Localization, analysis and evolution of transposed human immunoglobulin VK genes

The localization of Vκ gene regions to chromosome 2, on which the κ locus is located, and to other chromosomes is described. The Vκ genes that have been transposed to other chromosomes are called orphons. The finding of two new Vκ genes on chromosome 22 is reported. A Vκ II gene of this region and two Vκ I genes of the Chr 1 and the cos 118 regions were sequenced. The two Vκ I orphon sequences and two others that had been determined previously were 97.5% identical, indicating that they may have evolved from a common ancestor by amplification. A model of the evolution of the human Vκ orphons is discussed. Author Keywords: Human-rodent cell hybrids; cosmids; restriction maps; ligation artifacts; orphon; recombinant DNA Abbreviations: aa, amino acid(s); bp, base pair(s); Chr1, Vκ gene-containing regions of chromosomes 1; Chr22, Vκ gene-containing regions of chromosomes 22; FR, framework regions; CDR, complementary determining regions; kb, kilo-base(s) or 1000 bp; L, L′, parts of a leader gene segment; m219-1, the first subclone of the cosmid clone cos 219; orphon, Vκ gene outside the κ locus on chromosome 2pl2; SSC, 0.15 M NaCl, 0.015 M Na3-citrate, pH 7.6; V, variable gene segments; J, joining gene segments; C, constant gene segments; Vκ I to Vκ IV, variable gene segments of immunoglobulin light chains of the κ type belonging to subgroups I to IV; for reasons of simplicity Vκ gene segments are generally called Vκ gene

Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing

Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. Two draft genome assemblies already exist for this species but contain pervasive assembly errors and are highly fragmented, which limits their values. Our purpose here was to improve the assembly of the D. suzukii genome and to annotate it in a way that facilitates comparisons with D. melanogaster. For this, we generated PacBio long-read sequencing data and assembled a novel, high-quality D. suzukii genome assembly. It is one of the largest Drosophila genomes, notably because of the expansion of its repeatome. We found that despite 16 rounds of full-sib crossings the D. suzukii strain that we sequenced has maintained high levels of polymorphism in some regions of its genome. As a consequence, the quality of the assembly of these regions was reduced. We explored possible origins of this high residual diversity, including the presence of structural variants and a possible heterogeneous admixture pattern of North American and Asian ancestry. Overall, our assembly and annotation constitute a high-quality genomic resource that can be used for both high-throughput sequencing approaches, as well as manipulative genetic technologies to study D. suzukii

Revisiting the developmental and cellular role of the pigmentation gene yellow in Drosophila using a tagged allele

International audiencePigmentation is a diverse and ecologically relevant trait in insects. Pigment formation has been studied extensively at the genetic and biochemical levels. The temporality of pigment formation during animal development, however, is more elusive. Here, we examine this temporality, focusing on yellow, a gene involved in the formation of black melanin. We generated a protein-tagged yellow allele in the fruit fly Drosophila melanogaster, which allowed us to precisely describe Yellow expression pattern at the tissue and cellular levels throughout development. We found Yellow expressed in the pupal epidermis in patterns prefiguring black pigmentation. We also found Yellow expressed in a few central neurons from the second larval instar to adult stages, including a subset of neurons adjacent to the clock neurons marked by the gene Pdf. We then specifically examined the dynamics of Yellow expression domain and subcellular localization in relationship to pigment formation. In particular, we showed how a late step of re-internalization is regulated by the large low-density lipoprotein receptor-related protein Megalin. Finally we suggest a new function for Yellow in the establishment of sharp pigmentation pattern boundaries, whereby this protein may assume a structural role, anchoring pigment deposits or pigmentation enzymes in the cuticle

Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer

International audienceDevelopmental enhancers control the expression of genes prefiguring morphological patterns. The activity of an enhancer varies among cells of a tissue, but collectively, expression levels in individual cells constitute a spatial pattern of gene expression. How the spatial and quantitative regulatory information is encoded in an enhancer sequence is elusive. To link spatial pattern and activity levels of an enhancer, we used systematic mutations of the yellow spot enhancer, active in developing Drosophila wings, and tested their effect in a reporter assay. Moreover, we developed an analytic framework based on the comprehensive quantification of spatial reporter activity. We show that the quantitative enhancer activity results from densely packed regulatory information along the sequence, and that a complex interplay between activators and multiple tiers of repressors carves the spatial pattern. Our results shed light on how an enhancer reads and integrates trans-regulatory landscape information to encode a spatial quantitative pattern