History (Show revision history)

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The zebra finch DNA for shotgun sequencing, and for BAC and cosmid libraries, was derived from a single male (Black 17) domesticated zebra finch from the laboratory of Arthur P. Arnold in the Department of Physiological Science at UCLA, ... Los Angeles, CA, USA. The parents of this male hatched in the same clutch in an aviary of group-housed zebra finches, and therefore may have been brother-sister. A male BAC library was constructed from the same bird by Barbara Blackmon at the Clemson University Genomics Institute (this library is NOT the same as the BAC library available from the Arizona Genome Institute made from several individual females). The initial assembly was generated using PCAP (Huang et al., 2006) from about 6X coverage in whole-genome shotgun reads, a combination of plasmid, fosmid and bacterial artificial chromosome (BAC)-end read pairs. The sequence of 35 finished BAC clones were incorporated into the final assembly. The T. guttata physical map contains 108,725 clones for about 10X depth of coverage and is contained in 2,724 contigs. 

Of the 1.2 Gb genome, 1.0Gb was ordered and oriented along 33 zebra finch chromosomes and 1 linkage group. An additional 36 Mb was localized to specific chromosomes or linkage groups, but was not ordered and oriented. For the initial PCAP assembly (prior to removal of contaminants and contigs/supercontigs less than 2kb), there were 92,299 major contigs (126,053 total contigs) with an N50 contig length of 39kb (n=8,037). There were 37,252 major supercontigs (37,698 total supercontigs) with the N50 supercontig length of 10.4Mb (n=29).

The zebra finch chromosomes were named based on their homologous chromosomes in Gallus gallus. For those chromosomes where multiple zebra finch chromosomes correspond to a single chicken chromosome, a letter was appended to the chromosome name. The lookup table can be found below for cross-referencing the Gallus gallus homologous names with the current naming convention for the zebra finch.

AGP Generation Details
To create chromosomal sequences, data from the Sheffield Linkage Map and the physical map were integrated with the WGS assembly data. Using sequence comparison, T. guttata SNP marker sequences were assigned to contigs (contiguous stretches of DNA) in the WGS assembly. Based on these marker assignments, the supercontigs (sets of ordered/oriented contigs linked by virtue of read pairing data) were assigned to a chromosome based on a majority rule (>50% of markers assigned to the same chromosome). The supercontigs were initially positioned along chromosomes based on their median marker position, and initially oriented based on relative marker order along the supercontig. The physical map was also linked to the sequence assembly by using BAC end sequence links and in silico digests of the assembly to create "ultracontigs", ordered/oriented lists of "supercontigs". Following these initial placements, the WGS assembly read pairing data were used, where possible, to aid in orientation and confirm order. For the Z chromosome, marker order was also determined by FISH (Art Arnold, personal commuication) and integrated again with the linkage map, physical map and assembly. All discrepancies betwen the various maps were manually reviewed and a combined super/ultracontig order was established based on reconciling the data from the Sheffield, assembly and physical maps. Available EST data were also used in reviewing the assembly. Alignments with the chicken genome were also examined and used as aid in orientation particularly when available other zebra finch-specific data were inconclusive. The location of the centromere is known only for the Z chromosome. Thus no other centromeres were placed in the current chromosomal assemblies.

Cross-reference of zebra finch chromosome names used for this release, chicken and finch chromosome name suggested by Itoh et al, 2005*. 

TGU GGA Itoh et al., 2005 Chromosome Res. 2005;13(1):47-56.
Chr1 1 3 
Chr1A 1 4 
Chr1B 1 NA 
Chr2 2 1 
Chr3 3 2 
Chr4 4 5 
Chr4A 4 microchromosome 
Chr5 5 6 
Chr6 6 7 
Chr7 7 8 
Chr8 8 9 
Chr9 9 10 
Chr10 10 NA 
Chr11 11 NA 
Chr12 12 NA 
Chr13 13 NA 
Chr14 14 NA 
Chr15 15 NA 
Chr16 16 NA 
Chr17 17 NA 
Chr18 18 NA 
Chr19 19 NA 
Chr20 20 NA 
Chr21 21 NA 
Chr22 22 NA 
Chr23 23 NA 
Chr24 24 NA 
Chr25 25 NA 
Chr26 26 NA 
Chr27 27 NA 
Chr28 28 NA 
LGE22 LGE22C19W28_E50C23 NA 
LGE22A LGE22C19W28_E50C23 NA 
LG2 NA NA 
LG5 NA NA 
ChrZ Z Z

DNA source - Art Arnold, Department of Physiological Science, UCLA 
Genome Sequence - The Genome Center, Washington University School of Medicine 
Sequence Assembly and Chromosomal Sequence Construction - The Genome Center, Washington University School of Medicine 
Zebra finch linkage map - Jessica Stapley, Tim Birkhead, Terry Burke and Jon Slate, Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK 
Z Map/FISH Mapping - Itoh Yuichiro and Art Arnold, Department of Physiological Science, UCLA 
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