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Coturnix japonica 2.0 assembly release notes
 Background: Total assembled sequence coverage of Illumina instrument reads was 73X, including 41X fragments, and 32X long insert reads. The combined sequence reads were assembled using the ALLPATHS-LG software (Gnerre 2011). Additionally, 20X ... coverage of long PacBio reads were sequenced and used to close gaps, and extend sequence ends with PBJelly (English 2012). The estimated genome size is 1.17 Mb. This genome has an estimated 25% repeat content, which is high compared to other birds. For instance, the sparrow, Z. albicollis, has a repeat content of just 13%. SSPACE (Boetzer 2010) was used post assembly to improve scaffolding. This 2.0 version has been screened and cleaned of contaminating contigs, and all contigs 200bp or smaller were removed.
 The assembly is made up of a total of 2534 scaffolds with an N50 scaffold length of 3,247,718bp, which includes singletons (single contigs scaffolds). The N50 contig length is 511,434bp. This assembly spans 928Mb including gaps, and singleton scaffolds. The scaffolds were organized into chromosomal AGPs using primarily the Japanese quail genetic map (Recoquillay et al., 2015) with added information from alignments against galGal4 (Genbank accession: GCA_000002315.2).
 For questions regarding this Coturnix japonica 2.0 assembly please contact Dr. Wesley Warren or founding members of The International Quail Genome Consortium that include: 
 Dr. David W. Burt Dept. of Genomics and Genetics The Roslin Institute and Royal (Dick) School of Veterinary Studies The Roslin Institute Building University of Edinburgh Easter Bush Campus Midlothian EH25 9RG
 Dr. Parker B. Antin, Ph.D. Department of Cellular and Molecular Medicine College of Agriculture and Life Sciences University of Arizona MRB 318 1656 E. Mabel St. Tucson, AZ 85724
 Dr. Rusty Lanford CHLA-USC Saban Research Institute 4661 Sunset Blvd., MS #135 Los Angeles, CA ###90027
 Dr. Jarome Gros Institut Pasteur Department of Developmental and Stem Cell Biology### 25-28 rue du docteur Roux Email: jgros@pasteur.fr Tel: +33(0)1-45-68-81-45
 DNA samples can be obtained from: Dr. Alain Vignal UMR 1388 GenPhySE INRA, 24 Chemin de Borde-Rouge - Auzeville CS 52627 31326 CASTANET-TOLOSAN CEDEX FRANCE 
 Sequence and Assembly Credits:
 Source DNA - Dr. Alain Vignal, UMR 1388 GenPhySE,INRA, 24 Chemin de Borde-Rouge- Auzeville 
 Genome Sequence - McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO.
 Sequence Assembly - McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO.
 Genetic Map - Julien Recoquillay, Elisabeth Le Bihan-Duval, INRA of Nouzilly and Toulouse.(Recoquillay et al., 2015, BMC Genomics. 16:10. PMID: 25609057.
 Quail line selection and maintenance - UE1295 PEAT, INRA, Tours, 37380 NOUZILLY and UMR1313 GABI, Domaine de Vilvert 78352 JOUY-EN-JOSAS CEDEX.
 Citation upon use of this assembly in a manuscript:
It is requested that users of this Coturnix japonica 2.0 sequence assembly acknowledge The International Quail Genome Consortium and McDonnell Genome Institute, Washington University School of Medicine in any publications that result from use of this sequence assembly.
In January 2020 the chromosome assignment of scaffolds LSZS01008902 and KQ966558 was corrected from W to unplaced, and the chromosome W GenBank record CM003811 was suppressed because male quails do not have chromosome W. This updated assembly is "Coturnix japonica 2.1", GCA_001577835.2.  more

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