AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus

Srinivasan, Jagan

doi:10.1093/nar/gkh057

Cited by 5 publications

(3 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To obtain a first estimate of the number of collagen genes in P. pacificus, we used an "in silico" approach of the available P. pacificus sequence data. Three sequencing projects have been carried out in P. pacificus: an EST sequencing project of 12,000 reads (McCarter et al, 2002), a BAC end-sequencing project with more than 30,000 reads (Srinivasan et al, 2002(Srinivasan et al, , 2003 and a fosmid end-sequencing project with nearly 50,000 reads (Srinivasan et al, 2004). BLAST searches identified a number of collagens in P. pacificus.…”

Section: In Silico Characterization Of Collagens In P Pacificusmentioning

confidence: 99%

Isolation of mutations with dumpy‐like phenotypes and of collagen genes in the nematodePristionchus pacificus

Kenning

Kipping

Sommer

2004

Genesis

View full text Add to dashboard Cite

The nematode Pristionchus pacificus was developed as a satellite system in evolutionary developmental biology and forward and reverse genetic approaches allow a detailed comparison of various developmental processes between P. pacificus and Caenorhabditis elegans. To facilitate map-based cloning in P. pacificus, a genome map was generated including a genetic linkage map of approximately 300 molecular markers and a physical map of 10,000 BAC clones. Here, we describe the isolation and characterization of more than 40 morphological mutations that can be used as genetic markers. These mutations fall into 12 Dumpy genes and one Roller gene that represent morphological markers for all six P. pacificus chromosomes. Using an in silico approach, we identified approximately 150 hits of P. pacificus collagen genes in the available EST, BAC-end, and fosmid-end sequences. However, 1:1 orthologs could only be identified for fewer than 20 collagen genes.

show abstract

Section: In Silico Characterization Of Collagens In P Pacificusmentioning

confidence: 99%

Isolation of mutations with dumpy‐like phenotypes and of collagen genes in the nematodePristionchus pacificus

Kenning

Kipping

Sommer

2004

Genesis

View full text Add to dashboard Cite

show abstract

“…One biological process that has been studied in great detail in P.pacificus is the development of the vulva, the egg-laying structure of nematode females and hermaphrodites [for reviews see (5,7)]. In recent years, a genomic approach has complemented developmental studies by generating a physical and a genetic map and performing three sequencing projects [expressed sequence tag (EST), bacterial artificial chromosome (BAC) end and fosmid end sequencing] (8)(9)(10).…”

Section: Introductionmentioning

confidence: 99%

Evolution of dnmt-2 and mbd-2-like genes in the free-living nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae

Gutierrez

2004

Nucleic Acids Research

View full text Add to dashboard Cite

Whole genome sequencing of several metazoan model organisms provides a platform for studying genome evolution. How representative are the genomes of these model organisms for their respective phyla? Within nematodes, for example, the free-living soil nematode Caenorhabditis elegans is a highly derived species with unusual genomic characters, such as a reduced Hox cluster (Curr. Biol., 13, 37-40) and the absence of a Hedgehog signaling system. Here, we describe the recent loss of a DNA methyltransferase-2 gene (dnmt-2) in C.elegans. A dnmt-2-like gene is present in the satellite model organism Pristionchus pacificus, another free-living nematode that diverged from C.elegans 200-300 million years ago. In contrast, C.elegans, Caenorhabditis briggsae and P.pacificus all contain an mbd-2-like gene, which encodes another essential component of the methylation system of higher animals and fungi. Cel-mbd-2 is expressed throughout development and RNA interference (RNAi) experiments result in variable phenotypes. In contrast, Cbr-mbd-2 RNAi results in paralyzed larval or adult worms suggesting recent changes of gene function within the genus Caenorhabditis. We speculate that both genes were part of an ancestral DNA methylation system in nematodes and that gene loss and sequence divergence have abolished DNA methylation in C.elegans.

show abstract

“…All aforementioned genomics resources were bundled and made available online on , our web portal for P.pacificus genomics. Genetic and physical map services were moved from the discontinued AppaDB (8) to .…”

Section: Introductionmentioning

confidence: 99%

Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus

Dieterich

Roeseler

Sobetzko

et al. 2007

Nucleic Acids Research

View full text Add to dashboard Cite

Comparative studies have been of invaluable importance to the understanding of evolutionary biology. The evolution of developmental programs can be studied in nematodes at a single cell resolution given their fixed cell lineage. We have established Pristionchus pacificus as a major satellite organism for evolutionary developmental biology relative to Caenorhabditis elegans, the model nematode. Online genomic information to support studies in this satellite system can be accessed at . Our web resource offers diverse content covering genome browsing, genetic and physical maps, similarity searches, a community platform and assembly details. Content will be continuously improved as we annotate the P.pacificus genome, and will be an indispensable resource for P.pacificus genomics.

show abstract

AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus

Cited by 5 publications

References 9 publications

Isolation of mutations with dumpy‐like phenotypes and of collagen genes in the nematodePristionchus pacificus

Isolation of mutations with dumpy‐like phenotypes and of collagen genes in the nematodePristionchus pacificus

Evolution of dnmt-2 and mbd-2-like genes in the free-living nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae

Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus

Contact Info

Product

Resources

About