A gene-based SNP resource and linkage map for the copepod Tigriopus californicus

<p>Abstract</p> <p>Background</p> <p>As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. <it>Tigriopus californicus </it>is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for <it>T. californicus--</it>a first for copepods.</p> <p>Results</p> <p>One hundred and ninety Single Nucleotide Polymorphisms (SNPs) were used to genotype our mapping population of 250 F₂larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of <it>T. californicus</it>. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of <it>T. californicus</it>. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between <it>T. californicus </it>and the honeybee <it>Apis mellifera</it>, than expected by chance, suggesting preserved macrosynteny between Hymenoptera and Copepoda.</p> <p>Conclusions</p> <p>Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of <it>T. californicus</it>, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are currently under development.</p

Fusion of the BCR and the c-ABL genes in PH'-positive acute lymphoblastic leukemia with no rearrangement in the breakpoint cluster region

none5Two types of Philadelphia (Ph') chromosome positive acute lymphoblastic leukemias (ALL) have been described. One shows rearrangements within the 5.8 kb breakpoint cluster region (bcr), which forms the mid-portion of the bcr gene, on chromosome 22, while the other carries rearrangements involving a more proximal region on chromosome 22. To understand the nature of the breakpoints on chromosome 22 in bcr rearrangement negative, Ph'-positive ALLs, we have cloned and sequenced the cDNA of the c-abl oncogene in such ALL cells. The 5' ends of the cDNA clones correspond to the normal sequences of the bcr gene first exon with two of the clones extending beyond the GCCATGG consensus sequence for the initiation of translation. The bcr sequence stops at nucleotide 1813 of the coding sequence of the bcr gene, while the c-abl sequence starts at the beginning of the second c-abl exon (nucleotide 227). Thus the joining point between bcr and c-abl is at the boundary between two exons, suggesting intronic fusion and the occurrence of a splicing event. Our current observations indicate that the Ph' translocation in bcr negative ALL involves bcr gene sequences, albeit only a proximal portion of those involved in CML. These genomic differences may be important factors in the pathogenesis of the distinct phenotypes of ALL and CML.noneAR-RUSHDI A.; M. NEGRINI; KURZROCK R.; HUEBNER K.; CROCE C. M.AR RUSHDI, A.; Negrini, Massimo; Kurzrock, R.; Huebner, K.; Croce, C. M