Shownkeen R et al. (1992) Worm Breeder's Gazette "Clone Mapping"

Coulson AR, Shownkeen R

[Worm Breeder's Gazette, 1992]

We are continuing to map clones by fingerprinting, where appropriate. Polytene YAC filters are an additional mapping resource, not a replacement. Thus any clones that require mapping should be sent to Cambridge initially (preferably DNA and clone). There is greater than a 90% probability that a clone will be mapped by fingerprinting, provided that it has sufficient HindIII sites (generally more than 2 or 3) to generate an adequate fingerprint (i.e. essentially all cosmids and lambdas). Clones with insufficient HindIII sites for unequivocal mapping solely by fingerprinting ( many plasmids for example) may be mapped to the cosmid level by a combination of fingerprinting and polytene YAC probing (when the fingerprint comparison is to a smaller subset of cosmids as defined by the probing).

Shownkeen R et al. (1995) International C. elegans Meeting "THE CAENORHABDITIS ELEGANS PHYSICAL MAP"

Chissoe SL, Waterston RH, Fraser A, Sulston JE, Shownkeen R, Coulson AR

[International C. elegans Meeting, 1995]

Twelve contigs of cosmids and yeast artificial chromosomes (YACs) span more than 95Mb of the 100Mb C.elegans genome. 650 markers link the physical and genetic maps.Hybridisation of tag-sequenced cDNA clones to a map-representative set of YACs indicates that the map incorporates in excess of 99.8% of genes. The map is accessible in ACeDB. We (S.C.) are investigating the representation by bacterial artificial chromosomes (BACs) of regions of the genome not represented by cosmids. Two grids of YACs, of 958 clones ('Poly2') and 223 clones ('Suppoly') are available on request. The latter represents regions of the genome that have been characterised or better defined since the selection of clones for the former. Cosmid clones and YAC grids are available from the Sanger Centre (requests to alan@sanger.ac.uk; FAX 01223 494919). YAC clones and 'cm' series cDNA clones are available from the Sanger Centre or Washington University (rw@nematode. wustl.edu; FAX 314 362 2985).

Coulson AR et al. (1995) Methods Cell Biol "The physical map of the Caenorhabditis elegans genome."

Kozono Y, Shownkeen R, Coulson AR, Huynh C

[Methods Cell Biol, 1995]

The clone-based physical map of the 100-Mb Caenorhabditis elegans genome has evolved over a number of years. Although the detection of clone overlaps and construction of the map have of necessity been carried out centrally, it has been essentially a community project. Without the provision of cloned markers and relevant map information by the C. elegans community as a whole, the map would lack the genetic anchor points and coherent structure that make it a viable entity. Currently, the map consists of 13 mapped contigs totaling in excess of 95 Mb and 2 significant unmapped contigs totaling 1.3 Mb. Telomeric clones are not yet in place. The map carries 600 physically mapped loci, of which 262 have genetic map data. With one exception, the physical extents of the remaining gaps are not known. The exception is the remaining gap on linkage group (LG) II. This has been shown to be bridged by a 225-kb Sse83871 fragment. Because the clones constituting the map are a central resource, there is essentially no necessity for individuals to construct cosmid and yeast artificial chromosome (YAC) libraries. Consequently, such protocols are not included here. Similarly, protocols for clone fingerprinting, which forms the basis of the determination of cosmid overlaps and the mapping of clones received from outside sources and has to be a centralized operation, and YAC linkage are not give here. What follows is essentially a "user's guide" to the physical map. Details of map construction are given where required for interpretation of the map as distributed. The physical mapping has been a collaboration between the MRC Laboratory of Molecular Biology, Cambridge, United Kingdom (now at The Sanger Centre, Cambridge, UK) and Washington University School of Medicine, St. Louis, Missouri. Inquiries regarding map interpretation, information, and materials should be addressed to alan@sanger.ac.uk or rw@nematode.wustl.edu.

Galindo-Malagn XA et al. (2022) Zootaxa "New species, synonymies and records in the genus Rhagovelia Mayr, 1865 (Hemiptera: Heteroptera: Veliidae) from Colombia."

Moreira FFF, Morales I, Mondragn-F SP, Galindo-Malagn XA

[Zootaxa, 2022]

Rhagovelia medinae sp. nov., of the hambletoni group (angustipes complex), and R. utria sp. nov., of the hirtipes group (robusta complex), are described, illustrated, and compared with similar congeners. Based on the examination of type specimens, six new synonymies are proposed: R. elegans Uhler, 1894 = R. pediformis Padilla-Gil, 2010, syn. nov.; R. cauca Polhemus, 1997 = R. azulita Padilla-Gil, 2009, syn. nov., R. huila Padilla-Gil, 2009, syn. nov., R. oporapa Padilla-Gil, 2009, syn. nov, R. quilichaensis Padilla-Gil, 2011, syn. nov.; and R. gaigei, Drake Hussey, 1947 = R. victoria Padilla-Gil, 2012 syn. nov. The first record from Colombia is presented for R. trailii (White, 1879), and the distributions of the following species are extended in the country: R. cali Polhemus, 1997, R. castanea Gould, 1931, R. cauca Polhemus, 1997, R. gaigei Drake Hussey, 1957, R. elegans Uhler, 1894, R. femoralis Champion, 1898, R. malkini Polhemus, 1997, R. perija Polhemus, 1997, R. sinuata Gould, 1931, R. venezuelana Polhemus, 1997, R. williamsi Gould, 1931, and R. zeteki Drake, 1953.

Schrank B et al. (1991) International C. elegans Meeting "A POLYMORPHIC STS MAP FOR CAENORHABDITIS ELEGANS."

Shownkeen R, Waterston RH, Williams BD, Schrank B, Huynh C

[International C. elegans Meeting, 1991]

We have developed a polymorphic genetic STS map which includes 37 sites scattered over the six linkage groups. In many cases the assays can be combined into a single reaction so that multiple sites can be followed simultaneously. By using this map new mutations can be mapped rapidly to a small interval through analysis of the progeny of a single cross. To develop the map we exploited Tcl polymorphisms between the low copy number Bristol and high copy number Bergerac strains. In addition to previously identified sites we have located 80 Tcl containing sites by fingerprinting genomic clones from a Bergerac library to the physical map. Each PCR assay was designed to behave as a dominant genetic marker that gives a product of defined length from the 'filled' Tcl site in Bergerac DNA, but gives no product from the corresponding 'empty' site in Bristol DNA. This was accomplished by determining flanking sequence, and synthesizing an oligonucleotide primer for use in combination with a primer within Tcl. Since the reaction products from different sites were designed to be of different lengths, multiple sites can be assayed in a single reaction. We have used the polymorphic STS markers to map several lethal mutations. Bristol/Bergerac hybrid hermaphrodites are allowed to self and individual homozygous mutant progeny are selected for PCR. The first 20 - 30 animals are tested against markers from all five autosomes to assign the mutation to a linkage group. Additional animals are then assayed with a chromosome specific marker set to determine position along the chromosome. The polymorphic STS map should also be useful for mapping suppressor mutations and mapping loci involved in polygenic traits. In addition to genetic linkage data the map has improved the local contiguity of the genetic and physical maps.

Williams BD et al. (1992) Genetics "A genetic mapping system in Caenorhabditis elegans based on polymorphic sequence-tagged sites."

Schrank B, Waterston RH, Huynh C, Shownkeen R, Williams BD

[Genetics, 1992]

We devised an efficient genetic mapping system in the nematode Caenorhabditis elegans which is based upon the differences in number and location of the transposable element Tc1 between the Bristol and Bergerac strains. Using the nearly completed physical map of the C. elegans genome, we selected 40 widely distributed sites which contain a Tc1 element in the Bergerac strain, but not in the Bristol strain. For each site a polymerase chain reaction assay was designed that can distinguish between the Bergerac Tc1-containing site and the Bristol "empty" site. By combining appropriate assays in a single reaction, one can score multiple sites within single worms. This permits a mutation to be rapidly mapped, first to a linkage group and then to a chromosomal subregion, through analysis of only a small number of progeny from a single interstrain cross.

Coulson AR et al. (1993) Worm Breeder's Gazette "The Genome Map of C. elegans"

Lutterbach B, Sulston JE, Waterston RH, Kozono Y, Coulson AR, Shownkeen R

[Worm Breeder's Gazette, 1993]

See Figures 1-6

Coulson AR et al. (1992) Worm Breeder's Gazette "The Genome Map of C. elegans"

Lutterbach B, Waterston RH, Coulson AR, Kozono Y, Sulston JE, Shownkeen R

[Worm Breeder's Gazette, 1992]

Kozono Y et al. (1991) Worm Breeder's Gazette "The Genome Map of C. elegans."

Kozono Y, Coulson AR, Shownkeen R, Waterston RH, Lutterbach B, Sulston JE

[Worm Breeder's Gazette, 1991]

After the introduction of YAC libraries into the C. elegans mapping project, we pursued reciprocal hybridization of YACs and cosmids to link together the cosmid contigs (see Coulson et al., Nature 335, 184- 186). The YAC libraries have been increased to over 9000 clones, with over 3000 used in hybridization. A steady reduction in contig number resulted so that by the beginning of this year the number of contigs had fallen to 170 (from a starting number of 700) and the average size had risen from 125kb to more than 550kb. This greater continuity, combined with the ever increasing number of genetic loci placed on the physical map, increased the amount of DNA positioned on the genome map from less than 20 Mb to more than 75 Mb. The YAC coverage of the contigs was almost complete, and less than 1000 were required to give redundant (2 fold) coverage of the physical map. A grid of these clones (genomically ordered at the time of selection) has been prepared on a postcard sized piece of nylon (958 clones in all) and replicas made for distribution. Using the key provided and the electronic map (see WBG#10;3) it is now a straightforward procedure for a lab to locate any given DNA sequence on the genome map. They have been used successfully in a number of labs. These 'polytene' filters may be obtained from either St. Louis or Cambridge by request. By the beginning of the year, it had become clear that the reciprocal hybridization strategy was decreasingly useful and another approach was needed. The remaining contigs were largely of two classes: (1) contigs with YACs as the likely endmost clones; and (2) small contigs lacking YACs. The contigs with YAC ends were blocked from growth because the reciprocal hybridization strategy provides no way to recognize YAC-YAC overlaps. To obtain an end probe from the YACs, sequence was obtained via an adaptation of Engelke's genomic sequencing method (Methods in Enzymology). Primers were made and the PCR product used to probe to the YAC grids. Hybridizing YACs were tested with the same primer pairs by PCR to confirm the overlap. A total of 34 joins and rearrangements have resulted from the analysis of 186 ends. Because these joins involve just the ends of YACs they are particularly vulnerable to artifact; please inquire if you need to know the status of particular areas. The small YACless contigs were of a variety of types. Some contained only cosmids made in the pJB8 vector that had been left out of the above grids because sequences share with the YAC vector. Some had repeated sequences that led to ambiguous positioning. Others simply had failed to hybridize with YACs tested. To assign these cosmids to YACs, end sequence was obtained by direct sequencing of cosmid DNA, PCR was used to generate small probes and positive YACs were tested by PCR to confirm assignment. Of 50 cosmids from which we have useful data, 38 have been assigned to YACs. Currently, for 31 cases these YACs either had previously been placed on the physical map or have been subsequently linked to larger contigs, thereby locating the small contigs. Many of the remaining clones failed to give a PCR- product from nematode DNA and have been set aside. Only 2 clones were found which gave a PCR product from worm DNA and failed to identify any overlapping YAC. Together these efforts have reduced the contig number to 102. With the joins obtained and the continuing efforts of the community to clone and assign genetically mapped fragments on the physical map, 85 Mb of DNA is now aligned with the genetic map. [See Figures 1-4]

Kozono Y et al. (1991) International C. elegans Meeting "THE CAENORHABDITIS ELEGANS PHYSICAL MAP."

Kozono Y, Waterston RH, Sulston JE, Lutterbach B, Coulson AR, Shownkeen R

[International C. elegans Meeting, 1991]

The C. elegans physical map has been assembled with a combination of cosmid and yeast artificial chromosome (YAC) clones. In the first phase, cosmid clone overlaps were detected using a high resolution fingerprinting technique. This produced a map with more than 700 contigs. Next, YACs were used to link together the multiple cosmid contigs via hybridization of the YACs to colony grids of representative cosmids. By the time this approach reached its practical limits, the map had been reduced to about 170 contigs. The current phase has involved detecting overlaps between protruding YAC clones at the ends of existing contigs, and also between small cosmid contigs and YACs. End sequence from the clones was obtained by using flanking vector primers either on total yeast genomic DNA for YACs or miniprep DNA for cosmids. PCR was then used to get unique hybridization probes. Hybridizing YACs were checked by PCR to confirm overlaps. From these efforts, the map now contains less than 90 contigs. Through the supporting evidence of genetic and physical information from other sources, more than 85 Mb of the assembled DNA has been assigned to chromosomes in 35 large contigs. Since C. elegans genes are preferentially located in the centers of chromosomes and the continuity of the map is greatest in these locations, all but a few coding sequences are now covered by contigs. The results of the physical map effort are available to the community in three forms: The database can be accessed either via network or modem from several locations throughout the world; a colony grid of 958 YACs, genomically ordered at the time of selection, has been prepared in a postcard sized array and replicas have been distributed to interested labs; YACs and cosmid clones covering any region are available upon request.