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Open Access Research article

Insights into the genome structure and copy-number variation of Eimeria tenella

Lik-Sin Lim12, Yea-Ling Tay12, Halimah Alias1, Kiew-Lian Wan12* and Paul H Dear3*

Author Affiliations

1 School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor DE, Malaysia

2 Malaysia Genome Institute, Jalan Bangi, 43000, Kajang, Selangor DE, Malaysia

3 MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, United Kingdom

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BMC Genomics 2012, 13:389  doi:10.1186/1471-2164-13-389

Published: 13 August 2012

Additional files

Additional file 1:

Marker typing results according to stages. Summary of marker typing results for the initial (“First”) set of HAPPY markers, for redesigned markers (“Second” and “Third”), for markers designed against chromosomally-assigned genes (“Chr”), and for all markers combined ("Overall"). Based on the average DNA content of each aliquot in the mapping panel, and on the Poisson distribution, we expect a single-copy sequence to be represented in 30-55 of the aliquots (mean ±2 s.d.); markers in this range are classified as good (green). Markers giving <30 positives, probably due to poor amplification, are classified as low copy (yellow), whilst those giving >55 positives are presumed to represent multi-copy sequences (blue). Markers that did not amplify are considered failed (red).

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Additional file 2:

Details of Eimeria tenella HAPPY map markers. List of Eimeria tenella HAPPY map markers together with relevant details including mapping information, and primers and amplicon sequences.

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Open Data

Additional file 3:

Analysis of BAC-end sequences. Summary of results of BAC-end sequence analysis.

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Additional file 4:

Alignment of the integrated HAPPY map with WGS assemblies of the E. tenellagenome. Graphical representation of the alignment of the HAPPY map and sequence of the Eimeria tenella draft genome assembly contigs. For each map segment, labels “Cxxxxxxxx” are contig numbers in the 2007 assembly; labels “SCxx.y” indicate the supercontig (xx) and contig (y) of the 2010 assembly; HAPPY markers are named as “Ewgxxxxxx”; asterisks in 2010 assembly denote markers that mapped to more than one locus in the assembly.

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Additional file 5:

The comparison of the HAPPY map and sequence of (A) contig _00031646 and (B) contig_00031359. Graphical representation of the alignment of the HAPPY map and sequence of the two largest Eimeria tenella draft genome assembly contigs.

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Open Data