Why there is no chicken galGal1 reference genome
Yung-Chih Lai
Steve Heitner
Hello, Gary.
Typically when we release assemblies, we start with the number 1 for the first assembly and then continue numbering sequentially when an updated assembly becomes available at NCBI. The galGal2 assembly (WUGSC 1.0) was the assembly actually used for initial analysis and publication. There was originally a galGal1 assembly, but for whatever reason, it was quickly replaced by galGal2 before galGal1 ever made it to our public site.
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Steve Heitner
UCSC Genome Bioinformatics Group
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Yung-Chih Lai
Hi Steve,
Many thanks for your explanation. Based on the below description, the galGal2 on UCSC Genome Browser is the first chicken draft sequence published in 2004 (Hillier et al. 2004). If it is true, who is the galGal1? May I have three additional questions about the chicken genome on USCS?
1. Will UCSC make a UCSC know gene track for the chicken galGal4 reference genome?
2. Do you know about when UCSC will make a conservation track for the chicken galGal4 reference genome?
3. Do you know about when the galGal5 majorly based on 70X Illumina reads will be released in the future?
Thanks you so much.
Gary
http://ged.msu.edu/downloads/2013-chick-genome-improvement.pdf
II. Genome reference history
In 2003 a single, partially inbred Red Jungle Fowl female bird (the primary wild progenitor of domestic chickens) was sequenced with NHGRI support in response to a White Paper (see http://genome.wustl.edu/genomes/view/gallus_gallus/) by The
Genome Institute (GI), Washington University School of Medicine, with the first draft sequence published in 2004 [2]. That assembled draft based on 6.6X sequence (Sanger technology) coverage was then aligned to chromosomal linkage groups using comprehensive physical [3] and genetic linkage maps [4, 5]. Subsequently, a second build (WUGSC 2.1/galGal3) was generated (May, 2006). In this version an additional 198K reads focused on contig ends and regions of poor quality were added. Furthermore, the assembly order and orientation were improved using early SNP mapping data that better aligned contigs on chromosomes. Total sequence in galGal3 includes 1.1 Gb of sequence, about 95% of which is anchored to autosomes 1-28 and 32, along with the Z and W sex chromosomes. The Z and W sex chromosomes were sequenced only to ~3.3X due to their hemizygous state in the female bird used. Build galGal3 increased the size of chrZ from 33.6 to 74.6 Mb and decreased chrW from 4.9 Mb to 0.26 Mb due, in part, to several mistaken assignments of contigs to W in galGal2 that were actually on Z. A focused effort to improve the Z chromosome subsequently resulted in a nearly contiguous version of this chromosome, incorporated into galGal4 (see below) [6].
A third build of the genome (galGal4), performed by the University of Maryland in collaboration with the GI, was released in November 2011. This assembly included the use of next-generation sequencing technology (454 Titanium, 12X) in combination with previous read types. Using a combination of Sanger and 454 sequence resulted in an increase of N50 contig size by 460% to 252 Kb. The supercontig N50 increased to 17.6 Mb. In addition to the significantly improved Z chromosome sequence, the new assembly removes about 10 Mb of artifactual duplications. The total amount of sequence mapped to the chromosomes increased by 15 Mb, after accounting for duplication errors. These corrections derive from the fact that the bird used for sequencing was incompletely inbred, leading to heterozygous alleles being mistakenly called as duplications in earlier assemblies. This galGal4 assembly is currently being annotated for gene content at Ensembl and is already available through the UCSC and NCBI browsers. In addition, the GI currently has 70X Illumina coverage of the reference genome that isn’t part of the above assembly. To facilitate further evaluation of reference genome representation individual assemblies have been created for each sequencing technology, 454 and Illumina[7].
Reference
Hillier, L. W., W. Miller, E. Birney, W. Warren, R. C. Hardison, C. P. Ponting, P. Bork, D. W. Burt, M. A. M. Groenen, M. E. Delany, J. B. Dodgson, A. T. Chinwalla, P. F. Cliften, S. W. Clifton, K. D. Delehaunty, C. Fronick, R. S. Fulton, T. A. Graves, C. Kremitzki, D. Layman, V. Magrini, J. D. McPherson, T. L. Miner, P. Minx, W. E. Nash, M. N. Nhan, J. O. Nelson, L. G. Oddy, C. S. Pohl, J. Randall-Maher, S. M. Smith, J. W. Wallis, S. P. Yang, M. N. Romanov, C. M. Rondelli, B. Paton, J. Smith, D. Morrice, L. Daniels, H. G. Tempest, L. Robertson, J. S. Masabanda, D. K. Griffin, A. Vignal, V. Fillon, L. Jacobbson, S. Kerje, L. Andersson, R. P. M. Crooijmans, J. Aerts, J. J. van der Poel, H. Ellegren, R. B. Caldwell, S. J. Hubbard, D. V. Grafham, A. M. Kierzek, S. R. McLaren, I. M. Overton, H. Arakawa, K. J. Beattie, Y. Bezzubov, P. E. Boardman, J. K. Bonfield, M. D. R. Croning, R. M. Davies, M. D. Francis, S. J. Humphray, C. E. Scott, R. G. Taylor, C. Tickle, W. R. A. Brown, J. Rogers, J. M. Buerstedde, S. A. Wilson, L. Stubbs, I. Ovcharenko, L. Gordon, S. Lucas, M. M. Miller, H. Inoko, T. Shiina, J. Kaufman, J. Salomonsen, K. Skjoedt, G. K. S. Wong, J. Wang, B. Liu, J. Yu, H. M. Yang, M. Nefedov, M. Koriabine, P. J. deJong, L. Goodstadt, C. Webber, N. J. Dickens, I. Letunic, M. Suyama, D. Torrents, C. von Mering, E. M. Zdobnov, et al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695.
Luvina Guruvadoo
If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Luvina Guruvadoo
UCSC Genome Bioinformatics Group
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