对上述27对引物进行验证,有17对引物符合Hardy-Weinberg平衡且没有连锁不平衡现象。【结论】首次成功利用高通量测序技术开发的EST-SSR引物将会对今后黄绿蜜环菌遗传多样性的研究以及种质资源鉴定、遗传图谱构建等打下了坚实基础。     

Isolation and characterization of highly polymorphic microsatellite markers in Hypochaeris radicata (Asteraceae)

We developed five highly polymorphic dinucleotide microsatellite loci for the grassland species Hypochaeris radicata (Asteraceae). Polymorphism of these markers was examined in six populations in the Netherlands. All loci were polymorphic in all populations. The number of alleles per locus varied between 18 and 43. Expected heterozygosity was between 0.86 and 0.91. Cross‐species amplification was tested in six Hypochaeris species and was successful for three different loci in four species. These microsatellites are a useful tool in population genetic, dispersal and metapopulation studies or in testing levels of inbreeding.     

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.     

Development and characterization of nine polymorphic microsatellite markers in the sand goby Pomatoschistus minutus (Gobiidae)

A microsatellite‐enriched genomic library was constructed for the sand goby, Pomatoschistus minutus (Pallas 1770), and nine polymorphic DNA microsatellite markers of high quality were successfully optimized. Characterization of 96 individuals from the Vaccarès lagoon (France) showed moderate to high levels of polymorphism (two to 54 alleles). All the markers conformed to Hardy–Weinberg equilibrium and showed no evidence of null alleles, large allele dropout, stuttering and linkage disequilibrium between pairs of loci. These markers successfully amplify in three closely related species and can be employed to investigate population genetic structure and to clarify paternity in Pomatoschistus 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.