Whole genome shotgun (WGS) assembly or sequencing

5 Apr

Whole genome shotgun (WGS) assembly or sequencing

whole genome shotgun (WGS) assembly or se- quencing See shotgun sequencing. wild type the most frequently observed pheno- type, or the one arbitrarily designated as “normal.” Often symbolized by “+” or “wt.” wild-type gene the allele commonly found in na- ture or arbitrarily designated as “normal.” Wilms tumor a malignant kidney tumor of chil- dren often associated with deletions in the short arm of chromosome 11.

The WT1 gene, located at 11p13, encodes specific proteins synthesized during the de- velopment of the genitourinary tract. Four different proteins are produced by alternative splicing (q.v.) of WT1 mRNA.

These proteins contain zinc fingers which bind to and prevent transcription of certain genes that encode growth factors. The kidney tu- mors are named after Max Wilms, who described them in a monograph on tumor pathology he pub- lished in 1899.

See anti-oncogenes, zinc finger pro- teins. Wilson disease (WD) a hereditary human disease described in 1912 by the neurologist S.A.K. Wilson. WD is caused by mutations in the ATP7B gene (q.v.), and over 200 have been identified. Most mu- tations are of the missense variety. The gene product is an enzyme that transports copper through the plasma membranes of liver and brain cells.

The dis- ease is characterized by a reduction both in the bili- ary excretion of copper and in the incorporation of copper into ceruloplasmin (q.v.). Liver and brain damage result from the copper overload. The preva- lence of WD is 1 per 75,000 live births. See missense mutant. winter variety a variety of cereal which must be sown in the autumn of the year preceding that in which the plants should flower.

If sown in the spring, they will not flower in the same growing sea- son. See vernalization. Wnt the symbol for a group of homologous genes which encode proteins that regulate cell-to-cell in- teractions during development.

The Drosophila gene wingless (wg) controls the segmental pattern of the embryo, and the mouse was later shown to have a homologous gene called integration (int). Once it be- came clear that these genes were conserved in both invertebrates and vertebrates, the symbol Wnt was chosen, w from wg and nt from int, to reflect the widespread evolutionary distribution of this family.

The proteins encoded by Wnt genes are cysteine- rich, secreted glycoproteins which interact with spe- cific cell-surface receptors that in turn initiate a sig- naling cascade which turns on specific genes in target cells. In the mouse embryo the timing of Wnt ex- pression in the central nervous system indicates that Wnt genes regulate the differentiation of forebrain and spinal cord.

In Xenopus embryos the ectopic ex- pression of Wnt can cause a second neural axis to develop, and a two-headed larva will be produced. See cellular signal transduction. wobble hypothesis a hypothesis developed to ex- plain how one tRNA may recognize two codons. The anticodon in each tRNA is a base triplet. The first two bases of the mRNA codon pair according to the base pairing rules.

The third base in the anti- codon, however, has a certain amount of play or wobble that permits it to pair with any one of a vari- ety of bases occupying the third position of different codons. Thus, U in the third position would recog- nize A or G, for example, and transfer RNA with a CUU anticodon would bind to either of two codons (GAA or GAG).

See Appendix C, 1966, Crick. Wolbachia a genus of Gram-negative bacteria that resemble Rickettsia (q.v.) and live as endosymbionts in many invertebrates (including nematodes, mites, spiders, crustaceans, and insects). Wolbachia are in- herited maternally by transovarial transmission, and they often manipulate the reproductive behavior of their hosts.

For example, in some insects the infect- ing Wolbachia secrete toxins that kill Y-bearing sperm, and female-biased sex ratios result. In a strain of the beetle Callosobruchus chinensis the X chromo- some has been shown to contain a Wolbachia DNA fragment. This is about 11 kbp and contains 12 ORFs, somewhat more than 1% of the genome of the Wolbachia.

The structure of the transferred seg- ment is highly preserved which suggests that the transfer was recent. Wolbachia pipientis (wMel) is an obligate intracellular parasite of Drosophila melano- gaster. A recent survey of cultures kept at the Bloomington Drosophila Stock Center at Indiana University found that 30% of the strains were in- fected with Wolbachia. The wMel genome consists of a 1,267,782 bp circle of DNA.

It contains very high levels of repetitive DNA and mobile DNA ele- ments. However, there is no evidence for recent lat- eral gene transfer between wMel and its Drosophila host. See Appendix A, Prokaryotae, Bacteria, Proto- bacteria; Appendix C, 2002, Kondo et al.; horizontal transmission. wolf the gray wolf, Canis lupus, is the ancestor of the domestic dog. In Europe, what had been consid- ered pure wolf populations have turned out to be hybrids with domestic or feral dogs. See Canis famil- iaris; introgressive hybridization.

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