A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.)

<p>Abstract</p> <p>Background</p> <p>Atlantic salmon (<it>Salmo salar </it>L.) is an environmentally and economically important organism and its gene content is reasonably well characterized. From a transcriptional standpoint, it is important to characterize the changes in gene expression over the course of unperturbed early development, from fertilization through to the parr stage.</p> <p>Findings</p> <p><it>S. salar </it>samples were taken at 17 time points from 2 to 89 days post fertilization. Total RNA was extracted and cRNA was synthesized and hybridized to a newly developed 44K oligo salmonid microarray platform. Quantified results were subjected to preliminary data analysis and submitted to NCBI's Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE25938. <url>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25938</url></p> <p>Conclusions</p> <p>Throughout the entire period of development, several thousand genes were found to be differentially regulated. This work represents the trancriptional characterization of a very large geneset that will be extremely valuable in further examination of the transcriptional changes in Atlantic salmon during the first few months of development. The expression profiles can help to annotate salmon genes in addition to being used as references against any number of experimental variables to which developing salmonids might be subjected.</p

A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis

AbstractBluefin tunas are one of the most important fishery resources worldwide. Because of high market values, bluefin tuna farming has been rapidly growing during recent years. At present, the most common form of the tuna farming is based on the stocking of wild-caught fish. Therefore, concerns have been raised about the negative impact of the tuna farming on wild stocks. Recently, the Pacific bluefin tuna (PBT), Thunnus orientalis, has succeeded in completing the reproduction cycle under aquaculture conditions, but production bottlenecks remain to be solved because of very little biological information on bluefin tunas. Functional genomics approaches promise to rapidly increase our knowledge on biological processes in the bluefin tuna. Here, we describe the development of the first 44K PBT oligonucleotide microarray (oligo-array), based on whole-genome shotgun (WGS) sequencing and large-scale expressed sequence tags (ESTs) data. In addition, we also introduce an initial 44K PBT oligo-array experiment using in vitro grown peripheral blood leukocytes (PBLs) stimulated with immunostimulants such as lipopolysaccharide (LPS: a cell wall component of Gram-negative bacteria) or polyinosinic:polycytidylic acid (poly I:C: a synthetic mimic of viral infection). This pilot 44K PBT oligo-array analysis successfully addressed distinct immune processes between LPS- and poly I:C- stimulated PBLs. Thus, we expect that this oligo-array will provide an excellent opportunity to analyze global gene expression profiles for a better understanding of diseases and stress, as well as for reproduction, development and influence of nutrition on tuna aquaculture production

Regulation and Expression of Sexual Differentiation Factors in Embryonic and Extragonadal Tissues of Atlantic salmon

Background: The products of cyp19, dax, foxl2, mis, sf1 and sox9 have each been associated with sex-determiningprocesses among vertebrates. We provide evidence for expression of these regulators very early in salmoniddevelopment and in tissues outside of the hypothalamic-pituitary-adrenal/gonadal (HPAG) axis. Although thefunction of these factors in sexual differentiation have been defined, their roles in early development before sexualfate decisions and in tissues beyond the brain or gonad are essentially unknown.Results: Bacterial artificial chromosomes containing salmon dax1 and dax2, foxl2b and mis were isolated and theregulatory regions that control their expression were characterized. Transposon integrations are implicated in theshaping of the dax and foxl2 loci. Splice variants for cyp19b1 and mis in both embryonic and adult tissues weredetected and characterized. We found that cyp19b1 transcripts are generated that contain 5’-untranslated regionsof different lengths due to cryptic splicing of the 3’-end of intron 1. We also demonstrate that salmon mistranscripts can encode prodomain products that present different C-termini and terminate before translation of theMIS hormone. Regulatory differences in the expression of two distinct aromatases cyp19a and cyp19b1 are exerted,despite transcription of their transactivators (ie; dax1, foxl2, sf1) occurring much earlier during embryonicdevelopment.Conclusions: We report the embryonic and extragonadal expression of dax, foxl2, mis and other differentiationfactors that indicate that they have functions that are more general and not restricted to steroidogenesis andgonadogenesis. Spliced cyp19b1 and mis transcripts are generated that may provide regulatory controls for tissueordevelopment-specific activities. Selection of cyp19b1 transcripts may be regulated by DAX-1, FOXL2 and SF-1complexes that bind motifs in intron 1, or by signals within exon 2 that recruit splicing factors, or both. Thepotential translation of proteins bearing only the N-terminal MIS prodomain may modulate the functions of otherTGF b family members in different tissues. The expression patterns of dax1 early in salmon embryogenesisimplicate its role as a lineage determination factor. Other roles for these factors during embryogenesis and outsidethe HPAG axis are discussed

Evolution of duplicated IgH loci in Atlantic salmon, Salmo salar

<p>Abstract</p> <p>Background</p> <p>The Atlantic salmon (<it>Salmo salar</it>) immunoglobulin heavy chain (<it>IgH</it>) locus possesses two parallel <it>IgH </it>isoloci (<it>IGH-A </it>and <it>IGH-B</it>), that are related to the genomic duplication event in the family Salmonidae. These duplicated <it>IgH </it>loci in Atlantic salmon provide a unique opportunity to examine the mechanisms of genome diversity and genome evolution of the <it>IgH </it>loci in vertebrates. In this study, we defined the structure of these loci in Atlantic salmon, and sequenced 24 bacterial artificial chromosome (BAC) clones that were assembled into the <it>IGH-A </it>(1.1 Mb) and <it>IGH-B </it>(0.9 Mb) loci. In addition, over 7,000 cDNA clones from the <it>IgH </it>variable (V<smcaps>H</smcaps>) region have been sequenced and analyzed.</p> <p>Results</p> <p>The present study shows that the genomic organization of the duplicated <it>IgH </it>loci in Atlantic salmon differs from that in other teleosts and other vertebrates. The loci possess multiple Cτ genes upstream of the Cμ region, with three of the Cτ genes being functional. Moreover, the duplicated loci possess over 300 V<smcaps>H</smcaps> segments which could be classified into 18 families. This is the largest number of V<smcaps>H</smcaps> families currently defined in any vertebrate. There were significant structural differences between the two loci, indicating that both <it>IGH-A </it>and <it>-B </it>loci have evolved independently in the short time after the recent genome duplication approximately 60 mya.</p> <p>Conclusions</p> <p>Our results indicate that the duplication of the <it>IgH </it>loci in Atlantic salmon significantly contributes to the increased diversity of the antibody repertoire, as compared with the single <it>IgH </it>locus in other vertebrates.</p

Interaksi Masyarakat Keturunan Arab dengan Masyarakat Setempat di Pekalongan

Dalam penelitian ini penulis mengeksplorasi interaksi antara masyarakat keturunan Arab dengan masyarakat setempat di Kelurahan Klego Kota Pekalongan serta mengetahui faktor pendorong dan penghambat terjadinya interaksi antara masyarakat keturunan Arab dengan masyarakat setempat. Penelitian ini menggunakan metode kualitatif. Teknik pengumpulan data melalui metode wawancara, observasi, dan dokumentasi. Hasil penelitian menunjukan bahwa terjadi interaksi antara masyarakat keturunan Arab dengan masyarakat setempat dengan intensitas dan kegiatan kebudayaan tertentu. Faktor pendukung terjadinya interaksi adalah adanya perkawinan campuran, terutama pada masyarakat keturunan Arab non-sayyid, dengan masyarakat setempat serta adanya kerjasama dalam bidang perdagangan. Sedangkan faktor penghambat terjadinya proses interaksi adalah adanya prasangka dan stereotip pada masyarakat keturunan Arab yang merasa masyarakat setempat kurang Islami, sebaliknya masyarakat setempat merasa masyarakat keturunan Arab itu sombong. Keturunan Arab yang tinggal di Kelurahan Klego terdiri dari golongan sayyid dan golongan non-sayyid. Keturunan Arab dari golongan non-sayyid sudah dapat berbaur dengan masyarakat setempat sedangkan keturunan Arab dari golongan sayyid belum berbaur dengan masyarakat non-Arab. Masyarakat keturunan Arab memiliki simbol-simbol seperti bahasa, pakaian, bangunan yang sangat mempengaruhi interaksi antara masyarakat keturunan Arab dengan masyarakat setempat. In this study, the author explores the interaction between people of Arab descent and the local people in the village of Klego Pekalongan city and also the factors that drive and inhibit the interaction between them. This study uses qualitative methods. The technique of collecting data are interviews, observation, and documentation. The results show that there is a pattern of interaction between people of Arab descent with the local people. Factors supporting the occurrence of interactions are the presence of mixed marriages, especially in the Arab non-sayyid descent, with the local community as well as the cooperation in the field of trade. While the factors inhibiting the interaction process is the existence of prejudice and stereotypes of people of Arab descent at a local community as less Islami. On the other hand, the local people feel that people of Arab descent are exclusive. The Arab descent living in the Village Klego consists of groups and classes of non-sayyid and sayyid. Arab descent from the class of non-sayyid are able to mingle with the local people, whereas Arab descent of sayyid cannot mingle with non-Arab communities. Society of Arab descent has symbols such as language, clothing, and building that strongly influence the interaction of people of Arab descent with the local community

EST and mitochondrial DNA sequences support a distinct Pacific form of salmon louse, Lepeophtheirus salmonis.

Abstract Nuclear deoxyribonucleic acid sequences from approximately 1

Genomic Resources for Sea Lice: Analysis of ESTs and Mitochondrial Genomes

Sea lice are common parasites of both farmed and wild salmon. Salmon farming constitutes an important economic market in North America, South America, and Northern Europe. Infections with sea lice can result in significant production losses. A compilation of genomic information on different genera of sea lice is an important resource for understanding their biology as well as for the study of population genetics and control strategies. We report on over 150,000 expressed sequence tags (ESTs) from five different species (Pacific Lepeophtheirus salmonis (49,672 new ESTs in addition to 14,994 previously reported ESTs), Atlantic L. salmonis (57,349 ESTs), Caligus clemensi (14,821 ESTs), Caligus rogercresseyi (32,135 ESTs), and Lernaeocera branchialis (16,441 ESTs)). For each species, ESTs were assembled into complete or partial genes and annotated by comparisons to known proteins in public databases. In addition, whole mitochondrial (mt) genome sequences of C. clemensi (13,440 bp) and C. rogercresseyi (13,468 bp) were determined and compared to L. salmonis. Both nuclear and mtDNA genes show very high levels of sequence divergence between these ectoparastic copepods suggesting that the different species of sea lice have been in existence for 37–113 million years and that parasitic association with salmonids is also quite ancient. Our ESTs and mtDNA data provide a novel resource for the study of sea louse biology, population genetics, and control strategies. This genomic information provides the material basis for the development of a 38K sea louse microarray that can be used in conjunction with our existing 44K salmon microarray to study host–parasite interactions at the molecular level. This report represents the largest genomic resource for any copepod species to date

Comparative Genomic Characterization of Three Streptococcus parauberis Strains in Fish Pathogen, as Assessed by Wide-Genome Analyses

Streptococcus parauberis, which is the main causative agent of streptococcosis among olive flounder (Paralichthys olivaceus) in northeast Asia, can be distinctly divided into two groups (type I and type II) by an agglutination test. Here, the whole genome sequences of two Japanese strains (KRS-02083 and KRS-02109) were determined and compared with the previously determined genome of a Korean strain (KCTC 11537). The genomes of S. parauberis are intermediate in size and have lower GC contents than those of other streptococci. We annotated 2,236 and 2,048 genes in KRS-02083 and KRS-02109, respectively. Our results revealed that the three S. parauberis strains contain different genomic insertions and deletions. In particular, the genomes of Korean and Japanese strains encode different factors for sugar utilization; the former encodes the phosphotransferase system (PTS) for sorbose, whereas the latter encodes proteins for lactose hydrolysis, respectively. And the KRS-02109 strain, specifically, was the type II strain found to be able to resist phage infection through the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system and which might contribute valuably to serologically distribution. Thus, our genome-wide association study shows that polymorphisms can affect pathogen responses, providing insight into biological/biochemical pathways and phylogenetic diversity