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We previously showed that side population (SP) cells, characterized by specific Hoechst dye efflux pattern in flow cytometric analysis, were present in teleost kidney hematopoietic tissue, and that kidney SP cells were enriched in hematopoietic stem cells (HSCs). ABCG2/Abcg2 is an ATP-binding cassette (ABC) transporter that is known to be associated with Hoechst dye efflux activity of mammalian HSCs. In the present study, we examined the expression and function of Abcg2 in kidney SP cells from zebrafish (Danio rerio). Although the zebrafish genome has 4 paralogous copies of ABCG2 (zAbcg2a, b, c, and d), zAbcg2a and zAbcg2c mRNA was expressed in kidney SP cells. Transfection of COS-7 cells with zAbcg2a and zAbcg2c showed that zAbcg2a was directly associated with the SP phenotype. These results indicate that zAbcg2a mRNA is a useful marker for zebrafish HSCs. In situ hybridization in kidney tissue showed that zAbcg2a-posi- IntroductionSide population (SP) cells are identified from bone marrow based on their capacity to efflux of the fluorescent dye Hoechst 33342 (Hoechst), and are enriched in hematopoietic stem cells (HSCs). 1 Since the Hoechst dye efflux activity of HSCs is widely conserved in mammals, SP cell purification has been extensively used to enrich mammalian HSCs. [2][3][4] Recently, we showed that the hematopoietic activity of teleost SP cells isolated from kidney, the main hematopoietic organ in teleosts, 5,6 using the transplantation model system of clonal ginbuna (Carassius auratus langsdorfii, S3n strain) and ginbuna goldfish (Carassius auratus) hybrids (S4n strain). The SP cell population was clearly identified from ginbuna kidney. When the kidney SP cells from S3n were injected into S4n, all types of donor-derived blood cells (erythrocytes, neutrophils, basophils, monocytes, thrombocytes, and T and B lymphocytes) were detected in the recipient blood over a period of 9 months. 7 These findings indicate that SP cell purification can be used to enrich HSCs from not only mammals but also teleosts.Zebrafish (Danio rerio) has recently emerged as a powerful genetic model in which forward genetic screens can uncover novel genes involved in development, hematopoiesis, and human disease. 8 Although many homologues of human genes, including hematopoietic genes, have been identified, 9,10 stem-cell markers have not been shown in zebrafish. Therefore, little is known about the localization of HSCs and about stem-cell niche, a microenvironment supporting the maintenance and self-renewal of stem cells, in teleost kidney hematopoietic tissue. In murine bone marrow, ABCG2/Abcg2, an ATP-binding cassette (ABC) transporter associated with Hoechst dye efflux activity of HSCs, 11-15 is highly expressed in the most primitive HSCs and is sharply downregulated with differentiation. 11 In addition, the expression of Abcg2 gene in stem cells is highly conserved from various sources such as mouse skin, skeletal muscle, mammary grand, and testis, as well as human bone marrow. 11,[16][17][18] Abcg2 is thus used as a gener...

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BackgroundThe common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies.ResultsHere we have used 19 different tissues from an F1 hybrid strain of the common carp to perform transcriptome analyses using RNA-Seq. For a subset of the tissues we also have performed deep proteomic studies. As a reference, we updated the European common carp genome assembly using low coverage Pacific Biosciences sequencing to permit high-quality gene annotation. These annotated gene lists were linked to zebrafish homologs, enabling direct comparisons with published datasets. Using clustering, we have identified sets of genes that are potential selective markers for various types of tissues. In addition, we provide a script for a schematic anatomical viewer for visualizing organ-specific expression data.ConclusionsThe identified transcriptome and proteome data for carp tissues represent a useful resource for further translational studies of tissue-specific markers for this economically important fish species that can lead to new markers for organ development. The similarity to zebrafish expression patterns confirms the value of common carp as a resource for studying tissue-specific expression in cyprinid fish. The availability of the annotated gene set of common carp will enable further research with both applied and fundamental purposes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3038-y) contains supplementary material, which is available to authorized users.

The current information on the polymorphism variation and haplotype structure of the domestic dog leukocyte antigen (DLA) genes is limited in comparison to other experimental animals. In this paper, to better elucidate the degree and types of polymorphisms and genetic differences for DLA-88, DLA-12 and DLA-64, we genotyped four families of 38 beagles and another 404 unrelated dogs representing 49 breeds by RT-PCR based Sanger sequencing. We also sequenced and analyzed the genomic organization of the DLA-88 and DLA-12 gene segments to better define these two-gene DLA haplotypes more precisely. We identified 45 alleles for DLA-88, 15 for DLA-12 and six for DLA-64, of which 20, 14 and six, respectively, were newly described alleles. Therefore, this study shows that the DLA-12 and DLA-64 loci are far more polymorphic than previously reported. Phylogenetic analysis strongly supported that the DLA-88, DLA-12 and DLA-64 alleles were independently generated after the original divergence of the DLA-79 alleles. Two distinct DLA-88 and DLA-12 haplotype structures, tentatively named DLA-88-DLA-12 and DLA-88-DLA-88L, were identified, and the novel haplotype DLA-88-DLA-88L contributed to 32.7% of the unrelated dogs. Quantitative real-time PCR analysis showed that the gene expression levels of DLA-88L and DLA-88 were similar, and that the gene expression level of DLA-12 was significantly lower. In addition, haplotype frequency estimations using frequently occurring alleles revealed 45 different DLA-class I haplotypes (88-88L/12-64) overall, and 22 different DLA-class I haplotypes in homozygous dogs for 18 breeds and mongrels.