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A Second Generation Integrated Map of the Rainbow Trout (Oncorhynchus mykiss) Genome: Analysis of Conserved Synteny with Model Fish Genomes

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Abstract

DNA fingerprints and end sequences from bacterial artificial chromosomes (BACs) from two new libraries were generated to improve the first generation integrated physical and genetic map of the rainbow trout (Oncorhynchus mykiss) genome. The current version of the physical map is composed of 167,989 clones of which 158,670 are assembled into contigs and 9,319 are singletons. The number of contigs was reduced from 4,173 to 3,220. End sequencing of clones from the new libraries generated a total of 11,958 high quality sequence reads. The end sequences were used to develop 238 new microsatellites of which 42 were added to the genetic map. Conserved synteny between the rainbow trout genome and model fish genomes was analyzed using 188,443 BAC end sequence (BES) reads. The fractions of BES reads with significant BLASTN hits against the zebrafish, medaka, and stickleback genomes were 8.8%, 9.7%, and 10.5%, respectively, while the fractions of significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 6.2%, 5.8%, and 5.5%, respectively. The overall number of unique regions of conserved synteny identified through grouping of the rainbow trout BES into fingerprinting contigs was 2,259, 2,229, and 2,203 for stickleback, medaka, and zebrafish, respectively. These numbers are approximately three to five times greater than those we have previously identified using BAC paired ends. Clustering of the conserved synteny analysis results by linkage groups as derived from the integrated physical and genetic map revealed that despite the low sequence homology, large blocks of macrosynteny are conserved between chromosome arms of rainbow trout and the model fish species.

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Acknowledgments

This project was supported by National Research Initiative Competitive Grant number 2007-35616-17875 from the USDA National Institute of Food and Agriculture and by internal base funds provided by the Agricultural Research Service project number 1930-31000-009. Brian Smith, Kristy Shewbridge, and Roseanna Long carried out the microsatellites genotyping described in this manuscript. We thank Gary Thorgaard and Paul Wheeler (Washington State University) for the Swanson doubled haploid samples that were used to construct the new BAC libraries and Eric Peatman (Auburn University) for reviewing an earlier draft of the manuscript. We also thank anonymous reviewer 2 for his insightful comments on the blocks of conserved macro-synteny that can be identified through the chromosomes of the integrated map. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. USDA is an equal opportunity provider and employer.

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  1. Frank M. You

    Present address: Cereal Research Center, Agriculture and Agri-Food Canada, Winnipeg, MB, R3T 2M9, Canada

Authors and Affiliations

  1. National Center for Cool and Cold Water Aquaculture, ARS-USDA, 11861 Leetown Road, Kearneysville, WV, 25430, USA

    Yniv Palti, Guangtu Gao & Caird E. Rexroad III

  2. INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352, Jouy en Josas Cedex, France

    Carine Genet & Mekki Boussaha

  3. Department of Plant Sciences, University of California, One Shields Ave., Davis, CA, 95616, USA

    Yuqin Hu, Frank M. You & Ming-Cheng Luo

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Electronic supplementary material

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File 1

Microsatellite markers information in Excel file. (XLS 32 kb)

File 2

Genetic map data and statistics in excel sheets. (XLS 208 kb)

File 3

A schematic drawing of the genetic map linkage groups. (PDF 5331 kb)

File 4

Detailed results of the BlastN conserved synteny analyses in excel sheets. (XLS 868 kb)

File 5

Detailed results of the BlastX conserved synteny analyses in excel sheets. (XLS 741 kb)

File 6

Statistics of BlastN and BlastX hits on all three species. (XLS 19 kb)

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Palti, Y., Genet, C., Gao, G. et al. A Second Generation Integrated Map of the Rainbow Trout (Oncorhynchus mykiss) Genome: Analysis of Conserved Synteny with Model Fish Genomes. Mar Biotechnol 14, 343–357 (2012). https://doi.org/10.1007/s10126-011-9418-z

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