Open Access Research article

A duck RH panel and its potential for assisting NGS genome assembly

Man Rao1, Mireille Morisson1, Thomas Faraut1, Suzanne Bardes1, Katia Fève1, Emmanuelle Labarthe1, Valérie Fillon1, Yinhua Huang2, Ning Li1 and Alain Vignal1*

Author Affiliations

1 UMR INRA/ENVT Laboratoire de Génétique Cellulaire, INRA, Castanet-Tolosan, 31326, France

2 State key laboratory for agro-biotechnology, China Agricultural University, Beijing, 100193, People's Republic of China

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BMC Genomics 2012, 13:513  doi:10.1186/1471-2164-13-513

Published: 28 September 2012

Additional files

Additional File 1:

Table S1. Genotyping results of 39 scaffold markers and 8 no hit ESTs for the three different methods. The panel contained 90 hybrids.

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Additional File 2:

Figure S1. Checking the 13 largest scaffolds by RH mapping. Each thick horizontal line represents a scaffold; arrows point to the names of the markers which were genotyped on the duck RH panel. The approximate position of the markers is shown as well as the scaffold lengths. Markers in the same color and contained within the same box are linked by RH mapping. For the 12 first scaffolds shown, the RH mapping data confirm the scaffold assembly. The last one, scaffold504, was the only one which was detected to be discontinuous, as marker sca504F is not linked by RH mapping to the five other markers sca504A, sca504B, sca504C, sca504D and sca504E. Comparative analysis with chicken shows that the portion of the scaffold containing sca504F aligns to GGA2, whereas the rest aligns to GGA1.

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Additional File 3:

Figure S2. Testing duck scaffolds aligning to two chicken chromosomes. Duck scaffolds are represented together with the portions of chicken chromosomes to which they show high sequence similarity in the Narcisse database. The approximate position of the markers on the scaffolds and on the chicken genome is shown as well as the scaffold lengths To test if the synteny breakpoints are due to an evolutionary chromosomal rearrangement or a problem in the assembly of scaffolds, a pair of markers was chosen close together on the scaffolds, but spanning the break points. Whenever markers are linked together by RH mapping, they are contained in the same box and are represented in the same colour.

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Additional File 4:

Table S2. The 41 disrupted scaffolds which could be aligned on two different chicken chromosomes. Break1: the right-most coordinate of the alignment of the left part of the scaffold to one chicken chromosome. Break 2: the left-most coordinate of the alignment of the left right part of the scaffold to another chicken chromosome. Chicken 1 and Chicken 2: chicken chromosomes to which the left and right parts of the duck scaffold align to respectively. Pair-end support: refers to the reliability of paired-end sequence data.

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Additional File 5:

Table S3. Data on all markers genotyped in the study. Primer pairs, PCR conditions, and accession numbers (where applicable) are given.

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