Wilson RK (1999) Trends Genet "How the worm was won. The C. elegans genome sequencing project."

Wilson RK

[Trends Genet, 1999]

The genome sequence of the free-living nematode Caenorhabiditis elegans is nearly complete, with resolution of the final difficult regions expected over the next few months. This will represent the first genome of a multicellular organism to be sequenced to completion. The genome is approximately 97 Mb in total, and encodes more than 19 099 proteins, considerably more than expected before sequencing began. The sequencing project - a collaboration between the Genome Sequencing Center in St Louis and the Sanger Centre in Hinxton - has lasted eight years, with the majority of the sequence generated in the past four years. Analysis of the genome sequence is just beginning and represents an effort that will undoubtedly last more than another decade. However, some interesting findings are already apparent, indicating that the scope of the project, the approach taken, and the usefulness of having the genetic blueprint for this small organism have been well worth the effort.

Wilson RK et al. (1994) Nature "2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans."

Weinstock L, Waterston RH, Cooper JA, Coulson AR, Jones M, Hillier L, Wohldmann P, Green P, Roopra A, Smalldon N, Hawkins TL, Favello A, Durbin RM, Bonfield J, Saunders D, Anderson K, Kershaw JK, Sonnhammer ELL, Kirsten J, Berks M, Burton J, Thomas K, Fulton LL, Copsey T, Rifken L, Lightning J, Sims MA, O'Callaghan M, Jier M, Vaudin M, Johnstone L, Percy CM, Fraser A, Dear S, Gardner AE, Ainscough R, Smith M, Lloyd CR, Latreille P, Laisster N, Wilkinson-Sproat J, Connell M, Thierry-Mieg J, Staden R, Baynes C, Vaughan K, Du Z, Craxton M, Sulston JE, Mortimore BJ, Shownkeen R, Parsons JT, Watson A, Smith A, Wilson RK

[Nature, 1994]

As part of our effort to sequence the 100-megabase (Mb) genome of the nematode Caenorhabditis elegans, we have completed the nucleotide sequence of a contiguous 2,181,032 base pairs in the central gene cluster of chromosome III. Analysis of the finished sequence has indicated an average density of about one gene per five kilobases; comparison with the public sequence databases reveals similarities to previously known genes for about one gene in three. In addition, the genomic sequence contains several intriguing features, including putative gene duplications and a variety of other repeats with potential evolutionary

Wilson RK et al. (1991) International C. elegans Meeting "C. ELEGANS GENOME SEQUENCING: DNA SEQUENCING OF A SERIES OF OVERLAPPING COSMIDS ON CHROMOSOME III"

Wilson RK, Halloran N, Sulston JE, Hawkins TL, Coulson AR, Waterston RH, Ainscough R, Du Z, Craxton M, Metzstein MM, Qui QQ

[International C. elegans Meeting, 1991]

A project initiated in 1990, to sequence 3 Mb of contiguous C. elegans genomic DNA in three years, is being undertaken jointly by laboratories in SL Louis U.S.A. and Cambridge U.K. This is intended to serve as a pilot project for the subsequent complete genome sequencing. During the first year or so we hope to work out details of our sequencing stratagy and methods with which to implement it. Our strategy must allow a considerable increase in the rate of sequence determination. The main tenents behind our strategy are that reduction of the redundancy typical of shotgun sequencing, together with increased automation and computer control (of sequencing tasks as well as sequence analysis) as much as is practical, are essential for the increase in throughput required for genome sized projects. We have started sequencing in the large gene cluster on chromosome III, with the St. Louis and Cambridge laboratories working on independent but adjacent regions. Thanks to the physical map, we can take a logical, ordered approach and are currently working out the most effective methods for generating the sequence, cosmid by cosmid. We use a high efficiency cosmid subcloning routine which generates an evenly distributed array of overlapping clones of various sizes, thus providing suitably spaced startpoints for sequencing enzymatically, with both vector and custom primers. This combination of shotgun and primer walking methods should drive down redundancy whilst circumventing the problems of repetitive elements and template secondary structure which would hamper a completely directed sequencing strategy. We initially sequence randomly generated clones, using M13 vectors with 1-2 Kb inserts and phagemid vectors with 6-15 Kb inserts. Fluorescent sequencing machines (Applied Biosystems and Pharmacia LKB) are used for data collection and the analysed data from each gel run is transferred via ethemet, to Sun sparcstations where sequence assembly, editing and further sequence analysis is carried out. Here we describe the methods used on the first completed cosmid and the additional seven cosmids being sequenced in the Cambridge and St. Louis laboratories. We shall include results of sequence analysis of cosmid ZK637 which appears to have at least four genes with similarity to known genes, two of which are quite striking: Glutathione reductase (E. coli and human) and TJ6 immune suppressor ( mouse).

Favello A et al. (1995) Methods Cell Biol "Genomic DNA sequencing methods."

Wilson RK, Hillier L, Favello A

[Methods Cell Biol, 1995]

Sequence analysis of cosmids from C. elegans and other organisms currently is best done using the random or "shotgun" strategy (Wilson et al., 1994). After shearing by sonication, DNA is used to prepare M13 subclone libraries which provide good coverage and high-quality sequence data. The subclones are assembled and the data edited using software tools developed especially for C. elegans genomic sequencing. These same tools facilitate much of the subsequent work to complete both strands of the sequence and resolve any remaining ambiguities. Analysis of the finished sequence is then accomplished using several additional computer tools including Genefinder and ACeDB. Taken together, these methods and tools provide a powerful means for genome analysis in the nematode.

Zafra, Isabella et al. (2021) MicroPubl Biol

Zafra, Isabella, Nebenfuehr, Benjamin, Golden, Andy

[MicroPubl Biol, 2021]

For Zafra, I; Nebenfuehr, B; Golden, A (2021). Saul-Wilson Syndrome Missense Allele Does Not Show Obvious Golgi Defects in a C. elegans Model. microPublication Biology. 10.17912/micropub.biology.000373.

Sulston JE et al. (1992) Nature "The C. elegans genome sequencing project: a beginning."

Wilson RK, Metzstein MM, Ainscough R, Waterston RH, Coulson AR, Craxton M, Thomas K, Dear S, Qiu L, Staden R, Berks M, Halloran N, Thierry-Mieg J, Hillier L, Sulston JE, Du Z, Durbin RM, Hawkins TL, Green P

[Nature, 1992]

The long-term goal of this project is the elucidation of the complete sequence of the Caenorhabditis elegans genome. During the first year methods have been developed and a strategy implemented that is amenable to large-scale sequencing. The three cosmids sequenced in this initial phase are surprisingly rich in genes, many of which have mammalian homologues.AD - MRC Laboratory of Molecular Biology, Cambridge, UK.FAU - Sulston, JAU - Sulston JFAU - Du, ZAU - Du ZFAU - Thomas, KAU - Thomas KFAU - Wilson, RAU - Wilson RFAU - Hillier, LAU - Hillier LFAU - Staden, RAU - Staden RFAU - Halloran, NAU - Halloran NFAU - Green, PAU - Green PFAU - Thierry-Mieg, JAU - Thierry-Mieg JFAU - Qiu, LAU - Qiu LAU - et al.LA - engPT - Journal ArticleCY - ENGLANDTA - NatureJID - 0410462RN - 0 (Cosmids)SB - IM

Tan EH et al. (2012) EMBO J "A new tumour suppressor enters the network of intestinal progenitor cell homeostasis."

Tan EH, Sansom OJ

[EMBO J, 2012]

In this issue of The EMBO Journal, Wilson et al (2012) elegantly discovered an important new axis for intestinal homeostasis and cancer, using an RNAi screen to enhance the RAS-induced multivulva (MUV) phenotype in Caenorhabditis elegans.

Lye RJ et al. (1993) International C. elegans Meeting "Cloning and sequencing of the cytoplasmic dynein heavy chain."

Wilson RK, Lye RJ, Waterston RH

[International C. elegans Meeting, 1993]

Fulton LL et al. (1995) Methods Cell Biol "Large-scale complementary DNA sequencing methods."

Hillier L, Fulton LL, Wilson RK

[Methods Cell Biol, 1995]

Complementary DNA libraries are useful tools for uncovering genes of interest in C. elegans and finding specific homologies to genes in other organisms (Waterston et al., 1992; McCombie et al., 1992). When working with existing cDNA libraries, be sure to carefully choose which libraries would be most beneficial to the type of research being done. Some libraries may be specific for genes that are present in lower copy numbers, whereas others may be of a more general nature. It is important to fully understand the source and construction of the library you will be working with. Once an appropriate library has been chosen, work may begin to isolate a specific cDNA and sequence it completely or to survey many cDNAs by single-pass DNA sequencing. Whatever the project, it is important to develop a specific strategy for both the sequencing and the organization of the clones being characterized. The strategies and procedures we have outlined in this chapter have proven effective for rapid and comprehensive cDNA characterization.

Lye RJ et al. (1995) Cell Motil Cytoskeleton "Genomic structure of a cytoplasmic dynein heavy chain gene from the nematode Caenorhabditis elegans."

Waterston RH, Wilson RK, Lye RJ

[Cell Motil Cytoskeleton, 1995]

We report the cloning and sequencing of genomic DNA encoding a cytoplasmic dynein heavy chain from the nematode Caenorhabditis elegans. In a contiguous stretch of 35,103 bp of DNA from the left arm of linkage group I, we have found a gene that is predicted to encode a protein of 4,568 amino acids. This gene is composed of 15 exons and 14 relatively short introns, and it has significant homology to the other dynein heavy chains in the databases. The deduced molecular mass of the derived polypeptide is 512,624 Da. As with other dynein heavy chains that have been sequenced to date. it contains four GXXGXGK(S/T) motifs that form part of the consensus sequence for nucleotide triphosphate-binding domains. Comparison of axonemal and cytoplasmic dynein heavy chains shows that regions of homology among all dyneins are clustered in the carboxyl terminal two-thirds of the polypeptide, whereas the amino terminal one-third of the heavy chains may contain domains that specify functions that differ between axonemal and cytoplasmic forms of the dynein heavy chain.