A gene-based radiation hybrid map   of chicken microchromosome 14:  
 Comparison to human and alignment  to the assembled chicken sequence

Morisson, Mireille; Leroux, Sophie; Jiguet-Jiglaire, Carine; Assaf, Sirine; Pitel, Frédérique; Lagarrigue, Sandrine; Bardes, Suzanne; Fève, Katia; Faraut, Thomas; Milan, Denis; Vignal, Alain

doi:10.1051/gse:2004046

Cited by 11 publications

(12 citation statements)

References 34 publications

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“…The distance between the URP gene and the SS1 gene was 52 centiRays, with a logarithm of odds score of 4.4. Because RH maps were available for only a limited number of chromosomes (32)(33)(34)(35)(36)(37), the chromosomal assignment of the two genes could not be determined. They were finally localized on chromosome 9, owing to the data from the first draft sequence assembly of the whole chicken genome, available in ENSEMBL (www.ensembl.org͞index.html).…”

Section: Struture Of Predictive Peptides and Phylogenetical Relationsmentioning

confidence: 99%

Comparative genomics provides evidence for close evolutionary relationships between the urotensin II and somatostatin gene families

Tostivint

Joly

Lihrmann

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Although urotensin II (UII) and somatostatin 1 (SS1) exhibit some structural similarities, their precursors do not show any appreciable sequence identity and, thus, it is widely accepted that the UII and SS1 genes do not derive from a common ancestral gene. The recent characterization of novel isoforms of these two peptides, namely urotensin II-related peptide (URP) and somatostatin 2 (SS2)͞ cortistatin (CST), provides new opportunity to revisit the phylogenetic relationships of UII and SS1 using a comparative genomics approach. In the present study, by radiation hybrid mapping and in silico sequence analysis, we have determined the chromosomal localization of the genes encoding UII-and somatostatin-related peptides in several vertebrate species, including human, chicken, and zebrafish. In most of the species investigated, the UII and URP genes are closely linked to the SS2͞CST and SS1 genes, respectively. We also found that the UII-SS2͞CST locus and the URP͞SS1 locus are paralogous. Taken together, these data indicate that the UII and URP genes, on the one hand, and the SS1 and SS2͞CST genes, on the other hand, arose through a segmental duplication of two ancestral genes that were already physically linked to each other. Our results also suggest that these two genes arose themselves through a tandem duplication of a single ancestral gene. It thus appears that the genes encoding UII-and somatostatinrelated peptides belong to the same superfamily.duplication ͉ multigenic family ͉ neuropeptides ͉ radiation hybrid mapping

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Section: Struture Of Predictive Peptides and Phylogenetical Relationsmentioning

confidence: 99%

Comparative genomics provides evidence for close evolutionary relationships between the urotensin II and somatostatin gene families

Tostivint

Joly

Lihrmann

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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“…As a result, a number of gaps remain and the RH map of GGA1 is composed of several small linkage groups. Contrariwise, RH maps were developed specifically for the four other chromosomes presented (Jennen et al, 2004;Pitel et al, 2004;Rabie et al, 2004;Morisson et al, 2005). For GGA1, GGA4 and GGA5, higher retention frequencies are observed around the centromeric regions with maximum values at 78.4, 23.0 and 2.8 Mb respectively.…”

Section: Current State Of Progressmentioning

confidence: 99%

The chicken RH map: current state of progress and microchromosome mapping

Morisson

Denis²,

Milan³

et al. 2007

Cytogenet Genome Res

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The ChickRH6 radiation hybrid panel has been used to construct consensus chromosome radiation hybrid (RH) maps of the chicken genome. Markers genotyped were either from throughout the genome or targeted to specific chromosomes and a large proportion (one third) of data was the result of collaborative efforts. Altogether, 2,531 markers were genotyped, allowing the construction of RH reference maps for 20 chromosomes and linkage groups for four other chromosomes. Amongst the markers, 581 belong to the framework maps, while 1,721 are on the comprehensive maps. Around 800 markers still have to be assigned to linkage groups. Our attempt to assign the supercontigs from the chrun (virtual chromosome containing all the genome sequence that could not be attributed to a chromosome) as well as EST (Expressed Sequence Tag) contigs that do not have a BLAST hit in the genome assembly led to the construction of new maps for microchromosomes either absent or for which very little data is present in the genome assembly. RH data is presented through our ChickRH webserver (http://chickrh.toulouse.inra.fr/), which is a mapping tool as well as the official repository RH database for genotypes. It also displays the RH reference maps and comparison charts with the sequence thus highlighting the possible discrepancies. Future improvements of the RH maps include complete coverage of the sequence assigned to chromosomes, further mapping of the chrun and mapping of EST contigs absent from the assembly. This will help finish the mapping of the smallest gene-rich microchromosomes.

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“…In this method, the presence or absence of a marker is only required (usually based on a PCR assay) and there is no need to identify polymorphisms. A chicken RH panel and this issue) has been used to construct maps of chromosomes 2, 7, 14 and 15, which are co-linear with the genetic map (Morisson et al, , 2005Jennen et al, 2004;Leroux et al, 2005). Recently this RH panel has been used to complement the sequencing effort to create a robust assembly for the Z sex chromosome (Alain Vignal, unpublished data).…”

Section: Introduction Avian Genomics and The Build Up To The Genome Smentioning

confidence: 99%

Avian genomics in the 21st century

Burt¹,

White²

2007

Cytogenet Genome Res

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The chicken has long been an important model organism for developmental biology, as well as a major source of protein with billions of birds used in meat and egg production each year. Chicken genomics has been transformed in recent years, with the characterisation of large EST collections and most recently with the assembly of the chicken genome sequence. As the first livestock genome to be fully sequenced it leads the way for others to follow – with zebra finch later this year. The genome sequence and the availability of three million genetic polymorphisms are expected to aid the identification of genes that control traits of importance in poultry. As the first bird genome to be sequenced it is a model for the remaining 9,600 species thought to exist today. Many of the features of avian biology and organisation of the chicken genome make it an ideal model organism for phylogenetics and embryology, along with applications in agriculture and medicine. The availability of new tools such as whole-genome gene expression arrays and SNP panels, coupled with information resources on the genes and proteins are likely to enhance this position.

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A gene-based radiation hybrid map of chicken microchromosome 14: Comparison to human and alignment to the assembled chicken sequence

Cited by 11 publications

References 34 publications

Comparative genomics provides evidence for close evolutionary relationships between the urotensin II and somatostatin gene families

Comparative genomics provides evidence for close evolutionary relationships between the urotensin II and somatostatin gene families

The chicken RH map: current state of progress and microchromosome mapping

Avian genomics in the 21st century

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