The female (XX) and male (YY) genomes provide insights into the sex determination mechanism in spinach

Sexual reproduction is the primary means of reproduction for the vast majority of macroscopic organisms, including almost all animals and plants. Sex chromosomes are predicted to play a central role in sexual dimorphism. Sex determination in spinach is controlled by a pair of sex chromosomes. However, the mechanisms of sex determination in spinach remain poorly understand. Here, we assembled the genomes of both a female (XX) and a male (YY) individual of spinach, and the genome sizes were 978 Mb with 28,320 predicted genes and 926 Mb with 26,537 predicted genes, respectively. Based on reported sex-linked markers, chromosomes 4 of the female and male genome were defined as the X and Y chromosomes, and a 10 Mb male-specific region of the Y chromosome (MSY) from approximately 95– 105 Mb, was identified that contains abundant transposable elements (92.32%). Importantly, a large-scale inversion of about 13 Mb in length was detected on the X chromosome, corresponding to ~9 Mb and ~4 Mb on the Y chromosome, which were located on both sides of the MSY with two distinct evolutionary strata. Almost all sex-linked/Y-specific markers were enriched on the inversions/MSY, suggesting that the flanked inversions might result in recombination suppression between the X and Y chromosomes to maintain the MSY. Forty-nine genes within the MSY had functional homologs elsewhere in the autosomal region, suggesting movement of genes onto the MSY. The X and Y chromosomes of spinach provide a valuable resource for investigating spinach sex chromosomes evolution from wild to cultivated spinach and also provide a broader understanding of the sex determination model in the Amaranthaceae family.

Locating the Sex Determining Region of Linkage Group 12 of Guppy (Poecilia reticulata)

Despite over 100 years of study, the location of the fully sex-linked region of the guppy (Poecilia reticulata) carrying the male-determining locus, and the regions where the XY pair recombine, remain unclear. Previous population genomics studies to determine these regions used small samples from recently bottlenecked captive populations, which increase the false positive rate of associations between individuals’ sexes and SNPs. Using new data from multiple natural populations, we show that a recently proposed candidate for this species’ male-determining gene is probably not completely sex-linked, leaving the maleness factor still unidentified. Variants in the chromosome 12 region carrying the candidate gene sometimes show linkage disequilibrium with the sex-determining factor, but no consistently male-specific variant has yet been found. Our genetic mapping with molecular markers spread across chromosome 12 confirms that this is the guppy XY pair. We describe two families with recombinants between the X and Y chromosomes, which confirm that the male-determining locus is in the region identified by all previous studies, near the terminal pseudo-autosomal region (PAR), which crosses over at a very high rate in males. We correct the PAR marker order, and assign two unplaced scaffolds to the PAR. We also detect a duplication, with one copy in the male-determining region, explaining signals of sex linkage in a more proximal region.

Locating the sex determining region of linkage group 12 of guppy (Poecilia reticulata)

We describe new genetic mapping results from 6 full-sib families in the guppy (Poecilia reticulata), two of which included recombinants between the X and Y chromosomes. These recombinants confirm that the guppy sex-determining locus is in the region identified by all previous studies, including a recent report suggesting a candidate sex-determining gene in this fish, close to the pseudo-autosomal region (or PAR) at the chromosome terminus. Our results suggest the presence of some errors in the current assembly of the guppy genome. In males, crossing over occurs at a very high rate in the PAR, and our genetic map of the region allows us to correct the marker order. We also identified two unplaced scaffolds carrying genes that map to the PAR. Genetic mapping cannot be used to order markers in the region where crossing over is infrequent. However, our recombinant male is informative about the order, under the reasonable assumption that crossovers are infrequent. Our mapping families and natural population samples also show that the recently proposed candidate for this species’ sex-determining gene is not completely sex-linked. We detect an association between individuals’ sex and an SNP in the sex-determining region, but not with a marker 0.9 Mb away from it, suggesting that variants in this region may be in linkage disequilibrium with the actual sex-determining factor, but that the factor itself has not yet been identified. So far, no consistently male-specific variant has been identified in the guppy sex-determining region.

A female patient with retinoblastoma and severe intellectual disability carrying an X;13 balanced translocation without rearrangement in the RB1 gene: a case report

Background Female carriers of a balanced X; autosome translocation generally undergo selective inactivation of the normal X chromosome. This is because inactivation of critical genes within the autosomal region of the derivative translocation chromosome would compromise cellular function. We here report a female patient with bilateral retinoblastoma and a severe intellectual disability who carries a reciprocal X-autosomal translocation. Case presentation Cytogenetic and molecular analyses, a HUMARA (Human androgen receptor) assay, and methylation specific PCR (MSP) and bisulfite sequencing were performed using peripheral blood samples from the patient. The patient’s karyotype was 46,X,t(X;13)(q28;q14.1) by G-banding analysis. Further cytogenetic analysis located the entire RB1 gene and its regulatory region on der(X) with no translocation disruption. The X-inactivation pattern in the peripheral blood was highly skewed but not completely selected. MSP and deep sequencing of bisulfite-treated DNA revealed that an extensive 13q region, including the RB1 promoter, was unusually methylated in a subset of cells. Conclusions The der(X) region harboring the RB1 gene was inactivated in a subset of somatic cells, including the retinal cells, in the patient subject which acted as the first hit in the development of her retinoblastoma. In addition, the patient’s intellectual disability may be attributable to the inactivation of the der(X), leading to a 13q deletion syndrome-like phenotype, or to an active X-linked gene on der (13) leading to Xq28 functional disomy.

MP7: FAMILIES WITH BOTH NON-HODGKIN'S LYMPHOMA (NHL) AND MYELOMA (MM): ANTICIPATION AND MALE TRANSMISSION

Purpose of StudyTo determine whether genetic rather than environmental factors may be responsible for the occurrence of these neoplasms in families.Methods UsedWe interrogated our registry of >700 pedigrees of families (fams) with multiple hematologic malignancies. We identified 31 fams with both NHL and MM in their pedigrees. In 16 pedigrees a parent and child were affected (12 father-child pairs and 4 mother-child pairs). Fifteen affected sib pairs were identified in the 31 fams, 10 same sex pairs and 5 male-female pairs. Six of the 31 pedigrees had only 1 affected pair. More distant relationships were observed in other fams.Summary of ResultsMale transmission was evident in 25 fams and female transmission was observed in 6. NHL and MM cases had at least 1 unaffected generation (gen) between them in 8 pedigrees, and the diseases occurrred in sequential (13 fams) or the same gen in 10 fams. MM was the diagnosis (dx) in the youngest affected gen in 9 pedigrees, NHL in 13 pedigrees and both occurred in the youngest gen in 9 fams. The median age at dx of 29 NHL patients for whom data were available was 55 yrs (range, 20–99 yrs), and the median age at dx of 26 MM cases was 56 yrs (range, 30–82 yrs). Ten of 26 MM patients were <50 years old at dx. The presence or absence of anticipation could be assessed in 15 of the 31 pedigrees. All 15 displayed anticipation in terms of succeeding gens developing NHL or MM at an earlier age than did the previous gens (median −19 yrs, range −6 to −56 yrs).ConclusionsWe demonstrate anticipation in 15 assessible fams with both NHL and MM, a feature of familial MM that we previoiusly reported (Despande HA, et al: Br J Haematol 1998). More advanced, aggressive disease at dx in the youngest gen is another feature of anticipation, and was observed in 9 of 13 fams in which it could be assessed. Demonstration of anticipation in all 15 evaluable fams suggests a genetic basis for the relationship between these two B-cell disorders. The increase of same sex sib pairs among affected sib pairs implicates a locus on a pseudo-autosomal region of the X chromonsome as potentially responsible for this observation, as we have previously reported for Hodgkin's lymphoma (Horwitz M, Wiernik PH, Am J Hum Genet 1999). Myeloma and non-Hodgkin's lymphoma may have common genetic causation; molecular studies of these fams are planned.

Analysis of BAC clones containing homologous sequences on the end of the Xq arm and on chromosome 7 in the dioecious plant Silene latifolia

Silene latifolia is a model dioecious plant with morphologically distinguishable XY sex chromosomes. The end of the Xq arm is quite different from that of the Yp arm, although both are located at opposite ends of their respective chromosomes relative to a pseudo-autosomal region. The Xq arm does not seem to originate from the same autosome as the Yp arm. Bacterial artificial chromosome clone #15B12 has an insert containing a 130-kb stretch in which a 313-bp satellite DNA is repeated 420 times. PCR with a single primer revealed that this 130-kb stretch consists of three reversals of the orientation of the satellite DNA. A non-long terminal repeat retroelement and two sequences that share homology with an Oryza sativa RING zinc finger and a putative Arabidopsis thaliana protein, respectively, were found in the sequences that flank the satellite DNA. Fluorescence in situ hybridization carried out using this low-copy region of #15B12 as a probe confirmed that these sequences originated from the X chromosome and that homologous sequences exist at the end of chromosome 7. The region distal to DD44X on the Xq arm is postulated to have recombined with a region containing satellite DNA on chromosome 7 during the process of sex chromosome evolution.